From 206e383cfc6b60295eb105e2a39687552c537123 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Fri, 18 Aug 2023 19:07:23 +0100 Subject: [PATCH 01/38] Use OOP forcefields --- mdpow/equil.py | 441 ++++++++++++++++++------------ mdpow/forcefields.py | 377 +++++++++++++++++-------- mdpow/templates/system.top | 14 +- mdpow/templates/system_octwet.top | 16 +- mdpow/tests/test_forcefields.py | 2 +- 5 files changed, 547 insertions(+), 303 deletions(-) diff --git a/mdpow/equil.py b/mdpow/equil.py index 56d79f40..6a18de9c 100644 --- a/mdpow/equil.py +++ b/mdpow/equil.py @@ -29,9 +29,12 @@ .. autodata:: DIST """ import pickle +import re import os, errno import shutil +from string import Template +from typing import Optional import MDAnalysis as mda @@ -47,7 +50,8 @@ from .restart import Journalled import logging -logger = logging.getLogger('mdpow.equil') + +logger = logging.getLogger("mdpow.equil") # ITP <-- forcefields.get_solvent_model(id).itp # BOX <-- forcefields.get_solvent_model(id).coordinates @@ -56,7 +60,14 @@ # TODO: change to water distance 1.2 in the future (1.0 for # compatibility with our SAMPL5 runs) #: minimum distance between solute and box surface (in nm) -DIST = {'water': 1.0, 'octanol': 1.5, 'cyclohexane': 1.5, 'wetoctanol': 1.5, 'toluene': 1.5} +DIST = { + "water": 1.0, + "octanol": 1.5, + "cyclohexane": 1.5, + "wetoctanol": 1.5, + "toluene": 1.5, +} + class Simulation(Journalled): """Simple MD simulation of a single compound molecule in water. @@ -76,35 +87,64 @@ class Simulation(Journalled): """ #: Keyword arguments to pre-set some file names; they are keys in :attr:`Simulation.files`. - filekeys = ('topology', 'processed_topology', 'structure', 'solvated', 'ndx', - 'energy_minimized', 'MD_relaxed', 'MD_restrained', 'MD_NPT') + filekeys = ( + "topology", + "processed_topology", + "structure", + "solvated", + "ndx", + "energy_minimized", + "MD_relaxed", + "MD_restrained", + "MD_NPT", + ) topdir_default = "Equilibrium" dirname_default = os.path.curdir - solvent_default = 'water' + solvent_default = "water" #: Coordinate files of the full system in increasing order of advancement of #: the protocol; the later the better. The values are keys into :attr:`Simulation.files`. - coordinate_structures = ('solvated', 'energy_minimized', 'MD_relaxed', - 'MD_restrained', 'MD_NPT') - checkpoints = ('solvated','energy_minimized','MD_relaxed','MD_restrained','MD_NPT') - + coordinate_structures = ( + "solvated", + "energy_minimized", + "MD_relaxed", + "MD_restrained", + "MD_NPT", + ) + checkpoints = ( + "solvated", + "energy_minimized", + "MD_relaxed", + "MD_restrained", + "MD_NPT", + ) #: Check list of all methods that can be run as an independent protocol; see also #: :meth:`Simulation.get_protocol` and :class:`restart.Journal` - protocols = ("MD_NPT", "MD_NPT_run", # *_run as dummies for the ... - "MD_relaxed", "MD_relaxed_run", # ...checkpointing logic - "MD_restrained", "MD_restrained_run", - "energy_minimize", "solvate", "topology") + protocols = ( + "MD_NPT", + "MD_NPT_run", # *_run as dummies for the ... + "MD_relaxed", + "MD_relaxed_run", # ...checkpointing logic + "MD_restrained", + "MD_restrained_run", + "energy_minimize", + "solvate", + "topology", + ) #: Default Gromacs *MDP* run parameter files for the different stages. #: (All are part of the package and are found with :func:`mdpow.config.get_template`.) - mdp_defaults = {'MD_relaxed': 'NPT_opls.mdp', - 'MD_restrained': 'NPT_opls.mdp', - 'MD_NPT': 'NPT_opls.mdp', - 'energy_minimize': 'em_opls.mdp', - } - - def __init__(self, molecule=None, **kwargs): + mdp_defaults = { + "MD_relaxed": "NPT_opls.mdp", + "MD_restrained": "NPT_opls.mdp", + "MD_NPT": "NPT_opls.mdp", + "energy_minimize": "em_opls.mdp", + } + + def __init__( + self, molecule=None, ff_class: Optional[forcefields.Forcefield] = None, **kwargs + ): """Set up Simulation instance. The *molecule* of the compound molecule should be supplied. Existing files @@ -120,8 +160,11 @@ def __init__(self, molecule=None, **kwargs): :meth:`~mdpow.equil.Simulation.save`. *dirname* base directory; all other directories are created under it + *ff_class* + A :class:`mdpow.forcefields.Forcefield` instance. *forcefield* - 'OPLS-AA' or 'CHARMM' or 'AMBER' + A string representation of the forcefield, when using one of the defaults: + 'OPLS-AA' or 'CHARMM' or 'AMBER'. Not needed when :arg:`ff_class` is specified. *solvent* 'water' or 'octanol' or 'cyclohexane' or 'wetoctanol' or 'toluene' *solventmodel* @@ -142,11 +185,21 @@ def __init__(self, molecule=None, **kwargs): """ self.__cache = {} - filename = kwargs.pop('filename', None) - dirname = kwargs.pop('dirname', self.dirname_default) + filename = kwargs.pop("filename", None) + dirname = kwargs.pop("dirname", self.dirname_default) - forcefield = kwargs.pop('forcefield', 'OPLS-AA') - solvent = kwargs.pop('solvent', self.solvent_default) + if ff_class is not None: + assert isinstance(ff_class, forcefields.Forcefield) + forcefield: forcefields.Forcefield = ff_class + else: + forcefield_name = kwargs.pop("forcefield", "OPLS-AA") + try: + forcefield = forcefields.ALL_FORCEFIELDS[forcefield_name] + except KeyError: + raise ValueError( + f"No forcefield called `{forcefield_name}` is implemented. Please amend the `mdpow.forcefields.ALL_FORCEFIELDS` dictionary if you think it should be." + ) + solvent = kwargs.pop("solvent", self.solvent_default) # mdp files --- should get values from default runinput.cfg # None values in the kwarg mdp dict are ignored # self.mdp: key = stage, value = path to MDP file @@ -154,25 +207,36 @@ def __init__(self, molecule=None, **kwargs): # 'water' will choose the default ('tip4p'), other choices are # 'tip3p', 'spc', 'spce', 'm24', for water; no choices # available for 'cyclohexane' and 'octanol' - solventmodel = kwargs.pop('solventmodel', None) - - mdp_kw = kwargs.pop('mdp', {}) - self.mdp = dict((stage, config.get_template(fn)) for stage,fn in self.mdp_defaults.items()) - self.mdp.update(dict((stage, config.get_template(fn)) for stage,fn in mdp_kw.items() if fn is not None)) + solventmodel = kwargs.pop("solventmodel", None) + + mdp_kw = kwargs.pop("mdp", {}) + self.mdp = dict( + (stage, config.get_template(fn)) for stage, fn in self.mdp_defaults.items() + ) + self.mdp.update( + dict( + (stage, config.get_template(fn)) + for stage, fn in mdp_kw.items() + if fn is not None + ) + ) if molecule is None and filename is not None: # load from pickle file self.load(filename) self.filename = filename - kwargs = {} # for super + kwargs = {} # for super else: - self.molecule = molecule or 'DRUG' + self.molecule = molecule or "DRUG" self.dirs = AttributeDict( - basedir=realpath(dirname), # .../Equilibrium/ - includes=list(asiterable(kwargs.pop('includes',[]))) + [config.includedir], - ) + basedir=realpath(dirname), # .../Equilibrium/ + includes=list(asiterable(kwargs.pop("includes", []))) + + [config.includedir], + ) # pre-set filenames: keyword == variable name - self.files = AttributeDict([(k, kwargs.pop(k, None)) for k in self.filekeys]) + self.files = AttributeDict( + [(k, kwargs.pop(k, None)) for k in self.filekeys] + ) self.deffnm = kwargs.pop("deffnm", "md") if self.files.topology: @@ -184,28 +248,31 @@ def __init__(self, molecule=None, **kwargs): self.forcefield = forcefield self.solvent_type = solvent self.solventmodel_identifier = forcefields.get_solvent_identifier( - solvent, - model=solventmodel, - forcefield=forcefield, - ) + solvent, + model=solventmodel, + forcefield=forcefield, + ) if self.solventmodel_identifier is None: msg = "No parameters for solvent {0} and solventmodel {1} available.".format( - solvent, solventmodel) + solvent, solventmodel + ) logger.error(msg) raise ValueError(msg) self.solventmodel = forcefields.get_solvent_model( self.solventmodel_identifier, forcefield=forcefield, - ) + ) - distance = kwargs.pop('distance', None) + distance = kwargs.pop("distance", None) distance = distance if distance is not None else DIST[solvent] - self.solvent = AttributeDict(itp=self.solventmodel.itp, - box=self.solventmodel.coordinates, - distance=distance) + self.solvent = AttributeDict( + itp=self.solventmodel.itp, + box=self.solventmodel.coordinates, + distance=distance, + ) - self.filename = filename or self.solvent_type+'.simulation' + self.filename = filename or self.solvent_type + ".simulation" super(Simulation, self).__init__(**kwargs) @@ -220,12 +287,14 @@ def save(self, filename=None): """ if filename is None: if self.filename is None: - self.filename = filename or self.solvent_type+'.simulation' - logger.warning("No filename known, saving instance under name %r", self.filename) + self.filename = filename or self.solvent_type + ".simulation" + logger.warning( + "No filename known, saving instance under name %r", self.filename + ) filename = self.filename else: self.filename = filename - with open(filename, 'wb') as f: + with open(filename, "wb") as f: pickle.dump(self, f) logger.debug("Instance pickled to %(filename)r" % vars()) @@ -233,10 +302,10 @@ def load(self, filename=None): """Re-instantiate class from pickled file.""" if filename is None: if self.filename is None: - self.filename = self.molecule.lower() + '.pickle' + self.filename = self.molecule.lower() + ".pickle" logger.warning("No filename known, trying name %r", self.filename) filename = self.filename - with open(filename, 'rb') as f: + with open(filename, "rb") as f: instance = pickle.load(f) self.__dict__.update(instance.__dict__) logger.debug("Instance loaded from %(filename)r" % vars()) @@ -248,6 +317,7 @@ def make_paths_relative(self, prefix=os.path.curdir): check :attr:`mdpow.equil.Simulation.dirs.includes` and adjust manually if necessary. """ + def assinglet(m): if len(m) == 1: return m[0] @@ -272,10 +342,13 @@ def assinglet(m): self.mdp[key] = fn.replace(basedir, prefix) except AttributeError: pass - logger.warning("make_paths_relative(): check/manually adjust %s.dirs.includes = %r !", - self.__class__.__name__, self.dirs.includes) + logger.warning( + "make_paths_relative(): check/manually adjust %s.dirs.includes = %r !", + self.__class__.__name__, + self.dirs.includes, + ) - def topology(self, itp='drug.itp', prm=None, **kwargs): + def topology(self, itp="drug.itp", prm=None, **kwargs): """Generate a topology for compound *molecule*. :Keywords: @@ -290,70 +363,55 @@ def topology(self, itp='drug.itp', prm=None, **kwargs): *kwargs* see source for *top_template*, *topol* """ - self.journal.start('topology') + self.journal.start("topology") - dirname = kwargs.pop('dirname', self.BASEDIR('top')) + dirname = kwargs.pop("dirname", self.BASEDIR("top")) self.dirs.topology = realpath(dirname) - setting = forcefields.get_ff_paths(self.forcefield) template = forcefields.get_top_template(self.solvent_type) - top_template = config.get_template(kwargs.pop('top_template', template)) - topol = kwargs.pop('topol', os.path.basename(top_template)) + top_template = config.get_template(kwargs.pop("top_template", template)) + topol = kwargs.pop("topol", os.path.basename(top_template)) self.top_template = top_template itp = os.path.realpath(itp) _itp = os.path.basename(itp) if prm is None: - prm_kw = '' + prm_kw = "" else: prm = os.path.realpath(prm) _prm = os.path.basename(prm) prm_kw = '#include "{}"'.format(_prm) with in_dir(dirname): + with open(top_template, "r") as f: + top_string_template = Template(f.read()) + top_string_formatted = top_string_template.substitute( + forcefield_itp=self.forcefield.forcefield_dir / "forcefield.itp", + prm_line=f'#include "{prm_kw}"' if prm_kw else "", + compound_itp=_itp, + solvent_itp=self.forcefield.forcefield_dir / self.solvent.itp, + ions_itp=self.forcefield.ions_itp, + water_itp=self.forcefield.default_water_itp, + compound_name=self.molecule, + solvent=self.solvent_type, + ) + with open(topol, "w") as f: + f.write(top_string_formatted) shutil.copy(itp, _itp) if prm is not None: shutil.copy(prm, _prm) - gromacs.cbook.edit_txt(top_template, - [(r'#include +"oplsaa\.ff/forcefield\.itp"', - r'oplsaa\.ff/', - setting[0]), - (r'#include +"compound\.itp"', - r'compound\.itp', - _itp), - (r'#include +"oplsaa\.ff/tip4p\.itp"', - r'oplsaa\.ff/tip4p\.itp', - setting[0] + self.solvent.itp), - (r'#include +"oplsaa\.ff/ions_opls\.itp"', - r'oplsaa\.ff/ions_opls\.itp', - setting[1]), - (r'#include +"compound\.prm"', - r'#include +"compound\.prm"', - prm_kw), - (r'#include +"water\.itp"', - r'water\.itp', - setting[2]), - (r'Compound', - 'solvent', - self.solvent_type), - (r'Compound', - 'DRUG', - self.molecule), - (r'DRUG\s*1', - 'DRUG', - self.molecule), - ], - newname=topol) - logger.info('[%(dirname)s] Created topology %(topol)r that includes %(_itp)r', vars()) + logger.info( + "[%(dirname)s] Created topology %(topol)r that includes %(_itp)r", vars() + ) # update known files and dirs self.files.topology = realpath(dirname, topol) if not self.dirs.topology in self.dirs.includes: self.dirs.includes.append(self.dirs.topology) - self.journal.completed('topology') - return {'dirname': dirname, 'topol': topol} + self.journal.completed("topology") + return {"dirname": dirname, "topol": topol} @staticmethod def _setup_solvate(**kwargs): @@ -385,43 +443,49 @@ def solvate(self, struct=None, **kwargs): All other arguments are passed on to :func:`gromacs.setup.solvate`, but set to sensible default values. *top* and *water* are always fixed. """ - self.journal.start('solvate') - - self.dirs.solvation = realpath(kwargs.setdefault('dirname', self.BASEDIR('solvation'))) - kwargs['struct'] = self._checknotempty(struct or self.files.structure, 'struct') - kwargs['top'] = self._checknotempty(self.files.topology, 'top') - kwargs['water'] = self.solvent.box - kwargs.setdefault('mainselection', '"%s"' % self.molecule) # quotes are needed for make_ndx - kwargs.setdefault('distance', self.solvent.distance) - - boxtype = kwargs.pop('bt', None) + self.journal.start("solvate") + + self.dirs.solvation = realpath( + kwargs.setdefault("dirname", self.BASEDIR("solvation")) + ) + kwargs["struct"] = self._checknotempty(struct or self.files.structure, "struct") + kwargs["top"] = self._checknotempty(self.files.topology, "top") + kwargs["water"] = self.solvent.box + kwargs.setdefault( + "mainselection", '"%s"' % self.molecule + ) # quotes are needed for make_ndx + kwargs.setdefault("distance", self.solvent.distance) + + boxtype = kwargs.pop("bt", None) boxtype = boxtype if boxtype is not None else "dodecahedron" if boxtype not in ("dodecahedron", "triclinic", "cubic", "octahedron"): - msg = "Invalid boxtype '{0}', not suitable for 'gmx editconf'.".format(boxtype) + msg = "Invalid boxtype '{0}', not suitable for 'gmx editconf'.".format( + boxtype + ) logger.error(msg) raise ValueError(msg) - kwargs['bt'] = boxtype + kwargs["bt"] = boxtype - kwargs['includes'] = asiterable(kwargs.pop('includes',[])) + self.dirs.includes + kwargs["includes"] = asiterable(kwargs.pop("includes", [])) + self.dirs.includes params = self._setup_solvate(**kwargs) - self.files.structure = kwargs['struct'] - self.files.solvated = params['struct'] - self.files.ndx = params['ndx'] + self.files.structure = kwargs["struct"] + self.files.solvated = params["struct"] + self.files.ndx = params["ndx"] # we can also make a processed topology right now self.processed_topology(**kwargs) - self.journal.completed('solvate') + self.journal.completed("solvate") return params def processed_topology(self, **kwargs): """Create a portable topology file from the topology and the solvated system.""" if self.files.solvated is None or not os.path.exists(self.files.solvated): self.solvate(**kwargs) - kwargs['topol'] = self.files.topology - kwargs['struct'] = self.files.solvated - kwargs['includes'] = self.dirs.includes + kwargs["topol"] = self.files.topology + kwargs["struct"] = self.files.solvated + kwargs["includes"] = self.dirs.includes self.files.processed_topology = gromacs.cbook.create_portable_topology(**kwargs) return self.files.processed_topology @@ -432,55 +496,71 @@ def energy_minimize(self, **kwargs): :meth:`~mdpow.equil.Simulation.solvate` step has been carried out previously all the defaults should just work. """ - self.journal.start('energy_minimize') + self.journal.start("energy_minimize") - self.dirs.energy_minimization = realpath(kwargs.setdefault('dirname', self.BASEDIR('em'))) - kwargs['top'] = self.files.topology - kwargs.setdefault('struct', self.files.solvated) - kwargs.setdefault('mdp', self.mdp['energy_minimize']) - kwargs['mainselection'] = None - kwargs['includes'] = asiterable(kwargs.pop('includes',[])) + self.dirs.includes + self.dirs.energy_minimization = realpath( + kwargs.setdefault("dirname", self.BASEDIR("em")) + ) + kwargs["top"] = self.files.topology + kwargs.setdefault("struct", self.files.solvated) + kwargs.setdefault("mdp", self.mdp["energy_minimize"]) + kwargs["mainselection"] = None + kwargs["includes"] = asiterable(kwargs.pop("includes", [])) + self.dirs.includes params = gromacs.setup.energy_minimize(**kwargs) - self.files.energy_minimized = params['struct'] + self.files.energy_minimized = params["struct"] - self.journal.completed('energy_minimize') + self.journal.completed("energy_minimize") return params def _MD(self, protocol, **kwargs): """Basic MD driver for this Simulation. Do not call directly.""" self.journal.start(protocol) - kwargs.setdefault('dirname', self.BASEDIR(protocol)) - kwargs.setdefault('deffnm', self.deffnm) - kwargs.setdefault('mdp', config.get_template('NPT_opls.mdp')) - self.dirs[protocol] = realpath(kwargs['dirname']) - setupMD = kwargs.pop('MDfunc', gromacs.setup.MD) - kwargs['top'] = self.files.topology - kwargs['includes'] = asiterable(kwargs.pop('includes',[])) + self.dirs.includes - kwargs['ndx'] = self.files.ndx - kwargs['mainselection'] = None # important for SD (use custom mdp and ndx!, gromacs.setup._MD) - self._checknotempty(kwargs['struct'], 'struct') - if not os.path.exists(kwargs['struct']): + kwargs.setdefault("dirname", self.BASEDIR(protocol)) + kwargs.setdefault("deffnm", self.deffnm) + kwargs.setdefault("mdp", config.get_template("NPT_opls.mdp")) + self.dirs[protocol] = realpath(kwargs["dirname"]) + setupMD = kwargs.pop("MDfunc", gromacs.setup.MD) + kwargs["top"] = self.files.topology + kwargs["includes"] = asiterable(kwargs.pop("includes", [])) + self.dirs.includes + kwargs["ndx"] = self.files.ndx + kwargs[ + "mainselection" + ] = None # important for SD (use custom mdp and ndx!, gromacs.setup._MD) + self._checknotempty(kwargs["struct"], "struct") + if not os.path.exists(kwargs["struct"]): # struct is not reliable as it depends on qscript so now we just try everything... - struct = gromacs.utilities.find_first(kwargs['struct'], suffices=['pdb', 'gro']) + struct = gromacs.utilities.find_first( + kwargs["struct"], suffices=["pdb", "gro"] + ) if struct is None: - logger.error("Starting structure %(struct)r does not exist (yet)" % kwargs) - raise IOError(errno.ENOENT, "Starting structure not found", kwargs['struct']) + logger.error( + "Starting structure %(struct)r does not exist (yet)" % kwargs + ) + raise IOError( + errno.ENOENT, "Starting structure not found", kwargs["struct"] + ) else: - logger.info("Found starting structure %r (instead of %r).", struct, kwargs['struct']) - kwargs['struct'] = struct + logger.info( + "Found starting structure %r (instead of %r).", + struct, + kwargs["struct"], + ) + kwargs["struct"] = struct # now setup the whole simulation (this is typically gromacs.setup.MD() ) - params = setupMD(**kwargs) + params = setupMD(**kwargs) # params['struct'] is md.gro but could also be md.pdb --- depends entirely on qscript - self.files[protocol] = params['struct'] + self.files[protocol] = params["struct"] # Gromacs 4.5.x 'mdrun -c PDB' fails if it cannot find 'residuetypes.dat' # so instead of fuffing with GMXLIB we just dump it into the directory try: - shutil.copy(config.topfiles['residuetypes.dat'], self.dirs[protocol]) + shutil.copy(config.topfiles["residuetypes.dat"], self.dirs[protocol]) except IOError: - logger.warning("Failed to copy 'residuetypes.dat': mdrun will likely fail to write a final structure") + logger.warning( + "Failed to copy 'residuetypes.dat': mdrun will likely fail to write a final structure" + ) self.journal.completed(protocol) return params @@ -513,11 +593,11 @@ def MD_relaxed(self, **kwargs): """ # user structure or restrained or solvated - kwargs.setdefault('struct', self.files.energy_minimized) - kwargs.setdefault('dt', 0.0001) # ps - kwargs.setdefault('runtime', 5) # ps - kwargs.setdefault('mdp', self.mdp['MD_relaxed']) - return self._MD('MD_relaxed', **kwargs) + kwargs.setdefault("struct", self.files.energy_minimized) + kwargs.setdefault("dt", 0.0001) # ps + kwargs.setdefault("runtime", 5) # ps + kwargs.setdefault("mdp", self.mdp["MD_relaxed"]) + return self._MD("MD_relaxed", **kwargs) def MD_restrained(self, **kwargs): """Short MD simulation with position restraints on compound. @@ -551,11 +631,13 @@ def MD_restrained(self, **kwargs): :class:`gromacs.manager.Manager` """ - kwargs.setdefault('struct', - self._lastnotempty([self.files.energy_minimized, self.files.MD_relaxed])) - kwargs.setdefault('mdp', self.mdp['MD_restrained']) - kwargs['MDfunc'] = gromacs.setup.MD_restrained - return self._MD('MD_restrained', **kwargs) + kwargs.setdefault( + "struct", + self._lastnotempty([self.files.energy_minimized, self.files.MD_relaxed]), + ) + kwargs.setdefault("mdp", self.mdp["MD_restrained"]) + kwargs["MDfunc"] = gromacs.setup.MD_restrained + return self._MD("MD_restrained", **kwargs) def MD_NPT(self, **kwargs): """Short NPT MD simulation. @@ -595,10 +677,12 @@ def MD_NPT(self, **kwargs): """ # user structure or relaxed or restrained or solvated - kwargs.setdefault('struct', self.get_last_structure()) - kwargs.setdefault('t',self.get_last_checkpoint()) # Pass checkpoint file from md_relaxed - kwargs.setdefault('mdp', self.mdp['MD_NPT']) - return self._MD('MD_NPT', **kwargs) + kwargs.setdefault("struct", self.get_last_structure()) + kwargs.setdefault( + "t", self.get_last_checkpoint() + ) # Pass checkpoint file from md_relaxed + kwargs.setdefault("mdp", self.mdp["MD_NPT"]) + return self._MD("MD_NPT", **kwargs) # for convenience and compatibility MD = MD_NPT @@ -617,49 +701,64 @@ def _lastnotempty(l): def get_last_structure(self): """Returns the coordinates of the most advanced step in the protocol.""" - return self._lastnotempty([self.files[name] for name in self.coordinate_structures]) + return self._lastnotempty( + [self.files[name] for name in self.coordinate_structures] + ) def get_last_checkpoint(self): """Returns the checkpoint of the most advanced step in the protocol. Relies on md.gro being present from previous simulation, assumes that checkpoint is then present. """ - return self._lastnotempty([self.files[name] for name in self.checkpoints]).replace('.gro','.cpt') + return self._lastnotempty( + [self.files[name] for name in self.checkpoints] + ).replace(".gro", ".cpt") + class WaterSimulation(Simulation): """Equilibrium MD of a solute in a box of water.""" - solvent_default = 'water' + + solvent_default = "water" dirname_default = os.path.join(Simulation.topdir_default, solvent_default) + class CyclohexaneSimulation(Simulation): """Equilibrium MD of a solute in a box of cyclohexane.""" - solvent_default = 'cyclohexane' + + solvent_default = "cyclohexane" dirname_default = os.path.join(Simulation.topdir_default, solvent_default) + class OctanolSimulation(Simulation): """Equilibrium MD of a solute in a box of octanol.""" - solvent_default = 'octanol' + + solvent_default = "octanol" dirname_default = os.path.join(Simulation.topdir_default, solvent_default) + class WetOctanolSimulation(Simulation): """Equilibrium MD of a solute in a box of wet octanol.""" - solvent_default = 'wetoctanol' + + solvent_default = "wetoctanol" dirname_default = os.path.join(Simulation.topdir_default, solvent_default) - def _setup_solvate(self, **kwargs): + def _setup_solvate(self, **kwargs): sol = gromacs.setup.solvate_sol(**kwargs) with in_dir(self.dirs.solvation, create=False): - u = mda.Universe('solvated.gro') - octanol = u.select_atoms('resname OcOH') + u = mda.Universe("solvated.gro") + octanol = u.select_atoms("resname OcOH") n = octanol.n_residues with in_dir(self.dirs.topology, create=False): - gromacs.cbook.edit_txt(self.files.topology, - [('OcOH 1', '1', n)]) + gromacs.cbook.edit_txt( + self.files.topology, [("OcOH 1", "1", n)] + ) ionkwargs = kwargs - ionkwargs['struct'] = sol['struct'] + ionkwargs["struct"] = sol["struct"] params = gromacs.setup.solvate_ion(**ionkwargs) return params + class TolueneSimulation(Simulation): """Equilibrium MD of a solute in a box of toluene.""" - solvent_default = 'toluene' - dirname_default = os.path.join(Simulation.topdir_default, solvent_default) \ No newline at end of file + + solvent_default = "toluene" + dirname_default = os.path.join(Simulation.topdir_default, solvent_default) diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index 7ad9ebe3..e06e95a9 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -55,41 +55,43 @@ """ import os +from dataclasses import dataclass from collections import defaultdict +from pathlib import Path +from typing import Dict, List, Union import logging + logger = logging.getLogger("mdpow.forecefields") +HERE = Path(__file__).parent +TOP_DIR = HERE / "top" + #: Default force field. At the moment, OPLS-AA, CHARMM/CGENFF, and AMBER/GAFF #: are directly supported. However, it is not recommended to change the #: default here as this behavior is not tested. DEFAULT_FORCEFIELD = "OPLS-AA" -#------------------------------------------------------------ -# Gromacs water models -#------------------------------------------------------------ - -#: See the file ``top/oplsaa.ff/watermodels.dat`` for a description of -#: available water models that are bundled with MDPOW. -GMX_WATERMODELS_DAT=""" -tip4p TIP4P TIP 4-point, recommended -tip3p TIP3P TIP 3-point -tip5p TIP5P TIP 5-point -spc SPC simple point charge -spce SPC/E extended simple point charge -m24 M24 TIP 3-point with modified LJ (M24) -tip4pd TIP4P-D TIP 4-point with modified dispersion (TIP4P-D) -tip4pew TIP4PEW TIP 4-point modified for use with Ewald techniques (TIP4PEW) -""" +@dataclass class GromacsSolventModel(object): """Data for a solvent model in Gromacs.""" - def __init__(self, identifier, name=None, itp=None, coordinates=None, - description=None, forcefield="OPLS-AA"): + + def __init__( + self, + identifier, + name=None, + itp=None, + coordinates=None, + description=None, + forcefield="OPLS-AA", + ): self.identifier = identifier self.name = name if name is not None else str(identifier).upper() - self.itp = itp if itp is not None else self.guess_filename('itp') - self.coordinates = coordinates if coordinates is not None else self.guess_filename('gro') + self.itp = itp if itp is not None else self.guess_filename("itp") + self.coordinates = ( + coordinates if coordinates is not None else self.guess_filename("gro") + ) self.description = description self.forcefield = forcefield @@ -98,23 +100,45 @@ def guess_filename(self, extension): return self.identifier.lower() + os.extsep + str(extension) def __repr__(self): - return "<{0[name]} water: identifier={0[identifier]}, ff={0[forcefield]}>".format(vars(self)) + return ( + "<{0[name]} water: identifier={0[identifier]}, ff={0[forcefield]}>".format( + vars(self) + ) + ) + +# ------------------------------------------------------------ +# Gromacs water models +# ------------------------------------------------------------ + +#: See the file ``top/oplsaa.ff/watermodels.dat`` for a description of +#: available water models that are bundled with MDPOW. +GMX_WATERMODELS_DAT=""" +tip4p TIP4P TIP 4-point, recommended +tip3p TIP3P TIP 3-point +tip5p TIP5P TIP 5-point +spc SPC simple point charge +spce SPC/E extended simple point charge +m24 M24 TIP 3-point with modified LJ (M24) +tip4pd TIP4P-D TIP 4-point with modified dispersion (TIP4P-D) +tip4pew TIP4PEW TIP 4-point modified for use with Ewald techniques (TIP4PEW) +""" #: For some water models we cannot derive the filename for the equilibrated box #: so we supply them explicitly. SPECIAL_WATER_COORDINATE_FILES = defaultdict( lambda: None, - spc='spc216.gro', - spce='spc216.gro', - tip3p='spc216.gro', - m24='spc216.gro', - tip4pd='tip4p.gro', - tip4pew='tip4p.gro', + spc="spc216.gro", + spce="spc216.gro", + tip3p="spc216.gro", + m24="spc216.gro", + tip4pd="tip4p.gro", + tip4pew="tip4p.gro", ) -def _create_water_models(watermodelsdat): +def _create_water_models(watermodelsdat: Path) -> Dict[str, GromacsSolventModel]: models = {} - for line in GMX_WATERMODELS_DAT.split('\n'): + data = watermodelsdat.read_text() + for line in data.split('\n'): line = line.strip() if not line or line.startswith('#'): continue @@ -127,6 +151,64 @@ def _create_water_models(watermodelsdat): description=description) return models +#: See the file ``top/oplsaa.ff/watermodels.dat`` for a description of +#: available water models that are bundled with MDPOW. + +#: Dictionary of :class:`GromacsSolventModel` instances, one for each Gromacs water +#: model available under the force field directory. The keys are the water model +#: identifiers. +#: For OPLS-AA the following ones are available. +GROMACS_WATER_MODELS: Dict[str, GromacsSolventModel] = { + "tip4p": GromacsSolventModel( + "tip4p", + name="TIP4P", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip4p"], + description="TIP 4-point, recommended", + ), + "tip3p": GromacsSolventModel( + "tip3p", + name="TIP3P", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip3p"], + description="TIP 3-point", + ), + "tip5p": GromacsSolventModel( + "tip5p", + name="TIP5P", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip5p"], + description="TIP 5-point", + ), + "spc": GromacsSolventModel( + "spc", + name="SPC", + coordinates=SPECIAL_WATER_COORDINATE_FILES["spc"], + description="simple point charge", + ), + "spce": GromacsSolventModel( + "spce", + name="SPC/E", + coordinates=SPECIAL_WATER_COORDINATE_FILES["spce"], + description="extended simple point charge", + ), + "m24": GromacsSolventModel( + "m24", + name="M24", + coordinates=SPECIAL_WATER_COORDINATE_FILES["m24"], + description="TIP 3-point with modified LJ (M24)", + ), + "tip4pd": GromacsSolventModel( + "tip4pd", + name="TIP4P-D", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip4pd"], + description="TIP 4-point with modified dispersion (TIP4P-D)", + ), + "tip4pew": GromacsSolventModel( + "tip4pew", + name="TIP4PEW", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip4pew"], + description="TIP 4-point modified for use with Ewald techniques (TIP4PEW)", + ), +} + #: Use the default water model unless another water model is chosen in the #: :ref:`run input file ` file by setting the #: ``setup.watermodel`` parameter. @@ -139,11 +221,6 @@ def _create_water_models(watermodelsdat): #: DEFAULT_WATER_MODEL = "tip4p" -#: Dictionary of :class:`GromacsSolventModel` instances, one for each Gromacs water -#: model available under the force field directory. The keys are the water model -#: identifiers. -#: For OPLS-AA the following ones are available. -GROMACS_WATER_MODELS = _create_water_models(GMX_WATERMODELS_DAT) def get_water_model(watermodel=DEFAULT_WATER_MODEL): """Return a :class:`GromacsSolventModel` corresponding to identifier *watermodel*""" @@ -152,63 +229,143 @@ def get_water_model(watermodel=DEFAULT_WATER_MODEL): return GROMACS_WATER_MODELS[watermodel] except KeyError: msg = "{0} is not a valid water model: choose one from {1}".format( - watermodel, ", ".join(GROMACS_WATER_MODELS.keys())) + watermodel, ", ".join(GROMACS_WATER_MODELS.keys()) + ) logger.error(msg) raise ValueError(msg) + +@dataclass +class Forcefield: + """Contains information about files corresponding to a forcefield.""" + + name: str + solvent_models: Dict[str, GromacsSolventModel] + forcefield_dir: Path + ions_itp: Path + default_water_itp: Path + + def __post_init__(self): + """Check that the provided paths exist and populate the :attr:`water_models`.""" + for path_ in self.ff_paths: + if not path_.exists(): + raise ValueError(f"Could not find required forcefield files: {path_}") + + self.water_models: Dict[str, GromacsSolventModel] = _create_water_models(self.forcefield_dir / "watermodels.dat") + + @property + def ff_paths(self) -> List[Path]: + """Get the path to the forcefield directory and the ITP files for the ions and default water model.""" + return [self.forcefield_dir, self.ions_itp, self.default_water_itp] + + def __repr__(self) -> str: + """Get the name of the force field.""" + return self.name + + #: Other solvents (not water, see :data:`GROMACS_WATER_MODELS` for those). -new_octanol = '''Zangi R (2018) Refinement of the OPLSAA force-field - for liquid alcohols.; ACS Omega 3(12):18089-18099. - doi: 10.1021/acsomega.8b03132''' - -OPLS_SOLVENT_MODELS = { - 'octanol': GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct.gro"), - 'octanolnew': GromacsSolventModel( - identifier="octanol", itp="1octnew.itp", coordinates="1oct.gro", - description=new_octanol), - 'cyclohexane': GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo.gro"), - 'wetoctanol': GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet.gro"), - 'wetoctanolnew': GromacsSolventModel( - identifier="wetoctanol", itp="1octwetnew.itp", coordinates="1octwet.gro", - description=new_octanol), - 'toluene': GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_oplsaa.gro"), - } +NEW_OCTANOL_DESC = "Zangi R (2018) Refinement of the OPLSAA force-field for liquid alcohols.; ACS Omega 3(12):18089-18099. doi: 10.1021/acsomega.8b03132" + +OPLS_AA_FF_DIR = TOP_DIR / "oplsaa.ff" +OPLS_AA = Forcefield( + "OPLS-AA", + { + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct.gro" + ), + "octanolnew": GromacsSolventModel( + identifier="octanol", + itp="1octnew.itp", + coordinates="1oct.gro", + description=NEW_OCTANOL_DESC, + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet.gro" + ), + "wetoctanolnew": GromacsSolventModel( + identifier="wetoctanol", + itp="1octwetnew.itp", + coordinates="1octwet.gro", + description=NEW_OCTANOL_DESC, + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_oplsaa.gro" + ), + }, + OPLS_AA_FF_DIR, + OPLS_AA_FF_DIR / "ions_opls.itp", + OPLS_AA_FF_DIR / "tip4p.itp", +) -CHARMM_SOLVENT_MODELS = { - 'octanol': GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct_charmm.gro"), - 'wetoctanol': GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_charmm.gro"), - 'cyclohexane': GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_charmm.gro"), - 'toluene': GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_charmm.gro"), - } +CHARMM_FF_DIR = TOP_DIR / "charmm36-mar2019.ff" +CHARMM = Forcefield( + "CHARMM", + { + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct_charmm.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_charmm.gro" + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_charmm.gro" + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_charmm.gro" + ), + }, + CHARMM_FF_DIR, + CHARMM_FF_DIR / "ions.itp", + CHARMM_FF_DIR / "tip3p.itp", +) -AMBER_SOLVENT_MODELS = { - 'octanol': GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct_amber.gro"), - 'wetoctanol': GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_amber.gro"), - 'cyclohexane': GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_amber.gro"), - 'toluene': GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_amber.gro"), - } +AMBER_FF_DIR = TOP_DIR / "amber99sb.ff" +AMBER = Forcefield( + "AMBER", + { + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct_amber.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_amber.gro" + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_amber.gro" + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_amber.gro" + ), + }, + AMBER_FF_DIR, + AMBER_FF_DIR / "ions.itp", + AMBER_FF_DIR / "tip3p.itp", +) + +ALL_FORCEFIELDS: Dict[str, Forcefield] = { + "OPLS-AA": OPLS_AA, + "CHARMM": CHARMM, + "AMBER": AMBER, +} #: Solvents available in GROMACS; the keys of the dictionary #: are the forcefields. GROMACS_SOLVENT_MODELS = { - 'OPLS-AA': OPLS_SOLVENT_MODELS, - 'CHARMM': CHARMM_SOLVENT_MODELS, - 'AMBER': AMBER_SOLVENT_MODELS, - } + "OPLS-AA": OPLS_AA.solvent_models, + "CHARMM": CHARMM.solvent_models, + "AMBER": AMBER.solvent_models, +} -def get_solvent_identifier(solvent_type, model=None, forcefield='OPLS-AA'): +def _get_forcefield(ff_name: str) -> Forcefield: + """Get the :class:`Forcefield` instance corresponding to a given name.""" + try: + return ALL_FORCEFIELDS[ff_name] + except KeyError: + raise ValueError(f"Forcefield `{ff_name}` not found.") + +def get_solvent_identifier(solvent_type, model=None, forcefield: Union[Forcefield, str] = OPLS_AA): """Get the identifier for a solvent model. The identifier is needed to access a water model (i.e., a @@ -230,66 +387,54 @@ def get_solvent_identifier(solvent_type, model=None, forcefield='OPLS-AA'): of OPLS-AA forcefield, the ``model`` is used to select a specific model. For other solvents and forcefields, "model" is not required. - :Returns: Either an identifier or ``None`` + :Raises ValueError: If there is no identifier found for the combination. + + :Returns: An identifier """ - + if isinstance(forcefield, str): + forcefield = _get_forcefield(forcefield) + if solvent_type == "water": - identifier = model if not model in (None, 'water') else DEFAULT_WATER_MODEL - return identifier if identifier in GROMACS_WATER_MODELS else None - if model not in GROMACS_SOLVENT_MODELS[forcefield]: - if solvent_type in GROMACS_SOLVENT_MODELS[forcefield]: + identifier = model if not model in (None, "water") else DEFAULT_WATER_MODEL + return identifier if identifier in forcefield.water_models else None + if model not in forcefield.solvent_models: + if solvent_type in forcefield.solvent_models: model = solvent_type else: model = None return model -def get_solvent_model(identifier, forcefield='OPLS-AA'): +def get_solvent_model(identifier, forcefield: Union[Forcefield, str] = OPLS_AA): """Return a :class:`GromacsSolventModel` corresponding to identifier *identifier*. If identifier is "water" then the :data:`DEFAULT_WATER_MODEL` is assumed. """ + if isinstance(forcefield, str): + forcefield = _get_forcefield(forcefield) if identifier == "water": identifier = DEFAULT_WATER_MODEL try: - return GROMACS_WATER_MODELS[identifier] + return forcefield.water_models[identifier] except KeyError: try: - return GROMACS_SOLVENT_MODELS[forcefield][identifier] + return forcefield.solvent_models[identifier] except KeyError: - msg = "No solvent model with name {0} is available.".format(identifier) + msg = "No solvent model with name {0} is available for forcefield {1}.".format(identifier, forcefield.name) logger.critical(msg) raise ValueError(msg) - -def get_ff_paths(forcefield='OPLS-AA'): - """Return a :list: containing the forcefield directory, paths of ions - and default watermodel itp files. - """ - - settings = { - 'OPLS-AA': ['oplsaa.ff/', 'oplsaa.ff/ions_opls.itp', - 'oplsaa.ff/tip4p.itp'], - 'AMBER': ['amber99sb.ff/', 'amber99sb.ff/ions.itp', - 'amber99sb.ff/tip3p.itp'], - 'CHARMM': ['charmm36-mar2019.ff/', 'charmm36-mar2019.ff/ions.itp', - 'charmm36-mar2019.ff/tip3p.itp'], - } - try: - return settings[forcefield] - except KeyError: - msg = "No forcefield with name {0} is available".format(forcefield) - logger.critical(msg) - raise ValueError(msg) - - def get_top_template(identifier): """Return the topology file template suitable for the solvent model.""" - - templates = {'water': 'system.top', 'octanol': 'system.top', - 'cyclohexane': 'system.top', 'wetoctanol': 'system_octwet.top', - 'toluene': 'system.top',} + + templates = { + "water": "system.top", + "octanol": "system.top", + "cyclohexane": "system.top", + "wetoctanol": "system_octwet.top", + "toluene": "system.top", + } try: return templates[identifier] except KeyError: diff --git a/mdpow/templates/system.top b/mdpow/templates/system.top index 21fa8baa..fefad275 100644 --- a/mdpow/templates/system.top +++ b/mdpow/templates/system.top @@ -6,22 +6,22 @@ ; to change it as needed. See the source mdpow/equil.py for details. ; Include forcefield parameters -#include "oplsaa.ff/forcefield.itp" +#include "$forcefield_itp" ; Include compound topology -#include "compound.prm" -#include "compound.itp" +$prm_line +#include "$compound_itp" ; Include solvent topology -#include "oplsaa.ff/tip4p.itp" +#include "$solvent_itp" ; Include topology for OPLS/AA ions -#include "oplsaa.ff/ions_opls.itp" +#include "$ions_itp" [ system ] ; Name -Compound DRUG in solvent +Compound $compound_name in $solvent [ molecules ] ; Compound #mols -DRUG 1 +$compound_name 1 diff --git a/mdpow/templates/system_octwet.top b/mdpow/templates/system_octwet.top index 4c8c6054..be32d0db 100644 --- a/mdpow/templates/system_octwet.top +++ b/mdpow/templates/system_octwet.top @@ -6,24 +6,24 @@ ; to change it as needed. See the source mdpow/equil.py for details. ; Include forcefield parameters -#include "oplsaa.ff/forcefield.itp" +#include "$forcefield_itp" ; Include compound topology -#include "compound.prm" -#include "compound.itp" +$prm_line +#include "$compound_itp" ; Include solvent topology -#include "oplsaa.ff/tip4p.itp" -#include "water.itp" +#include "$solvent_itp" ; Include topology for OPLS/AA ions -#include "oplsaa.ff/ions_opls.itp" +#include "$ions_itp" +#include "$water_itp" [ system ] ; Name -Compound DRUG in solvent +Compound $compound_name in $solvent [ molecules ] ; Compound #mols -DRUG 1 +$compound_name 1 ;OcOH 1 diff --git a/mdpow/tests/test_forcefields.py b/mdpow/tests/test_forcefields.py index 5e95be83..37966b5d 100644 --- a/mdpow/tests/test_forcefields.py +++ b/mdpow/tests/test_forcefields.py @@ -100,7 +100,7 @@ class TestSolventModels(object): def test_get_solvent_default_water(): model = "water" defaultmodel = mdpow.forcefields.DEFAULT_WATER_MODEL - assert (mdpow.forcefields.get_solvent_model(model) is + assert (mdpow.forcefields.get_solvent_model(model) == mdpow.forcefields.GROMACS_WATER_MODELS[defaultmodel]) @staticmethod From 954f0729e16078bdf2f7fb2275f97691e09a616b Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Fri, 18 Aug 2023 19:10:40 +0100 Subject: [PATCH 02/38] Add Sphinx docstring --- mdpow/forcefields.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index e06e95a9..2b8ae2db 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -47,6 +47,9 @@ .. autoclass:: GromacsSolventModel :members: +.. autoclass:: Forcefield + :members: + .. autofunction:: get_water_model .. autofunction:: get_solvent_identifier From 0f532046c998116ee392363c7755f01e00e244ab Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 21 Aug 2023 14:10:26 +0100 Subject: [PATCH 03/38] Change template file extensions --- mdpow/templates/{system.top => system.top.template} | 0 mdpow/templates/{system_octwet.top => system_octwet.top.template} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename mdpow/templates/{system.top => system.top.template} (100%) rename mdpow/templates/{system_octwet.top => system_octwet.top.template} (100%) diff --git a/mdpow/templates/system.top b/mdpow/templates/system.top.template similarity index 100% rename from mdpow/templates/system.top rename to mdpow/templates/system.top.template diff --git a/mdpow/templates/system_octwet.top b/mdpow/templates/system_octwet.top.template similarity index 100% rename from mdpow/templates/system_octwet.top rename to mdpow/templates/system_octwet.top.template From 2b7f3a94f11e596a9bd14414dbb93a8bd741282c Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 21 Aug 2023 17:51:32 +0100 Subject: [PATCH 04/38] [WIP] Boilerplate for Martini benzene Pow --- .gitignore | 6 + doc/examples/martini/em.mdp | 16 + doc/examples/martini/eq.mdp | 23 + doc/examples/martini/martini-benzene.ipynb | 122 + doc/examples/martini/run.mdp | 101 + doc/examples/martini/water.gro | 2707 ++++++++++++++++++++ 6 files changed, 2975 insertions(+) create mode 100644 doc/examples/martini/em.mdp create mode 100644 doc/examples/martini/eq.mdp create mode 100644 doc/examples/martini/martini-benzene.ipynb create mode 100644 doc/examples/martini/run.mdp create mode 100644 doc/examples/martini/water.gro diff --git a/.gitignore b/.gitignore index ed42a5df..53a68245 100644 --- a/.gitignore +++ b/.gitignore @@ -15,3 +15,9 @@ coverage.xml *.lock *.npz dir.csv + +# Files for the Martini example that can be downloaded at runtime +doc/examples/martini/* +!doc/examples/martini/*.mdp +!doc/examples/martini/*.ipynb +!doc/examples/martini/water.gro diff --git a/doc/examples/martini/em.mdp b/doc/examples/martini/em.mdp new file mode 100644 index 00000000..5035d5e6 --- /dev/null +++ b/doc/examples/martini/em.mdp @@ -0,0 +1,16 @@ +integrator = steep +dt = 0.02 +nsteps = 1000 +nstxout = 0 +nstvout = 0 +nstlog = 100 +nstxtcout = 100 +xtc-precision = 1000 +rlist = 1.4 +coulombtype = Reaction-Field +rcoulomb = 1.1 +epsilon_r = 15 +vdw-type = cutoff +vdw-modifier = Potential-shift-verlet +rvdw = 1.1 +constraints = none diff --git a/doc/examples/martini/eq.mdp b/doc/examples/martini/eq.mdp new file mode 100644 index 00000000..2a15bc2a --- /dev/null +++ b/doc/examples/martini/eq.mdp @@ -0,0 +1,23 @@ +dt = 0.005 +nsteps = 25000 +nstxout = 0 +nstvout = 0 +nstlog = 1000 +nstxout-compressed = 1000 +cutoff-scheme = Verlet +coulombtype = Reaction-Field +rcoulomb = 1.1 +epsilon_r = 15 +vdw-type = cutoff +vdw-modifier = Potential-shift-verlet +rvdw = 1.1 +tcoupl = v-rescale +tc-grps = System +tau-t = 1.0 +ref-t = 300 +Pcoupl = c-rescale +Pcoupltype = isotropic +tau-p = 3.0 +compressibility = 3e-4 +ref-p = 1.0 +refcoord_scaling = all diff --git a/doc/examples/martini/martini-benzene.ipynb b/doc/examples/martini/martini-benzene.ipynb new file mode 100644 index 00000000..0e0d1b28 --- /dev/null +++ b/doc/examples/martini/martini-benzene.ipynb @@ -0,0 +1,122 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Example: using a different force field\n", + "\n", + "Here we show how to use MDPOW to calculate partition coefficients using an force field that isn't included in the package. To follow along, install `jupyter` in your `mdpow` environment.\n", + "\n", + "To implement a new force field, you will need:\n", + "\n", + "* `ITP` files for the molecule, the solvents, ions and also the general atom type definitions file (usually just named after the force field itself).\n", + "* `MDP` files for the energy minimisation, initial relaxation, NPT ensemble run and free energy calculation.\n", + "* Structure files (`.gro` or `.pdb`) for the solute and non-aqueous solvent. If you are using a type of water that does not come bundled with GROMACS, like in this example, you will also need to create an equilibrated box of pure water.\n", + "\n", + "The first thing we'll do is to download the files we need for Martini 3.0." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "from typing import Optional\n", + "\n", + "import requests as req\n", + "from zipfile import ZipFile\n", + "\n", + "HERE = Path(\".\")\n", + "\n", + "MARTINI_ITP = HERE / \"martini_v3.0.0.itp\"\n", + "MARTINI_IONS = HERE / \"martini_v3.0.0_ions_v1.itp\"\n", + "MARTINI_SMALL_MOLS = HERE / \"martini_v3.0.0_small_molecules_v1.itp\"\n", + "MARTINI_SOLVENTS = HERE / \"martini_v3.0.0_solvents_v1.itp\"\n", + "MARTINI_WATER = HERE / \"water.gro\"\n", + "MARTINI_OCTANOL = HERE / \"octanol.gro\"\n", + "\n", + "EM_FILE = HERE / \"em.mdp\"\n", + "EQ_FILE = HERE / \"eq.mdp\"\n", + "RUN_FILE = HERE / \"run.mdp\"\n", + "\n", + "def download_file(\n", + " url: str, out: Optional[Path] = None, chunk_size: int = 128, overwrite: bool = False\n", + "):\n", + " \"\"\"Utility function to download files.\"\"\"\n", + " if out is None:\n", + " out = HERE / Path(url).name\n", + "\n", + " if out.exists() and not overwrite:\n", + " return\n", + "\n", + " r = req.get(url, stream=True)\n", + " r.raise_for_status()\n", + "\n", + " with out.open(\"wb\") as f:\n", + " for chunk in r.iter_content(chunk_size=chunk_size):\n", + " f.write(chunk)\n", + "\n", + "\n", + "ZIP_DOWNLOAD = {\n", + " HERE / \"BENZ.itp\": \"https://mad.ibcp.fr/api/molecule/download?id=731653322400583591&filename=BENZ.zip\"\n", + "}\n", + "DOWNLOADS = {\n", + " MARTINI_ITP: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0.itp\",\n", + " MARTINI_IONS: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_ions_v1.itp\",\n", + " MARTINI_SMALL_MOLS: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_small_molecules_v1.itp\",\n", + " MARTINI_SOLVENTS: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_solvents_v1.itp\",\n", + "}\n", + "DOWNLOADS.update(ZIP_DOWNLOAD)\n", + "\n", + "for fname, url in DOWNLOADS.items():\n", + " download_file(url, fname)\n", + "\n", + "for zip_file in ZIP_DOWNLOAD.keys():\n", + " with ZipFile(zip_file, \"r\") as zip_ref:\n", + " zip_ref.extractall(HERE)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This should have downloaded several files to your workspace." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import gromacs\n", + "from mdpow import equil, forcefields, fep" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "mdpow", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.4" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/doc/examples/martini/run.mdp b/doc/examples/martini/run.mdp new file mode 100644 index 00000000..aed06872 --- /dev/null +++ b/doc/examples/martini/run.mdp @@ -0,0 +1,101 @@ +integrator = sd +; start time and timestep in ps = +tinit = 0 +dt = 0.020 + +nsteps = 200000 + +; We remove center of mass motion. In periodic boundary conditions, the center of mass motion is spurious; the periodic system is the same in all translational directions. +comm-mode = Linear +; number of steps for center of mass motion removal = +nstcomm = 10 + +; Output frequency for energies to log file and energy file = +nstxout = 0 +nstvout = 0 +nstfout = 0 +nstlog = 10000 +nstenergy = 10000 +nstcalcenergy = 10 +nstxtcout = 10000 + +cutoff-scheme = Verlet +nstlist = 20 +;rlist = 1.2 + +coulombtype = cutoff +coulomb-modifier = Potential-shift-verlet +rcoulomb = 1.1 +epsilon_r = 15 ; 2.5 (with polarizable water) +vdw_type = cutoff +vdw-modifier = Potential-shift-verlet +rvdw = 1.1 + +;coulombtype = Shift +;rcoulomb_switch = 0.0 +;rcoulomb = 1.2 +;epsilon_r = 15 +;vdw_type = Shift +;rvdw_switch = 0.9 +;rvdw = 1.2 + + +gen-vel = no +gen_seed = 175547 +tc-grps = System +tcoupl = v-rescale +tau_t = 1.0 +ref_t = 300 +; Pressure coupling = +Pcoupl = Parrinello-Rahman +tau_p = 4.0 +compressibility = 4.5e-5 +ref_p = 1.0 + +;lincs-iter = 2 +;lincs-order = 8 + +;-------------------- +; Free energy parameters +free-energy = yes +sc-power = 1 +sc-alpha = 0.5 +sc-r-power = 6 + +; Which intermediate state do we start with? Doesn't really matter, it leaves soon +------- +init-lambda-state = 0 + +; What are the values of lambda at the intermediate states? +;------- +vdw-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 + +; This makes sure we print out the differences in Hamiltonians between all states, and not just the neighboring states +;-------- +calc-lambda-neighbors = -1 + +; the frequency the free energy information is calculated. This +; frequency (every 0.2 ps) is pretty good for small molecule solvation. +;------- +nstdhdl = 10 + +; not required, but useful if you are doing any temperature reweighting. Without +; temperature reweighting, you don't need the total energy -- differences are enough +dhdl-print-energy = yes + +; We are doing free energies with the solute molecule alone +couple-moltype = SOLUTE + +; decharging free energy +; couple-lambda0 = vdw-q +; couple-lambda1 = vdw +; LJ decoupling free energy +; couple-lambda0 = vdw +; couple-lambda1 = none +; +; fully coupled (change for BAR!) +couple-lambda0 = vdw-q +couple-lambda1 = vdw-q + +; we are keeping the intramolecular interactions ON in all the interactions from state 0 to state 8 +couple-intramol = no diff --git a/doc/examples/martini/water.gro b/doc/examples/martini/water.gro new file mode 100644 index 00000000..81cc49ef --- /dev/null +++ b/doc/examples/martini/water.gro @@ -0,0 +1,2707 @@ +Bulk water + 2704 + 2W W 9 0.623 6.453 2.746 -0.0737 -0.1789 -0.1413 + 3W W 10 1.495 0.821 3.127 -0.1418 -0.1647 0.0677 + 4W W 11 2.276 4.379 0.851 0.2728 0.0220 0.2236 + 5W W 12 5.055 4.688 2.860 0.0937 -0.3331 -0.0833 + 6W W 13 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2.818 3.653 1.065 -0.1807 0.2447 -0.2448 + 2691W W 2698 5.707 3.343 1.433 -0.1670 -0.0935 0.0519 + 2692W W 2699 6.606 0.655 4.026 -0.0801 0.1854 0.0575 + 2693W W 2700 6.573 1.203 4.149 0.1100 0.0042 -0.0778 + 2694W W 2701 6.420 0.823 6.145 -0.1045 -0.0272 -0.0958 + 2695W W 2702 1.048 5.973 1.363 -0.0304 -0.2457 0.0535 + 2696W W 2703 1.528 4.309 1.440 0.3895 -0.3613 -0.1011 + 2697W W 2704 2.350 4.015 1.670 -0.1132 0.2028 0.1334 + 2698W W 2705 4.812 1.911 4.112 -0.2072 -0.2805 0.0912 + 2699W W 2706 0.972 0.124 1.147 -0.2538 0.0397 0.0581 + 2700W W 2707 1.525 3.455 0.600 -0.1575 -0.2820 0.1895 + 2701W W 2708 1.975 6.201 6.625 0.0036 0.1664 -0.1642 + 2702W W 2709 4.301 3.342 1.379 -0.1293 -0.1352 -0.2467 + 2703W W 2710 3.671 2.397 6.009 0.0508 0.0352 0.0895 + 2704W W 2711 5.800 2.764 5.035 -0.1177 -0.1528 0.0000 + 2705W W 2712 6.639 3.898 1.301 0.0357 0.3257 -0.2098 + 6.85823 6.85823 6.85823 From 8f061e7da99eb78353e9392d6929673da5b352a3 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 21 Aug 2023 14:06:20 +0100 Subject: [PATCH 05/38] format ALL files with black No functional changes. --- doc/examples/benzene/session.py | 22 +- doc/sphinx/source/conf.py | 161 +-- mdpow/__init__.py | 29 +- mdpow/_version.py | 154 ++- mdpow/analysis/dihedral.py | 55 +- mdpow/analysis/ensemble.py | 185 ++- mdpow/analysis/solvation.py | 38 +- mdpow/config.py | 120 +- mdpow/equil.py | 433 ++++--- mdpow/fep.py | 755 +++++++----- mdpow/filelock.py | 47 +- mdpow/forcefields.py | 198 ++-- mdpow/log.py | 10 +- mdpow/restart.py | 38 +- mdpow/run.py | 215 ++-- mdpow/tests/__init__.py | 2 +- mdpow/tests/tempdir.py | 19 +- mdpow/tests/test_Gsolv.py | 33 +- mdpow/tests/test_analysis.py | 44 +- mdpow/tests/test_analysis_alchemlyb.py | 134 ++- .../tests/test_automated_dihedral_analysis.py | 300 +++-- mdpow/tests/test_config.py | 26 +- mdpow/tests/test_dihedral.py | 62 +- mdpow/tests/test_ensemble.py | 118 +- mdpow/tests/test_equilibration_script.py | 38 +- mdpow/tests/test_fep.py | 137 ++- mdpow/tests/test_fep_analysis.py | 45 +- mdpow/tests/test_fep_script.py | 57 +- mdpow/tests/test_filelock.py | 2 + mdpow/tests/test_forcefields.py | 129 +- mdpow/tests/test_run.py | 90 +- mdpow/tests/test_runinput.py | 149 ++- mdpow/tests/test_solv_shell.py | 41 +- mdpow/tests/test_solvation.py | 65 +- mdpow/tests/test_version.py | 5 +- mdpow/tests/test_workflows_base.py | 123 +- mdpow/tests/test_workflows_registry.py | 3 +- mdpow/workflows/base.py | 182 +-- mdpow/workflows/dihedrals.py | 1056 +++++++++-------- mdpow/workflows/registry.py | 4 +- scripts/mdpow-cfg2yaml.py | 25 +- setup.py | 136 ++- versioneer.py | 267 +++-- 43 files changed, 3451 insertions(+), 2301 deletions(-) diff --git a/doc/examples/benzene/session.py b/doc/examples/benzene/session.py index b0ff5276..da1ac8d9 100644 --- a/doc/examples/benzene/session.py +++ b/doc/examples/benzene/session.py @@ -1,31 +1,39 @@ import mdpow.equil + S = mdpow.equil.WaterSimulation(molecule="BNZ") S.topology("benzene.itp") S.solvate(struct="benzene.pdb") S.energy_minimize() -S.MD_relaxed(runtime=5) # should be at least 1e3 ps for production not just 5 ps +S.MD_relaxed(runtime=5) # should be at least 1e3 ps for production not just 5 ps # run simulation externally or use MDrunner # (see docs for using mpi etc) import gromacs -r = gromacs.run.MDrunner(dirname=S.dirs['MD_relaxed'], deffnm="md", c="md.pdb", cpi=True, append=True, v=True) -r.run() # runs mdrun in the python shell + +r = gromacs.run.MDrunner( + dirname=S.dirs["MD_relaxed"], deffnm="md", c="md.pdb", cpi=True, append=True, v=True +) +r.run() # runs mdrun in the python shell -S.MD(runtime=10, qscript=['local.sh']) # should be at least 10e3 ps for production, not just 10 ps +S.MD( + runtime=10, qscript=["local.sh"] +) # should be at least 10e3 ps for production, not just 10 ps # run simulation -r = gromacs.run.MDrunner(dirname=S.dirs['MD_NPT'], deffnm="md", c="md.pdb", cpi=True, append=True, v=True) -r.run() # runs mdrun in the python shell +r = gromacs.run.MDrunner( + dirname=S.dirs["MD_NPT"], deffnm="md", c="md.pdb", cpi=True, append=True, v=True +) +r.run() # runs mdrun in the python shell import mdpow.fep + gwat = mdpow.fep.Ghyd(simulation=S, runtime=10) gwat.setup() # run multiple simulations on cluster - O = mdpow.equil.OctanolSimulation(molecule="BNZ") O.topology("benzene.itp") O.solvate(struct="benzene.pdb") diff --git a/doc/sphinx/source/conf.py b/doc/sphinx/source/conf.py index d32857d0..b55c6df5 100644 --- a/doc/sphinx/source/conf.py +++ b/doc/sphinx/source/conf.py @@ -14,6 +14,7 @@ import sys import os import datetime + # https://sphinx-rtd-theme.readthedocs.io/en/stable/ import sphinx_rtd_theme @@ -22,45 +23,51 @@ # is relative to the documentation root, use os.path.abspath to make it # absolute, like shown here. # make sure sphinx always uses the current branch -sys.path.insert(0, os.path.abspath('../../..')) +sys.path.insert(0, os.path.abspath("../../..")) # -- General configuration ----------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. # 'sphinx.ext.pngmath', 'sphinx.ext.jsmath' -extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx', - 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', - 'sphinx_rtd_theme'] +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.intersphinx", + "sphinx.ext.mathjax", + "sphinx.ext.viewcode", + "sphinx_rtd_theme", +] -mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML' +mathjax_path = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML" # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # The suffix of source filenames. -source_suffix = '.txt' +source_suffix = ".txt" # The encoding of source files. -#source_encoding = 'utf-8' +# source_encoding = 'utf-8' # The master toctree document. -master_doc = 'index' +master_doc = "index" # General information about the project. -project = u'MDPOW' +project = "MDPOW" now = datetime.datetime.now() -copyright = u'2010–{}, Shujie Fan, Ian Kenney, Alia Lescoulie, Bogdan Iorga, and Oliver Beckstein'.format(now.year) +copyright = "2010–{}, Shujie Fan, Ian Kenney, Alia Lescoulie, Bogdan Iorga, and Oliver Beckstein".format( + now.year +) # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # Dynamically calculate the version -packageversion = __import__('mdpow').__version__ +packageversion = __import__("mdpow").__version__ # The short X.Y version. -version = '.'.join(packageversion.split('.')[:2]) +version = ".".join(packageversion.split(".")[:2]) # The full version, including alpha/beta/rc tags. ##release = packageversion @@ -73,7 +80,7 @@ except ValueError: ver, rc = packageversion, None -if not rc or rc.startswith('0'): +if not rc or rc.startswith("0"): release = ver else: release = ver + "+" + rc.replace(".dirty", "") @@ -81,73 +88,71 @@ # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. -#language = None +# language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: -#today = '' +# today = '' # Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' +# today_fmt = '%B %d, %Y' # List of documents that shouldn't be included in the build. -#unused_docs = [] +# unused_docs = [] # List of directories, relative to source directory, that shouldn't be searched # for source files. exclude_trees = [] # The reST default role (used for this markup: `text`) to use for all documents. -#default_role = None +# default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True +# add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). -#add_module_names = True +# add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. -#show_authors = False +# show_authors = False # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = "sphinx" # A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] +# modindex_common_prefix = [] # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'sphinx_rtd_theme' +html_theme = "sphinx_rtd_theme" html_theme_options = { - 'logo_only': False, - 'display_version': True, - 'prev_next_buttons_location': 'bottom', - 'style_external_links': False, - 'style_nav_header_background': 'white', + "logo_only": False, + "display_version": True, + "prev_next_buttons_location": "bottom", + "style_external_links": False, + "style_nav_header_background": "white", # Toc options - 'collapse_navigation': True, - 'sticky_navigation': True, - 'navigation_depth': 4, - 'includehidden': True, - 'titles_only': False, + "collapse_navigation": True, + "sticky_navigation": True, + "navigation_depth": 4, + "includehidden": True, + "titles_only": False, } # Add any paths that contain custom themes here, relative to this directory. -html_theme_path = [ - sphinx_rtd_theme.get_html_theme_path() -] +html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". -#html_title = None +# html_title = None # A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None +# html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. @@ -161,98 +166,102 @@ # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +html_static_path = ["_static"] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. -html_last_updated_fmt = '%b %d, %Y' +html_last_updated_fmt = "%b %d, %Y" # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. -#html_use_smartypants = True +# html_use_smartypants = True # Custom sidebar templates, maps document names to template names. -#html_sidebars = {} +# html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. -#html_additional_pages = {} +# html_additional_pages = {} # If false, no module index is generated. -#html_use_modindex = True +# html_use_modindex = True # If false, no index is generated. -#html_use_index = True +# html_use_index = True # If true, the index is split into individual pages for each letter. -#html_split_index = False +# html_split_index = False # If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True +# html_show_sourcelink = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. -#html_use_opensearch = '' +# html_use_opensearch = '' # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = '' +# html_file_suffix = '' # Output file base name for HTML help builder. -htmlhelp_basename = 'MDPOWdoc' +htmlhelp_basename = "MDPOWdoc" # -- Options for LaTeX output -------------------------------------------------- # The paper size ('letter' or 'a4'). -#latex_paper_size = 'letter' +# latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). -#latex_font_size = '10pt' +# latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('index', 'MDpow.tex', u'MDpow Documentation', - u'Ian Kenney, Bogdan Iorga, and Oliver Beckstein', 'manual'), + ( + "index", + "MDpow.tex", + "MDpow Documentation", + "Ian Kenney, Bogdan Iorga, and Oliver Beckstein", + "manual", + ), ] # The name of an image file (relative to this directory) to place at the top of # the title page. -#latex_logo = None +# latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. -#latex_use_parts = False +# latex_use_parts = False # Additional stuff for the LaTeX preamble. -#latex_preamble = '' +# latex_preamble = '' # Documents to append as an appendix to all manuals. -#latex_appendices = [] +# latex_appendices = [] # If false, no module index is generated. -#latex_use_modindex = True - +# latex_use_modindex = True # Options for ext.intersphinx # --------------------------- # intersphinx: reference standard lib and RecSQL # http://sphinx.pocoo.org/latest/ext/intersphinx.html -intersphinx_mapping = {'https://docs.python.org/': None, - 'https://numpy.org/doc/stable/': None, - 'https://docs.scipy.org/doc/scipy/reference/': None, - 'https://gromacswrapper.readthedocs.io/en/latest': None, - 'https://docs.mdanalysis.org/stable/': None, - 'https://www.rdkit.org/docs/': None, - 'https://pandas.pydata.org/docs/': None, - 'https://seaborn.pydata.org': None, - 'https://cairosvg.org/documentation/': None, - 'https://svgutils.readthedocs.io/en/latest/': None, - 'https://pypdf.readthedocs.io/en/stable/': None, - } - +intersphinx_mapping = { + "https://docs.python.org/": None, + "https://numpy.org/doc/stable/": None, + "https://docs.scipy.org/doc/scipy/reference/": None, + "https://gromacswrapper.readthedocs.io/en/latest": None, + "https://docs.mdanalysis.org/stable/": None, + "https://www.rdkit.org/docs/": None, + "https://pandas.pydata.org/docs/": None, + "https://seaborn.pydata.org": None, + "https://cairosvg.org/documentation/": None, + "https://svgutils.readthedocs.io/en/latest/": None, + "https://pypdf.readthedocs.io/en/stable/": None, +} # Options for ext.autodoc @@ -262,4 +271,4 @@ # This value selects what content will be inserted into the main body of an autoclass directive. # "class", "init", "both" autoclass_content = "both" -automodule_content = "both" \ No newline at end of file +automodule_content = "both" diff --git a/mdpow/__init__.py b/mdpow/__init__.py index 63e1a96f..371ec35f 100644 --- a/mdpow/__init__.py +++ b/mdpow/__init__.py @@ -5,10 +5,12 @@ from . import log from ._version import get_versions -__version__ = get_versions()['version'] + +__version__ = get_versions()["version"] del get_versions -__all__ = ['fep', 'equil'] +__all__ = ["fep", "equil"] + def create_logger(logfile="mdpow.log"): """Create the default logger. @@ -16,19 +18,25 @@ def create_logger(logfile="mdpow.log"): Channels the output from :mod:`mdpow`, :mod:`gromacs`, and :mod:`numkit` into the file *logfile*. """ - logger = log.create('mdpow', logfile) - log.create('numkit', logfile) # capture numkit messages to same file - log.create('gromacs', logfile) # and the GromacsWrapper messages + logger = log.create("mdpow", logfile) + log.create("numkit", logfile) # capture numkit messages to same file + log.create("gromacs", logfile) # and the GromacsWrapper messages return logger + def log_banner(logger): """Log program name and licence at INFO level.""" logger.info("MDPOW %s starting.", __version__) - logger.info("Copyright (c) 2010-2023 Shujie Fan, Ian Kenney, " - "Alia Lescoulie, Cade Duckworth, Bogdan Iorga, and " - "Oliver Beckstein") + logger.info( + "Copyright (c) 2010-2023 Shujie Fan, Ian Kenney, " + "Alia Lescoulie, Cade Duckworth, Bogdan Iorga, and " + "Oliver Beckstein" + ) logger.info("Released under the GNU Public Licence, version 3.") - logger.info("For bug reports and help: https://github.com/Becksteinlab/MDPOW/issues") + logger.info( + "For bug reports and help: https://github.com/Becksteinlab/MDPOW/issues" + ) + logger = create_logger() log_banner(logger) @@ -43,5 +51,4 @@ def log_banner(logger): #: Avogadro's constant |NA| in mol^-1 (`NA NIST value`_). N_AVOGADRO = 6.02214179e23 #: Boltzmann's constant |kB| in kJ mol^-1 (`kB NIST value`_). -kBOLTZ = 1.3806504e-23 *1e-3 * N_AVOGADRO - +kBOLTZ = 1.3806504e-23 * 1e-3 * N_AVOGADRO diff --git a/mdpow/_version.py b/mdpow/_version.py index 2484e7bd..e5328388 100644 --- a/mdpow/_version.py +++ b/mdpow/_version.py @@ -1,4 +1,3 @@ - # This file helps to compute a version number in source trees obtained from # git-archive tarball (such as those provided by githubs download-from-tag # feature). Distribution tarballs (built by setup.py sdist) and build @@ -57,17 +56,18 @@ class NotThisMethod(Exception): def register_vcs_handler(vcs, method): # decorator """Decorator to mark a method as the handler for a particular VCS.""" + def decorate(f): """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} HANDLERS[vcs][method] = f return f + return decorate -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): +def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): """Call the given command(s).""" assert isinstance(commands, list) p = None @@ -75,10 +75,13 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, try: dispcmd = str([c] + args) # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) + p = subprocess.Popen( + [c] + args, + cwd=cwd, + env=env, + stdout=subprocess.PIPE, + stderr=(subprocess.PIPE if hide_stderr else None), + ) break except EnvironmentError: e = sys.exc_info()[1] @@ -115,16 +118,22 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): for i in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} + return { + "version": dirname[len(parentdir_prefix) :], + "full-revisionid": None, + "dirty": False, + "error": None, + "date": None, + } else: rootdirs.append(root) root = os.path.dirname(root) # up a level if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) + print( + "Tried directories %s but none started with prefix %s" + % (str(rootdirs), parentdir_prefix) + ) raise NotThisMethod("rootdir doesn't start with parentdir_prefix") @@ -180,7 +189,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) + tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d @@ -189,7 +198,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) + tags = set([r for r in refs if re.search(r"\d", r)]) if verbose: print("discarding '%s', no digits" % ",".join(refs - tags)) if verbose: @@ -197,19 +206,26 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): for ref in sorted(tags): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] + r = ref[len(tag_prefix) :] if verbose: print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} + return { + "version": r, + "full-revisionid": keywords["full"].strip(), + "dirty": False, + "error": None, + "date": date, + } # no suitable tags, so version is "0+unknown", but full hex is still there if verbose: print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} + return { + "version": "0+unknown", + "full-revisionid": keywords["full"].strip(), + "dirty": False, + "error": "no suitable tags", + "date": None, + } @register_vcs_handler("git", "pieces_from_vcs") @@ -224,8 +240,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) + out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) if rc != 0: if verbose: print("Directory %s not under git control" % root) @@ -233,10 +248,19 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%s*" % tag_prefix], - cwd=root) + describe_out, rc = run_command( + GITS, + [ + "describe", + "--tags", + "--dirty", + "--always", + "--long", + "--match", + "%s*" % tag_prefix, + ], + cwd=root, + ) # --long was added in git-1.5.5 if describe_out is None: raise NotThisMethod("'git describe' failed") @@ -259,17 +283,16 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): dirty = git_describe.endswith("-dirty") pieces["dirty"] = dirty if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] + git_describe = git_describe[: git_describe.rindex("-dirty")] # now we have TAG-NUM-gHEX or HEX if "-" in git_describe: # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) + mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) if not mo: # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) + pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out return pieces # tag @@ -278,10 +301,12 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if verbose: fmt = "tag '%s' doesn't start with prefix '%s'" print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) + pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( + full_tag, + tag_prefix, + ) return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] + pieces["closest-tag"] = full_tag[len(tag_prefix) :] # distance: number of commits since tag pieces["distance"] = int(mo.group(2)) @@ -292,13 +317,13 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): else: # HEX: no tags pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) + count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) pieces["distance"] = int(count_out) # total number of commits # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], - cwd=root)[0].strip() + date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[ + 0 + ].strip() pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces @@ -329,8 +354,7 @@ def render_pep440(pieces): rendered += ".dirty" else: # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) + rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) if pieces["dirty"]: rendered += ".dirty" return rendered @@ -444,11 +468,13 @@ def render_git_describe_long(pieces): def render(pieces, style): """Render the given version pieces into the requested style.""" if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} + return { + "version": "unknown", + "full-revisionid": pieces.get("long"), + "dirty": None, + "error": pieces["error"], + "date": None, + } if not style or style == "default": style = "pep440" # the default @@ -468,9 +494,13 @@ def render(pieces, style): else: raise ValueError("unknown style '%s'" % style) - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} + return { + "version": rendered, + "full-revisionid": pieces["long"], + "dirty": pieces["dirty"], + "error": None, + "date": pieces.get("date"), + } def get_versions(): @@ -484,8 +514,7 @@ def get_versions(): verbose = cfg.verbose try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) + return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose) except NotThisMethod: pass @@ -494,13 +523,16 @@ def get_versions(): # versionfile_source is the relative path from the top of the source # tree (where the .git directory might live) to this file. Invert # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): + for i in cfg.versionfile_source.split("/"): root = os.path.dirname(root) except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} + return { + "version": "0+unknown", + "full-revisionid": None, + "dirty": None, + "error": "unable to find root of source tree", + "date": None, + } try: pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) @@ -514,6 +546,10 @@ def get_versions(): except NotThisMethod: pass - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} + return { + "version": "0+unknown", + "full-revisionid": None, + "dirty": None, + "error": "unable to compute version", + "date": None, + } diff --git a/mdpow/analysis/dihedral.py b/mdpow/analysis/dihedral.py index 41996f22..05ca6c53 100644 --- a/mdpow/analysis/dihedral.py +++ b/mdpow/analysis/dihedral.py @@ -14,7 +14,7 @@ import logging -logger = logging.getLogger('mdpow.analysis.dihedral') +logger = logging.getLogger("mdpow.analysis.dihedral") class DihedralAnalysis(EnsembleAnalysis): @@ -48,7 +48,9 @@ def __init__(self, dihedral_groups: List[EnsembleAtomGroup]): self.check_groups_from_common_ensemble(dihedral_groups) self.check_dihedral_inputs(dihedral_groups) super(DihedralAnalysis, self).__init__(dihedral_groups[0].ensemble) - self.g1, self.g2, self.g3, self.g4, self.names = self._reorg_groups(dihedral_groups) + self.g1, self.g2, self.g3, self.g4, self.names = self._reorg_groups( + dihedral_groups + ) @staticmethod def _reorg_groups(groups: List[EnsembleAtomGroup]): @@ -63,14 +65,30 @@ def _reorg_groups(groups: List[EnsembleAtomGroup]): ag2 += [mda.AtomGroup([ag[1]]) for ag in [group[k] for k in group.keys()]] ag3 += [mda.AtomGroup([ag[2]]) for ag in [group[k] for k in group.keys()]] ag4 += [mda.AtomGroup([ag[3]]) for ag in [group[k] for k in group.keys()]] - names.append('-'.join([ag1[-1].atoms[0].name, ag2[-1].atoms[0].name, - ag3[-1].atoms[0].name, ag4[-1].atoms[0].name])) + names.append( + "-".join( + [ + ag1[-1].atoms[0].name, + ag2[-1].atoms[0].name, + ag3[-1].atoms[0].name, + ag4[-1].atoms[0].name, + ] + ) + ) for k in group.keys(): ag_keys.append((names[-1], k[0], k[1], k[2])) - eag1 = EnsembleAtomGroup({ag_keys[i]: ag1[i] for i in range(len(ag_keys))}, groups[0].ensemble) - eag2 = EnsembleAtomGroup({ag_keys[i]: ag2[i] for i in range(len(ag_keys))}, groups[0].ensemble) - eag3 = EnsembleAtomGroup({ag_keys[i]: ag3[i] for i in range(len(ag_keys))}, groups[0].ensemble) - eag4 = EnsembleAtomGroup({ag_keys[i]: ag4[i] for i in range(len(ag_keys))}, groups[0].ensemble) + eag1 = EnsembleAtomGroup( + {ag_keys[i]: ag1[i] for i in range(len(ag_keys))}, groups[0].ensemble + ) + eag2 = EnsembleAtomGroup( + {ag_keys[i]: ag2[i] for i in range(len(ag_keys))}, groups[0].ensemble + ) + eag3 = EnsembleAtomGroup( + {ag_keys[i]: ag3[i] for i in range(len(ag_keys))}, groups[0].ensemble + ) + eag4 = EnsembleAtomGroup( + {ag_keys[i]: ag4[i] for i in range(len(ag_keys))}, groups[0].ensemble + ) return eag1, eag2, eag3, eag4, names @staticmethod @@ -78,14 +96,22 @@ def check_dihedral_inputs(selections): for group in selections: for k in group.keys(): if len(group[k]) != 4: - msg = ("Dihedral calculations require AtomGroups with " - f"only 4 atoms, {len(group)} selected") + msg = ( + "Dihedral calculations require AtomGroups with " + f"only 4 atoms, {len(group)} selected" + ) logger.error(msg) raise SelectionError(msg) def _prepare_ensemble(self): - self._col = ['selection', 'solvent', 'interaction', - 'lambda', 'time', 'dihedral'] + self._col = [ + "selection", + "solvent", + "interaction", + "lambda", + "time", + "dihedral", + ] self.results = pd.DataFrame(columns=self._col) self._res_dict = {key: [] for key in self._col} @@ -99,8 +125,9 @@ def _single_frame(self): cord2 = np.concatenate(tuple([cord_dict2[k] for k in key_list])) cord3 = np.concatenate(tuple([cord_dict3[k] for k in key_list])) cord4 = np.concatenate(tuple([cord_dict4[k] for k in key_list])) - angle = calc_dihedrals(cord1, cord2, cord3, cord4, - box=self.g1[key_list[0]].dimensions) + angle = calc_dihedrals( + cord1, cord2, cord3, cord4, box=self.g1[key_list[0]].dimensions + ) angle = np.rad2deg(angle) for i in range(len(self.names)): result = list(key_list[i]) + [self._ts.time, angle[i]] diff --git a/mdpow/analysis/ensemble.py b/mdpow/analysis/ensemble.py index d4ba40a6..308f5115 100644 --- a/mdpow/analysis/ensemble.py +++ b/mdpow/analysis/ensemble.py @@ -9,17 +9,22 @@ import MDAnalysis as mda from MDAnalysis.lib.log import ProgressBar -from MDAnalysis.exceptions import FileFormatWarning, NoDataError, MissingDataWarning, SelectionError +from MDAnalysis.exceptions import ( + FileFormatWarning, + NoDataError, + MissingDataWarning, + SelectionError, +) from gromacs.utilities import in_dir import logging -logger = logging.getLogger('mdpow._ensemble') +logger = logging.getLogger("mdpow._ensemble") class Ensemble(object): - """ Collection of related :class:`MDAnalysis.Universe ` + """Collection of related :class:`MDAnalysis.Universe ` objects. Stores systems produced by running mdpow-fep organized @@ -86,9 +91,14 @@ class Ensemble(object): .. versionadded:: 0.8.0 """ - def __init__(self, dirname=None, solvents=('octanol', 'water'), - topology_paths=None, interactions=('Coulomb', 'VDW'), - **universe_kwargs): + def __init__( + self, + dirname=None, + solvents=("octanol", "water"), + topology_paths=None, + interactions=("Coulomb", "VDW"), + **universe_kwargs, + ): self.top_dict = topology_paths self._num_systems = 0 self._ensemble = {} @@ -102,8 +112,7 @@ def __init__(self, dirname=None, solvents=('octanol', 'water'), if not os.path.exists(dirname): logger.error(f"Directory {dirname} does not exist") - raise FileNotFoundError(errno.ENOENT, 'Directory does not' - 'exist', dirname) + raise FileNotFoundError(errno.ENOENT, "Directory does not" "exist", dirname) self._ensemble_dir = dirname self._build_ensemble() @@ -119,7 +128,9 @@ def __getitem__(self, index): return self._ensemble[index] @staticmethod - def _load_universe_from_dir(solv_dir=None, **universe_kwargs) -> Optional[mda.Universe]: + def _load_universe_from_dir( + solv_dir=None, **universe_kwargs + ) -> Optional[mda.Universe]: """Loads system simulation files in directory into an :class:`MDAnalysis.Universe ` @@ -141,10 +152,12 @@ def _sort_trajectories(trajectories: list) -> list: def _sort_topologies(topologies: list) -> list: """sorts list of trajectory files with .tpr first""" tops = [] - logger.info('If more than one topology is present the tpr will be the one used') + logger.info( + "If more than one topology is present the tpr will be the one used" + ) for i in range(len(topologies)): f = topologies[i] - if f.endswith('.tpr'): + if f.endswith(".tpr"): topologies.pop(i) tops = [f] + topologies break @@ -159,16 +172,20 @@ def _sort_topologies(topologies: list) -> list: top = [solv_dir] for file in cur_dir: - if file.endswith('.xtc'): + if file.endswith(".xtc"): # Saving trajectory directories trj.append(file) - elif (file.endswith('gro') or file.endswith('.tpr') or file.endswith('gro.bz2') - or file.endswith('gro.gz')) and solv_dir is None: + elif ( + file.endswith("gro") + or file.endswith(".tpr") + or file.endswith("gro.bz2") + or file.endswith("gro.gz") + ) and solv_dir is None: # Saving topology directories top.append(file) if len(top) == 0 or len(trj) == 0: - logger.warning('No MD files detected in %s', os.curdir) + logger.warning("No MD files detected in %s", os.curdir) return trj = _sort_trajectories(trj) @@ -177,8 +194,14 @@ def _sort_topologies(topologies: list) -> list: try: return mda.Universe(os.path.abspath(top[0]), trj, **universe_kwargs) - except (ValueError, FileFormatWarning, NoDataError, MissingDataWarning, OSError) as err: - logger.error(f'{err} raised while loading {top[0]} {trj} in dir {cur_dir}') + except ( + ValueError, + FileFormatWarning, + NoDataError, + MissingDataWarning, + OSError, + ) as err: + logger.error(f"{err} raised while loading {top[0]} {trj} in dir {cur_dir}") raise NoDataError def keys(self): @@ -193,9 +216,11 @@ def _build_ensemble(self): Run if :code:`dirname` argument is given when initializing the class. First enters FEP directory, then traverses solvent and interaction directories to search lambda directories for system files.""" - fep_dir = os.path.join(self._ensemble_dir, 'FEP') + fep_dir = os.path.join(self._ensemble_dir, "FEP") solv_top_path = None - for solvent in self._solvents: # Ugly set of loops, may have to find way to clean up + for ( + solvent + ) in self._solvents: # Ugly set of loops, may have to find way to clean up if self.top_dict is not None: solv_top_path = self.top_dict[solvent] for dirs in self._interactions: # Attribute folder names @@ -206,10 +231,11 @@ def _build_ensemble(self): for file in sorted(files): # Traversing lambda directories if os.path.isdir(file): with in_dir(file, create=False): - u = self._load_universe_from_dir(solv_dir=solv_top_path, - **self.unv_kwargs) + u = self._load_universe_from_dir( + solv_dir=solv_top_path, **self.unv_kwargs + ) if u is None: - logger.warning(f'No system loaded in {file}') + logger.warning(f"No system loaded in {file}") else: self.add_system((solvent, dirs, file), u) @@ -236,20 +262,33 @@ def select_atoms(self, *args, **kwargs): Uses the same `selection commands `_ - as MDAnalysis, and has the same keys as the :class:`~mdpow.analysis.ensemble.Ensemble`""" + as MDAnalysis, and has the same keys as the :class:`~mdpow.analysis.ensemble.Ensemble` + """ selections = {} for key in self.keys(): try: ag = self[key].select_atoms(*args, **kwargs) except SelectionError as err: - logger.error("%r on system %r with selection settings %r %r", err, key, args, kwargs) + logger.error( + "%r on system %r with selection settings %r %r", + err, + key, + args, + kwargs, + ) raise else: selections[key] = ag return EnsembleAtomGroup(selections, ensemble=self) - def select_systems(self, keys=None, solvents=None, interactions=None, - lambdas=None, lambda_range=None): + def select_systems( + self, + keys=None, + solvents=None, + interactions=None, + lambdas=None, + lambda_range=None, + ): """ Select specific subset of systems and returns them in an Ensemble. @@ -318,10 +357,14 @@ def select_systems(self, keys=None, solvents=None, interactions=None, elif lambda_range is not None: # Selecting range of lambdas for k in self.keys(): - if lambda_range[0] <= int(k[2]) / 1000 <= lambda_range[1]: + if ( + lambda_range[0] + <= int(k[2]) / 1000 + <= lambda_range[1] + ): new_key.append((s, i, k[2])) for k in new_key: - logger.info('adding system %r to ensemble', k) + logger.info("adding system %r to ensemble", k) new_ens.add_system(k, universe=self[k]) new_ens._ensemble_dir = self._ensemble_dir return new_ens @@ -374,13 +417,20 @@ def select_atoms(self, *args, **kwargs): Uses the same `selection commands `_ - as MDAnalysis, and has the same keys as :class:`~mdpow.analysis.ensemble.EnsembleAtomGroup`""" + as MDAnalysis, and has the same keys as :class:`~mdpow.analysis.ensemble.EnsembleAtomGroup` + """ selections = {} for key in self.keys(): try: ag = self[key].select_atoms(*args, **kwargs) except SelectionError as err: - logger.error("%r on system %r with selection settings %r %r", err, key, args, kwargs) + logger.error( + "%r on system %r with selection settings %r %r", + err, + key, + args, + kwargs, + ) raise else: selections[key] = ag @@ -458,39 +508,41 @@ def _setup_system(self, key, start=None, stop=None, step=None): def _setup_frames(self, trajectory): self._trajectory = trajectory - start, stop, step = trajectory.check_slice_indices(self.start, self.stop, self.step) + start, stop, step = trajectory.check_slice_indices( + self.start, self.stop, self.step + ) self.n_frames = len(range(start, stop, step)) self.frames = np.zeros(self.n_frames, dtype=int) self.times = np.zeros(self.n_frames) def _single_universe(self): - """Calculations on a single :class:`MDAnalysis.Universe - ` object. - - Run on each :class:`MDAnalysis.Universe - ` - in the :class:`~mdpow.analysis.ensemble.Ensemble` - during when :meth:`run` in called. - :exc:`NotImplementedError` will detect whether - :meth:`~EnsembleAnalysis._single_universe` - or :meth:`~EnsembleAnalysis._single_frame` - should be implemented, based on which is defined - in the :class:`~mdpow.analysis.ensemble.EnsembleAnalysis`. + """Calculations on a single :class:`MDAnalysis.Universe + ` object. + + Run on each :class:`MDAnalysis.Universe + ` + in the :class:`~mdpow.analysis.ensemble.Ensemble` + during when :meth:`run` in called. + :exc:`NotImplementedError` will detect whether + :meth:`~EnsembleAnalysis._single_universe` + or :meth:`~EnsembleAnalysis._single_frame` + should be implemented, based on which is defined + in the :class:`~mdpow.analysis.ensemble.EnsembleAnalysis`. """ raise NotImplementedError def _single_frame(self): """Calculate data from a single frame of trajectory. - Called on each frame for each - :class:`MDAnalysis.Universe ` - in the :class:`~mdpow.analysis.ensemble.Ensemble`. - - :exc:`NotImplementedError` will detect whether - :meth:`~EnsembleAnalysis._single_universe` - or :meth:`~EnsembleAnalysis._single_frame` - should be implemented, based on which is defined - in the :class:`~mdpow.analysis.ensemble.EnsembleAnalysis`. + Called on each frame for each + :class:`MDAnalysis.Universe ` + in the :class:`~mdpow.analysis.ensemble.Ensemble`. + + :exc:`NotImplementedError` will detect whether + :meth:`~EnsembleAnalysis._single_universe` + or :meth:`~EnsembleAnalysis._single_frame` + should be implemented, based on which is defined + in the :class:`~mdpow.analysis.ensemble.EnsembleAnalysis`. """ raise NotImplementedError @@ -521,15 +573,15 @@ def _conclude_ensemble(self): pass # pragma: no cover def run(self, start=None, stop=None, step=None): - """Runs :meth:`~EnsembleAnalysis._single_universe` + """Runs :meth:`~EnsembleAnalysis._single_universe` on each system or :meth:`~EnsembleAnalysis._single_frame` on each frame in the system. - First iterates through keys of ensemble, then runs - :meth:`~EnsembleAnalysis._setup_system`which defines + First iterates through keys of ensemble, then runs + :meth:`~EnsembleAnalysis._setup_system`which defines the system and trajectory. Then iterates over each - system universe or trajectory frames of each universe - as defined by :meth:`~EnsembleAnalysis._single_universe` + system universe or trajectory frames of each universe + as defined by :meth:`~EnsembleAnalysis._single_universe` or :meth:`~EnsembleAnalysis._single_frame`. """ logger.info("Setting up systems") @@ -539,8 +591,13 @@ def run(self, start=None, stop=None, step=None): try: self._single_universe() except NotImplementedError: - for i, ts in enumerate(ProgressBar(self._trajectory[self.start:self.stop:self.step], verbose=True, - postfix=f'running system {self._key}')): + for i, ts in enumerate( + ProgressBar( + self._trajectory[self.start : self.stop : self.step], + verbose=True, + postfix=f"running system {self._key}", + ) + ): self._frame_index = i self._ts = ts self.frames[i] = ts.frame @@ -566,9 +623,11 @@ def check_groups_from_common_ensemble(groups: List[EnsembleAtomGroup]): for j in range(i + 1, len(groups)): # Checking if EnsembleAtomGroup.ensemble references same object in memory if groups[i].ensemble is not groups[j].ensemble: - msg = ('Dihedral selections from different Ensembles, ' - 'ensure that all EnsembleAtomGroups are created ' - 'from the same Ensemble. ' - f'mismatch: group[{i}].ensemble != group[{j}].ensemble') + msg = ( + "Dihedral selections from different Ensembles, " + "ensure that all EnsembleAtomGroups are created " + "from the same Ensemble. " + f"mismatch: group[{i}].ensemble != group[{j}].ensemble" + ) logger.error(msg) raise ValueError(msg) diff --git a/mdpow/analysis/solvation.py b/mdpow/analysis/solvation.py index 6ed6137a..47be995d 100644 --- a/mdpow/analysis/solvation.py +++ b/mdpow/analysis/solvation.py @@ -13,7 +13,7 @@ import logging -logger = logging.getLogger('mdpow.dihedral') +logger = logging.getLogger("mdpow.dihedral") class SolvationAnalysis(EnsembleAnalysis): @@ -48,7 +48,13 @@ class SolvationAnalysis(EnsembleAnalysis): solv_dist = SolvationAnalysis(solute, solvent, [1.2, 2.4]).run(stop=10) """ - def __init__(self, solute: EnsembleAtomGroup, solvent: EnsembleAtomGroup, distances: List[float]): + + def __init__( + self, + solute: EnsembleAtomGroup, + solvent: EnsembleAtomGroup, + distances: List[float], + ): self.check_groups_from_common_ensemble([solute, solvent]) super(SolvationAnalysis, self).__init__(solute.ensemble) self._solute = solute @@ -56,21 +62,37 @@ def __init__(self, solute: EnsembleAtomGroup, solvent: EnsembleAtomGroup, distan self._dists = distances def _prepare_ensemble(self): - self._col = ['distance', 'solvent', 'interaction', - 'lambda', 'time', 'N_solvent'] + self._col = [ + "distance", + "solvent", + "interaction", + "lambda", + "time", + "N_solvent", + ] self.results = pd.DataFrame(columns=self._col) self._res_dict = {key: [] for key in self._col} def _single_frame(self): solute = self._solute[self._key] solvent = self._solvent[self._key] - pairs, distances = capped_distance(solute.positions, solvent.positions, - max(self._dists), box=self._ts.dimensions) + pairs, distances = capped_distance( + solute.positions, + solvent.positions, + max(self._dists), + box=self._ts.dimensions, + ) solute_i, solvent_j = np.transpose(pairs) for d in self._dists: close_solv_atoms = solvent[solvent_j[distances < d]] - result = [d, self._key[0], self._key[1],self._key[2], - self._ts.time, close_solv_atoms.n_atoms] + result = [ + d, + self._key[0], + self._key[1], + self._key[2], + self._ts.time, + close_solv_atoms.n_atoms, + ] for i in range(len(self._col)): self._res_dict[self._col[i]].append(result[i]) diff --git a/mdpow/config.py b/mdpow/config.py index 3d2e2878..18f2890d 100644 --- a/mdpow/config.py +++ b/mdpow/config.py @@ -104,6 +104,7 @@ import warnings import logging + logger = logging.getLogger("mdpow.config") # Reading of configuration files @@ -112,7 +113,8 @@ #: Locations of default run input files and configurations. defaults = { "runinput": resource_filename(__name__, "templates/runinput.yml"), - } +} + class NoSectionError(ValueError): """Section entry is missing. @@ -120,13 +122,16 @@ class NoSectionError(ValueError): .. versionadded:: 0.8.0 """ + # not used at the moment # class NoOptionError(ValueError): # """Option entry is missing from section""" + class NoOptionWarning(UserWarning): """Warning that an option is missing.""" + def merge_dicts(user, default): """Merge two dictionaries recursively. @@ -186,7 +191,7 @@ def merge(self, fn): return self.conf def write(self, filename): - with open(filename, 'w') as f: + with open(filename, "w") as f: f.write(yaml.dump(self.conf)) def get(self, section, option): @@ -213,10 +218,12 @@ def get(self, section, option): value = value if value != "None" else None # still needed?? except KeyError: # Returning None has been standard behavior. - #raise NoOptionError(f"Config file section {section} contains " + # raise NoOptionError(f"Config file section {section} contains " # f"no option {option}.") - msg = (f"Config file section {section} contains " - f"no option {option}. Using 'None'.") + msg = ( + f"Config file section {section} contains " + f"no option {option}. Using 'None'." + ) warnings.warn(msg, category=NoOptionWarning) logger.warning(msg) value = None @@ -240,8 +247,9 @@ def getpath(self, section, option): instead of raising a :exc:`TypeError`. """ item = self.get(section, option) - return os.path.expanduser( - os.path.expandvars(item)) if item is not None else None + return ( + os.path.expanduser(os.path.expandvars(item)) if item is not None else None + ) def findfile(self, section, option): """Return location of a file ``option`` or ``None``. @@ -263,8 +271,7 @@ def getlist(self, section, option): instead of raising a :exc:`TypeError`. """ item = self.get(section, option) - return [x.strip() - for x in str(item).split(",")] if item is not None else [] + return [x.strip() for x in str(item).split(",")] if item is not None else [] def getarray(self, section, option): """Return option as a numpy array of floats or ``np.array([])``. @@ -277,6 +284,7 @@ def getarray(self, section, option): """ return np.asarray(self.getlist(section, option), dtype=float) + # def getintarray(self, section, option): # """Return option as a numpy array of integers. # @@ -285,6 +293,7 @@ def getarray(self, section, option): # """ # return np.asarray(self.getlist(section, option), dtype=int) + def get_configuration(filename=None): """Reads and parses a run input config file. @@ -294,47 +303,61 @@ def get_configuration(filename=None): cfg.readfp(open(defaults["runinput"])) logger.debug("Loaded runinput defaults from %r", defaults["runinput"]) if filename is not None: - cfg.merge(open(filename)) # override package defaults + cfg.merge(open(filename)) # override package defaults logger.debug("Loaded user runinput from %r (replacing defaults)", filename) else: - logger.warning("Running with package defaults for the run; you should supply a runinput file!") + logger.warning( + "Running with package defaults for the run; you should supply a runinput file!" + ) return cfg + def modify_gromacs_environment(name, value): from gromacs.environment import flags + if flags[name] != value: - logger.warning("Changing GromacsWrapper environment: flags[%(name)r] = %(value)r", vars()) + logger.warning( + "Changing GromacsWrapper environment: flags[%(name)r] = %(value)r", vars() + ) flags[name] = value + def set_gromacsoutput(cfg): # maybe allow setting this on a per protocol basis? - modify_gromacs_environment('capture_output', not cfg.getboolean('setup', 'gromacsoutput')) + modify_gromacs_environment( + "capture_output", not cfg.getboolean("setup", "gromacsoutput") + ) # Functions to locate template files # ---------------------------------- + def _generate_template_dict(dirname): """Generate a list of included top-level files *and* extract them to a temp space. Only lists files and directories at the *top level* of the *dirname*; however, all directories are extracted recursively and will be available. """ - return dict((resource_basename(fn), resource_filename(__name__, dirname+'/'+fn)) - for fn in resource_listdir(__name__, dirname) - if not fn.endswith('~')) + return dict( + (resource_basename(fn), resource_filename(__name__, dirname + "/" + fn)) + for fn in resource_listdir(__name__, dirname) + if not fn.endswith("~") + ) + def resource_basename(resource): - """Last component of a resource (which always uses '/' as sep).""" - if resource.endswith('/'): - resource = resource[:-1] - parts = resource.split('/') - return parts[-1] + """Last component of a resource (which always uses '/' as sep).""" + if resource.endswith("/"): + resource = resource[:-1] + parts = resource.split("/") + return parts[-1] # Functions to access configuration data # -------------------------------------- + def get_template(t): """Find template file *t* and return its real path. @@ -358,9 +381,10 @@ def get_template(t): # Not sure if this is the best way to get asiterables templates = [_get_template(s) for s in gromacs.utilities.asiterable(t)] if len(templates) == 1: - return templates[0] + return templates[0] return templates + def get_templates(t): """Find template file(s) *t* and return their real paths. @@ -381,26 +405,27 @@ def get_templates(t): """ return [_get_template(s) for s in gromacs.utilities.asiterable(t)] + def _get_template(t): """Return a single template *t*.""" - if os.path.exists(t): # 1) Is it an accessible file? + if os.path.exists(t): # 1) Is it an accessible file? pass - else: # 2) check the packaged template files + else: # 2) check the packaged template files _t = os.path.basename(t) _t_found = False for p in templates.values(): if _t == os.path.basename(p): t = p - _t_found = True # NOTE: in principle this could match multiple - break # times if more than one template dir existed. - if not _t_found: # 3) try it as a key into templates + _t_found = True # NOTE: in principle this could match multiple + break # times if more than one template dir existed. + if not _t_found: # 3) try it as a key into templates try: t = templates[t] except KeyError: pass else: _t_found = True - if not _t_found: # 4) nothing else to try... or introduce a PATH? + if not _t_found: # 4) nothing else to try... or introduce a PATH? raise ValueError("Failed to locate the template file %(t)r." % vars()) return os.path.realpath(t) @@ -408,19 +433,21 @@ def _get_template(t): # utility functions (from gromacs.utilities) # Copied so that config does not have a dependency on gromacs.utilities + def iterable(obj): """Returns ``True`` if *obj* can be iterated over and is *not* a string.""" if isinstance(obj, str): return False # avoid iterating over characters of a string - if hasattr(obj, 'next'): - return True # any iterator will do + if hasattr(obj, "next"): + return True # any iterator will do try: - len(obj) # anything else that might work + len(obj) # anything else that might work except TypeError: return False return True + def asiterable(obj): """Returns obj so that it can be iterated over; a string is *not* treated as iterable""" if not iterable(obj): @@ -429,9 +456,9 @@ def asiterable(obj): # Setting up configuration variables and paths -#--------------------------------------------- +# --------------------------------------------- -templates = _generate_template_dict('templates') +templates = _generate_template_dict("templates") """*POW* comes with a number of templates for run input files and queuing system scripts. They are provided as a convenience and examples but **WITHOUT ANY GUARANTEE FOR CORRECTNESS OR SUITABILITY FOR @@ -459,8 +486,8 @@ def asiterable(obj): #: List of all topology files that are included in the package. #: (includes force field files under ``top/oplsaa.ff``) -topfiles = _generate_template_dict('top') -topfiles.update(_generate_template_dict('top/oplsaa.ff')) # added manually! +topfiles = _generate_template_dict("top") +topfiles.update(_generate_template_dict("top/oplsaa.ff")) # added manually! # Find the top include dir by looking for an important file 'ffoplsaa.itp'. # Since Gromacs 4.5.x, force fields are ONLY found in @@ -471,21 +498,30 @@ def asiterable(obj): #: The package's include directory for :func:`gromacs.grompp`; the #: environment variable :envvar:`GMXLIB` is set to :data:`includedir` #: so that the bundled version of the force field is picked up. - includedir = os.path.dirname(topfiles['ffoplsaa.itp']) + includedir = os.path.dirname(topfiles["ffoplsaa.itp"]) except KeyError: errmsg = "Missing required data files (ffoplsaa.itp). Check your installation." logger.fatal(errmsg) raise ImportError(errmsg) -if not 'GMXLIB' in os.environ: +if not "GMXLIB" in os.environ: if not os.path.exists(includedir): - errmsg = "Likely installation problem: cannot access the package GMXLIB " \ + errmsg = ( + "Likely installation problem: cannot access the package GMXLIB " "directory (try re-installing): " + ) logger.fatal(errmsg + includedir) raise OSError(errno.ENOENT, errmsg, includedir) - os.environ['GMXLIB'] = includedir + os.environ["GMXLIB"] = includedir logger.info("Using the bundled force fields from GMXLIB=%(includedir)r.", vars()) - logger.info("If required, override this behaviour by setting the environment variable GMXLIB yourself.") + logger.info( + "If required, override this behaviour by setting the environment variable GMXLIB yourself." + ) else: - logger.warning("Using user-supplied environment variable GMXLIB=%r to find force fields", os.environ['GMXLIB']) - logger.info("(You can use the MDPOW default by executing 'unset GMXLIB' in your shell before running MDPOW.)") + logger.warning( + "Using user-supplied environment variable GMXLIB=%r to find force fields", + os.environ["GMXLIB"], + ) + logger.info( + "(You can use the MDPOW default by executing 'unset GMXLIB' in your shell before running MDPOW.)" + ) diff --git a/mdpow/equil.py b/mdpow/equil.py index 56d79f40..d1ac36ff 100644 --- a/mdpow/equil.py +++ b/mdpow/equil.py @@ -47,7 +47,8 @@ from .restart import Journalled import logging -logger = logging.getLogger('mdpow.equil') + +logger = logging.getLogger("mdpow.equil") # ITP <-- forcefields.get_solvent_model(id).itp # BOX <-- forcefields.get_solvent_model(id).coordinates @@ -56,7 +57,14 @@ # TODO: change to water distance 1.2 in the future (1.0 for # compatibility with our SAMPL5 runs) #: minimum distance between solute and box surface (in nm) -DIST = {'water': 1.0, 'octanol': 1.5, 'cyclohexane': 1.5, 'wetoctanol': 1.5, 'toluene': 1.5} +DIST = { + "water": 1.0, + "octanol": 1.5, + "cyclohexane": 1.5, + "wetoctanol": 1.5, + "toluene": 1.5, +} + class Simulation(Journalled): """Simple MD simulation of a single compound molecule in water. @@ -76,33 +84,60 @@ class Simulation(Journalled): """ #: Keyword arguments to pre-set some file names; they are keys in :attr:`Simulation.files`. - filekeys = ('topology', 'processed_topology', 'structure', 'solvated', 'ndx', - 'energy_minimized', 'MD_relaxed', 'MD_restrained', 'MD_NPT') + filekeys = ( + "topology", + "processed_topology", + "structure", + "solvated", + "ndx", + "energy_minimized", + "MD_relaxed", + "MD_restrained", + "MD_NPT", + ) topdir_default = "Equilibrium" dirname_default = os.path.curdir - solvent_default = 'water' + solvent_default = "water" #: Coordinate files of the full system in increasing order of advancement of #: the protocol; the later the better. The values are keys into :attr:`Simulation.files`. - coordinate_structures = ('solvated', 'energy_minimized', 'MD_relaxed', - 'MD_restrained', 'MD_NPT') - checkpoints = ('solvated','energy_minimized','MD_relaxed','MD_restrained','MD_NPT') - + coordinate_structures = ( + "solvated", + "energy_minimized", + "MD_relaxed", + "MD_restrained", + "MD_NPT", + ) + checkpoints = ( + "solvated", + "energy_minimized", + "MD_relaxed", + "MD_restrained", + "MD_NPT", + ) #: Check list of all methods that can be run as an independent protocol; see also #: :meth:`Simulation.get_protocol` and :class:`restart.Journal` - protocols = ("MD_NPT", "MD_NPT_run", # *_run as dummies for the ... - "MD_relaxed", "MD_relaxed_run", # ...checkpointing logic - "MD_restrained", "MD_restrained_run", - "energy_minimize", "solvate", "topology") + protocols = ( + "MD_NPT", + "MD_NPT_run", # *_run as dummies for the ... + "MD_relaxed", + "MD_relaxed_run", # ...checkpointing logic + "MD_restrained", + "MD_restrained_run", + "energy_minimize", + "solvate", + "topology", + ) #: Default Gromacs *MDP* run parameter files for the different stages. #: (All are part of the package and are found with :func:`mdpow.config.get_template`.) - mdp_defaults = {'MD_relaxed': 'NPT_opls.mdp', - 'MD_restrained': 'NPT_opls.mdp', - 'MD_NPT': 'NPT_opls.mdp', - 'energy_minimize': 'em_opls.mdp', - } + mdp_defaults = { + "MD_relaxed": "NPT_opls.mdp", + "MD_restrained": "NPT_opls.mdp", + "MD_NPT": "NPT_opls.mdp", + "energy_minimize": "em_opls.mdp", + } def __init__(self, molecule=None, **kwargs): """Set up Simulation instance. @@ -142,11 +177,11 @@ def __init__(self, molecule=None, **kwargs): """ self.__cache = {} - filename = kwargs.pop('filename', None) - dirname = kwargs.pop('dirname', self.dirname_default) + filename = kwargs.pop("filename", None) + dirname = kwargs.pop("dirname", self.dirname_default) - forcefield = kwargs.pop('forcefield', 'OPLS-AA') - solvent = kwargs.pop('solvent', self.solvent_default) + forcefield = kwargs.pop("forcefield", "OPLS-AA") + solvent = kwargs.pop("solvent", self.solvent_default) # mdp files --- should get values from default runinput.cfg # None values in the kwarg mdp dict are ignored # self.mdp: key = stage, value = path to MDP file @@ -154,25 +189,36 @@ def __init__(self, molecule=None, **kwargs): # 'water' will choose the default ('tip4p'), other choices are # 'tip3p', 'spc', 'spce', 'm24', for water; no choices # available for 'cyclohexane' and 'octanol' - solventmodel = kwargs.pop('solventmodel', None) - - mdp_kw = kwargs.pop('mdp', {}) - self.mdp = dict((stage, config.get_template(fn)) for stage,fn in self.mdp_defaults.items()) - self.mdp.update(dict((stage, config.get_template(fn)) for stage,fn in mdp_kw.items() if fn is not None)) + solventmodel = kwargs.pop("solventmodel", None) + + mdp_kw = kwargs.pop("mdp", {}) + self.mdp = dict( + (stage, config.get_template(fn)) for stage, fn in self.mdp_defaults.items() + ) + self.mdp.update( + dict( + (stage, config.get_template(fn)) + for stage, fn in mdp_kw.items() + if fn is not None + ) + ) if molecule is None and filename is not None: # load from pickle file self.load(filename) self.filename = filename - kwargs = {} # for super + kwargs = {} # for super else: - self.molecule = molecule or 'DRUG' + self.molecule = molecule or "DRUG" self.dirs = AttributeDict( - basedir=realpath(dirname), # .../Equilibrium/ - includes=list(asiterable(kwargs.pop('includes',[]))) + [config.includedir], - ) + basedir=realpath(dirname), # .../Equilibrium/ + includes=list(asiterable(kwargs.pop("includes", []))) + + [config.includedir], + ) # pre-set filenames: keyword == variable name - self.files = AttributeDict([(k, kwargs.pop(k, None)) for k in self.filekeys]) + self.files = AttributeDict( + [(k, kwargs.pop(k, None)) for k in self.filekeys] + ) self.deffnm = kwargs.pop("deffnm", "md") if self.files.topology: @@ -184,28 +230,31 @@ def __init__(self, molecule=None, **kwargs): self.forcefield = forcefield self.solvent_type = solvent self.solventmodel_identifier = forcefields.get_solvent_identifier( - solvent, - model=solventmodel, - forcefield=forcefield, - ) + solvent, + model=solventmodel, + forcefield=forcefield, + ) if self.solventmodel_identifier is None: msg = "No parameters for solvent {0} and solventmodel {1} available.".format( - solvent, solventmodel) + solvent, solventmodel + ) logger.error(msg) raise ValueError(msg) self.solventmodel = forcefields.get_solvent_model( self.solventmodel_identifier, forcefield=forcefield, - ) + ) - distance = kwargs.pop('distance', None) + distance = kwargs.pop("distance", None) distance = distance if distance is not None else DIST[solvent] - self.solvent = AttributeDict(itp=self.solventmodel.itp, - box=self.solventmodel.coordinates, - distance=distance) + self.solvent = AttributeDict( + itp=self.solventmodel.itp, + box=self.solventmodel.coordinates, + distance=distance, + ) - self.filename = filename or self.solvent_type+'.simulation' + self.filename = filename or self.solvent_type + ".simulation" super(Simulation, self).__init__(**kwargs) @@ -220,12 +269,14 @@ def save(self, filename=None): """ if filename is None: if self.filename is None: - self.filename = filename or self.solvent_type+'.simulation' - logger.warning("No filename known, saving instance under name %r", self.filename) + self.filename = filename or self.solvent_type + ".simulation" + logger.warning( + "No filename known, saving instance under name %r", self.filename + ) filename = self.filename else: self.filename = filename - with open(filename, 'wb') as f: + with open(filename, "wb") as f: pickle.dump(self, f) logger.debug("Instance pickled to %(filename)r" % vars()) @@ -233,10 +284,10 @@ def load(self, filename=None): """Re-instantiate class from pickled file.""" if filename is None: if self.filename is None: - self.filename = self.molecule.lower() + '.pickle' + self.filename = self.molecule.lower() + ".pickle" logger.warning("No filename known, trying name %r", self.filename) filename = self.filename - with open(filename, 'rb') as f: + with open(filename, "rb") as f: instance = pickle.load(f) self.__dict__.update(instance.__dict__) logger.debug("Instance loaded from %(filename)r" % vars()) @@ -248,6 +299,7 @@ def make_paths_relative(self, prefix=os.path.curdir): check :attr:`mdpow.equil.Simulation.dirs.includes` and adjust manually if necessary. """ + def assinglet(m): if len(m) == 1: return m[0] @@ -272,10 +324,13 @@ def assinglet(m): self.mdp[key] = fn.replace(basedir, prefix) except AttributeError: pass - logger.warning("make_paths_relative(): check/manually adjust %s.dirs.includes = %r !", - self.__class__.__name__, self.dirs.includes) + logger.warning( + "make_paths_relative(): check/manually adjust %s.dirs.includes = %r !", + self.__class__.__name__, + self.dirs.includes, + ) - def topology(self, itp='drug.itp', prm=None, **kwargs): + def topology(self, itp="drug.itp", prm=None, **kwargs): """Generate a topology for compound *molecule*. :Keywords: @@ -290,22 +345,22 @@ def topology(self, itp='drug.itp', prm=None, **kwargs): *kwargs* see source for *top_template*, *topol* """ - self.journal.start('topology') + self.journal.start("topology") - dirname = kwargs.pop('dirname', self.BASEDIR('top')) + dirname = kwargs.pop("dirname", self.BASEDIR("top")) self.dirs.topology = realpath(dirname) setting = forcefields.get_ff_paths(self.forcefield) template = forcefields.get_top_template(self.solvent_type) - top_template = config.get_template(kwargs.pop('top_template', template)) - topol = kwargs.pop('topol', os.path.basename(top_template)) + top_template = config.get_template(kwargs.pop("top_template", template)) + topol = kwargs.pop("topol", os.path.basename(top_template)) self.top_template = top_template itp = os.path.realpath(itp) _itp = os.path.basename(itp) if prm is None: - prm_kw = '' + prm_kw = "" else: prm = os.path.realpath(prm) _prm = os.path.basename(prm) @@ -315,45 +370,48 @@ def topology(self, itp='drug.itp', prm=None, **kwargs): shutil.copy(itp, _itp) if prm is not None: shutil.copy(prm, _prm) - gromacs.cbook.edit_txt(top_template, - [(r'#include +"oplsaa\.ff/forcefield\.itp"', - r'oplsaa\.ff/', - setting[0]), - (r'#include +"compound\.itp"', - r'compound\.itp', - _itp), - (r'#include +"oplsaa\.ff/tip4p\.itp"', - r'oplsaa\.ff/tip4p\.itp', - setting[0] + self.solvent.itp), - (r'#include +"oplsaa\.ff/ions_opls\.itp"', - r'oplsaa\.ff/ions_opls\.itp', - setting[1]), - (r'#include +"compound\.prm"', - r'#include +"compound\.prm"', - prm_kw), - (r'#include +"water\.itp"', - r'water\.itp', - setting[2]), - (r'Compound', - 'solvent', - self.solvent_type), - (r'Compound', - 'DRUG', - self.molecule), - (r'DRUG\s*1', - 'DRUG', - self.molecule), - ], - newname=topol) - logger.info('[%(dirname)s] Created topology %(topol)r that includes %(_itp)r', vars()) + gromacs.cbook.edit_txt( + top_template, + [ + ( + r'#include +"oplsaa\.ff/forcefield\.itp"', + r"oplsaa\.ff/", + setting[0], + ), + (r'#include +"compound\.itp"', r"compound\.itp", _itp), + ( + r'#include +"oplsaa\.ff/tip4p\.itp"', + r"oplsaa\.ff/tip4p\.itp", + setting[0] + self.solvent.itp, + ), + ( + r'#include +"oplsaa\.ff/ions_opls\.itp"', + r"oplsaa\.ff/ions_opls\.itp", + setting[1], + ), + ( + r'#include +"compound\.prm"', + r'#include +"compound\.prm"', + prm_kw, + ), + (r'#include +"water\.itp"', r"water\.itp", setting[2]), + (r"Compound", "solvent", self.solvent_type), + (r"Compound", "DRUG", self.molecule), + (r"DRUG\s*1", "DRUG", self.molecule), + ], + newname=topol, + ) + logger.info( + "[%(dirname)s] Created topology %(topol)r that includes %(_itp)r", vars() + ) # update known files and dirs self.files.topology = realpath(dirname, topol) if not self.dirs.topology in self.dirs.includes: self.dirs.includes.append(self.dirs.topology) - self.journal.completed('topology') - return {'dirname': dirname, 'topol': topol} + self.journal.completed("topology") + return {"dirname": dirname, "topol": topol} @staticmethod def _setup_solvate(**kwargs): @@ -385,43 +443,49 @@ def solvate(self, struct=None, **kwargs): All other arguments are passed on to :func:`gromacs.setup.solvate`, but set to sensible default values. *top* and *water* are always fixed. """ - self.journal.start('solvate') - - self.dirs.solvation = realpath(kwargs.setdefault('dirname', self.BASEDIR('solvation'))) - kwargs['struct'] = self._checknotempty(struct or self.files.structure, 'struct') - kwargs['top'] = self._checknotempty(self.files.topology, 'top') - kwargs['water'] = self.solvent.box - kwargs.setdefault('mainselection', '"%s"' % self.molecule) # quotes are needed for make_ndx - kwargs.setdefault('distance', self.solvent.distance) - - boxtype = kwargs.pop('bt', None) + self.journal.start("solvate") + + self.dirs.solvation = realpath( + kwargs.setdefault("dirname", self.BASEDIR("solvation")) + ) + kwargs["struct"] = self._checknotempty(struct or self.files.structure, "struct") + kwargs["top"] = self._checknotempty(self.files.topology, "top") + kwargs["water"] = self.solvent.box + kwargs.setdefault( + "mainselection", '"%s"' % self.molecule + ) # quotes are needed for make_ndx + kwargs.setdefault("distance", self.solvent.distance) + + boxtype = kwargs.pop("bt", None) boxtype = boxtype if boxtype is not None else "dodecahedron" if boxtype not in ("dodecahedron", "triclinic", "cubic", "octahedron"): - msg = "Invalid boxtype '{0}', not suitable for 'gmx editconf'.".format(boxtype) + msg = "Invalid boxtype '{0}', not suitable for 'gmx editconf'.".format( + boxtype + ) logger.error(msg) raise ValueError(msg) - kwargs['bt'] = boxtype + kwargs["bt"] = boxtype - kwargs['includes'] = asiterable(kwargs.pop('includes',[])) + self.dirs.includes + kwargs["includes"] = asiterable(kwargs.pop("includes", [])) + self.dirs.includes params = self._setup_solvate(**kwargs) - self.files.structure = kwargs['struct'] - self.files.solvated = params['struct'] - self.files.ndx = params['ndx'] + self.files.structure = kwargs["struct"] + self.files.solvated = params["struct"] + self.files.ndx = params["ndx"] # we can also make a processed topology right now self.processed_topology(**kwargs) - self.journal.completed('solvate') + self.journal.completed("solvate") return params def processed_topology(self, **kwargs): """Create a portable topology file from the topology and the solvated system.""" if self.files.solvated is None or not os.path.exists(self.files.solvated): self.solvate(**kwargs) - kwargs['topol'] = self.files.topology - kwargs['struct'] = self.files.solvated - kwargs['includes'] = self.dirs.includes + kwargs["topol"] = self.files.topology + kwargs["struct"] = self.files.solvated + kwargs["includes"] = self.dirs.includes self.files.processed_topology = gromacs.cbook.create_portable_topology(**kwargs) return self.files.processed_topology @@ -432,55 +496,71 @@ def energy_minimize(self, **kwargs): :meth:`~mdpow.equil.Simulation.solvate` step has been carried out previously all the defaults should just work. """ - self.journal.start('energy_minimize') + self.journal.start("energy_minimize") - self.dirs.energy_minimization = realpath(kwargs.setdefault('dirname', self.BASEDIR('em'))) - kwargs['top'] = self.files.topology - kwargs.setdefault('struct', self.files.solvated) - kwargs.setdefault('mdp', self.mdp['energy_minimize']) - kwargs['mainselection'] = None - kwargs['includes'] = asiterable(kwargs.pop('includes',[])) + self.dirs.includes + self.dirs.energy_minimization = realpath( + kwargs.setdefault("dirname", self.BASEDIR("em")) + ) + kwargs["top"] = self.files.topology + kwargs.setdefault("struct", self.files.solvated) + kwargs.setdefault("mdp", self.mdp["energy_minimize"]) + kwargs["mainselection"] = None + kwargs["includes"] = asiterable(kwargs.pop("includes", [])) + self.dirs.includes params = gromacs.setup.energy_minimize(**kwargs) - self.files.energy_minimized = params['struct'] + self.files.energy_minimized = params["struct"] - self.journal.completed('energy_minimize') + self.journal.completed("energy_minimize") return params def _MD(self, protocol, **kwargs): """Basic MD driver for this Simulation. Do not call directly.""" self.journal.start(protocol) - kwargs.setdefault('dirname', self.BASEDIR(protocol)) - kwargs.setdefault('deffnm', self.deffnm) - kwargs.setdefault('mdp', config.get_template('NPT_opls.mdp')) - self.dirs[protocol] = realpath(kwargs['dirname']) - setupMD = kwargs.pop('MDfunc', gromacs.setup.MD) - kwargs['top'] = self.files.topology - kwargs['includes'] = asiterable(kwargs.pop('includes',[])) + self.dirs.includes - kwargs['ndx'] = self.files.ndx - kwargs['mainselection'] = None # important for SD (use custom mdp and ndx!, gromacs.setup._MD) - self._checknotempty(kwargs['struct'], 'struct') - if not os.path.exists(kwargs['struct']): + kwargs.setdefault("dirname", self.BASEDIR(protocol)) + kwargs.setdefault("deffnm", self.deffnm) + kwargs.setdefault("mdp", config.get_template("NPT_opls.mdp")) + self.dirs[protocol] = realpath(kwargs["dirname"]) + setupMD = kwargs.pop("MDfunc", gromacs.setup.MD) + kwargs["top"] = self.files.topology + kwargs["includes"] = asiterable(kwargs.pop("includes", [])) + self.dirs.includes + kwargs["ndx"] = self.files.ndx + kwargs[ + "mainselection" + ] = None # important for SD (use custom mdp and ndx!, gromacs.setup._MD) + self._checknotempty(kwargs["struct"], "struct") + if not os.path.exists(kwargs["struct"]): # struct is not reliable as it depends on qscript so now we just try everything... - struct = gromacs.utilities.find_first(kwargs['struct'], suffices=['pdb', 'gro']) + struct = gromacs.utilities.find_first( + kwargs["struct"], suffices=["pdb", "gro"] + ) if struct is None: - logger.error("Starting structure %(struct)r does not exist (yet)" % kwargs) - raise IOError(errno.ENOENT, "Starting structure not found", kwargs['struct']) + logger.error( + "Starting structure %(struct)r does not exist (yet)" % kwargs + ) + raise IOError( + errno.ENOENT, "Starting structure not found", kwargs["struct"] + ) else: - logger.info("Found starting structure %r (instead of %r).", struct, kwargs['struct']) - kwargs['struct'] = struct + logger.info( + "Found starting structure %r (instead of %r).", + struct, + kwargs["struct"], + ) + kwargs["struct"] = struct # now setup the whole simulation (this is typically gromacs.setup.MD() ) - params = setupMD(**kwargs) + params = setupMD(**kwargs) # params['struct'] is md.gro but could also be md.pdb --- depends entirely on qscript - self.files[protocol] = params['struct'] + self.files[protocol] = params["struct"] # Gromacs 4.5.x 'mdrun -c PDB' fails if it cannot find 'residuetypes.dat' # so instead of fuffing with GMXLIB we just dump it into the directory try: - shutil.copy(config.topfiles['residuetypes.dat'], self.dirs[protocol]) + shutil.copy(config.topfiles["residuetypes.dat"], self.dirs[protocol]) except IOError: - logger.warning("Failed to copy 'residuetypes.dat': mdrun will likely fail to write a final structure") + logger.warning( + "Failed to copy 'residuetypes.dat': mdrun will likely fail to write a final structure" + ) self.journal.completed(protocol) return params @@ -513,11 +593,11 @@ def MD_relaxed(self, **kwargs): """ # user structure or restrained or solvated - kwargs.setdefault('struct', self.files.energy_minimized) - kwargs.setdefault('dt', 0.0001) # ps - kwargs.setdefault('runtime', 5) # ps - kwargs.setdefault('mdp', self.mdp['MD_relaxed']) - return self._MD('MD_relaxed', **kwargs) + kwargs.setdefault("struct", self.files.energy_minimized) + kwargs.setdefault("dt", 0.0001) # ps + kwargs.setdefault("runtime", 5) # ps + kwargs.setdefault("mdp", self.mdp["MD_relaxed"]) + return self._MD("MD_relaxed", **kwargs) def MD_restrained(self, **kwargs): """Short MD simulation with position restraints on compound. @@ -551,11 +631,13 @@ def MD_restrained(self, **kwargs): :class:`gromacs.manager.Manager` """ - kwargs.setdefault('struct', - self._lastnotempty([self.files.energy_minimized, self.files.MD_relaxed])) - kwargs.setdefault('mdp', self.mdp['MD_restrained']) - kwargs['MDfunc'] = gromacs.setup.MD_restrained - return self._MD('MD_restrained', **kwargs) + kwargs.setdefault( + "struct", + self._lastnotempty([self.files.energy_minimized, self.files.MD_relaxed]), + ) + kwargs.setdefault("mdp", self.mdp["MD_restrained"]) + kwargs["MDfunc"] = gromacs.setup.MD_restrained + return self._MD("MD_restrained", **kwargs) def MD_NPT(self, **kwargs): """Short NPT MD simulation. @@ -595,10 +677,12 @@ def MD_NPT(self, **kwargs): """ # user structure or relaxed or restrained or solvated - kwargs.setdefault('struct', self.get_last_structure()) - kwargs.setdefault('t',self.get_last_checkpoint()) # Pass checkpoint file from md_relaxed - kwargs.setdefault('mdp', self.mdp['MD_NPT']) - return self._MD('MD_NPT', **kwargs) + kwargs.setdefault("struct", self.get_last_structure()) + kwargs.setdefault( + "t", self.get_last_checkpoint() + ) # Pass checkpoint file from md_relaxed + kwargs.setdefault("mdp", self.mdp["MD_NPT"]) + return self._MD("MD_NPT", **kwargs) # for convenience and compatibility MD = MD_NPT @@ -617,49 +701,64 @@ def _lastnotempty(l): def get_last_structure(self): """Returns the coordinates of the most advanced step in the protocol.""" - return self._lastnotempty([self.files[name] for name in self.coordinate_structures]) + return self._lastnotempty( + [self.files[name] for name in self.coordinate_structures] + ) def get_last_checkpoint(self): """Returns the checkpoint of the most advanced step in the protocol. Relies on md.gro being present from previous simulation, assumes that checkpoint is then present. """ - return self._lastnotempty([self.files[name] for name in self.checkpoints]).replace('.gro','.cpt') + return self._lastnotempty( + [self.files[name] for name in self.checkpoints] + ).replace(".gro", ".cpt") + class WaterSimulation(Simulation): """Equilibrium MD of a solute in a box of water.""" - solvent_default = 'water' + + solvent_default = "water" dirname_default = os.path.join(Simulation.topdir_default, solvent_default) + class CyclohexaneSimulation(Simulation): """Equilibrium MD of a solute in a box of cyclohexane.""" - solvent_default = 'cyclohexane' + + solvent_default = "cyclohexane" dirname_default = os.path.join(Simulation.topdir_default, solvent_default) + class OctanolSimulation(Simulation): """Equilibrium MD of a solute in a box of octanol.""" - solvent_default = 'octanol' + + solvent_default = "octanol" dirname_default = os.path.join(Simulation.topdir_default, solvent_default) + class WetOctanolSimulation(Simulation): """Equilibrium MD of a solute in a box of wet octanol.""" - solvent_default = 'wetoctanol' + + solvent_default = "wetoctanol" dirname_default = os.path.join(Simulation.topdir_default, solvent_default) - def _setup_solvate(self, **kwargs): + def _setup_solvate(self, **kwargs): sol = gromacs.setup.solvate_sol(**kwargs) with in_dir(self.dirs.solvation, create=False): - u = mda.Universe('solvated.gro') - octanol = u.select_atoms('resname OcOH') + u = mda.Universe("solvated.gro") + octanol = u.select_atoms("resname OcOH") n = octanol.n_residues with in_dir(self.dirs.topology, create=False): - gromacs.cbook.edit_txt(self.files.topology, - [('OcOH 1', '1', n)]) + gromacs.cbook.edit_txt( + self.files.topology, [("OcOH 1", "1", n)] + ) ionkwargs = kwargs - ionkwargs['struct'] = sol['struct'] + ionkwargs["struct"] = sol["struct"] params = gromacs.setup.solvate_ion(**ionkwargs) return params + class TolueneSimulation(Simulation): """Equilibrium MD of a solute in a box of toluene.""" - solvent_default = 'toluene' - dirname_default = os.path.join(Simulation.topdir_default, solvent_default) \ No newline at end of file + + solvent_default = "toluene" + dirname_default = os.path.join(Simulation.topdir_default, solvent_default) diff --git a/mdpow/fep.py b/mdpow/fep.py index b5b7e406..4edd0362 100644 --- a/mdpow/fep.py +++ b/mdpow/fep.py @@ -163,6 +163,7 @@ import gromacs import gromacs.utilities + try: import gromacs.setup except (ImportError, OSError): @@ -170,16 +171,19 @@ from gromacs.utilities import asiterable, AttributeDict, in_dir, openany import logging -logger = logging.getLogger('mdpow.fep') + +logger = logging.getLogger("mdpow.fep") from . import config from .restart import Journalled from . import kBOLTZ, N_AVOGADRO + def molar_to_nm3(c): """Convert a concentration in Molar to nm|^-3|.""" return c * N_AVOGADRO * 1e-24 + def bar_to_kJmolnm3(p): """Convert pressure in bar to kJ mol|^-1| nm|^-3|. @@ -187,17 +191,20 @@ def bar_to_kJmolnm3(p): """ return p * N_AVOGADRO * 1e-25 + def kcal_to_kJ(x): """Convert a energy in kcal to kJ.""" return 4.184 * x + def kJ_to_kcal(x): """Convert a energy in kJ to kcal.""" return x / 4.184 + def kBT_to_kJ(x, T): """Convert a energy in kBT to kJ/mol.""" - return x * constants.N_A*constants.k*T*1e-3 + return x * constants.N_A * constants.k * T * 1e-3 class FEPschedule(AttributeDict): @@ -232,19 +239,23 @@ class FEPschedule(AttributeDict): lambdas = 0.0, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1 """ - mdp_keywords = dict((('sc_alpha', float), - ('sc_power', int), - ('sc_sigma', float), - ('couple_lambda0', str), - ('couple_lambda1', str), - )) - meta_keywords = dict((('name', str), ('description', str), ('label', str))) - other_keywords = dict((('lambdas', list), )) + + mdp_keywords = dict( + ( + ("sc_alpha", float), + ("sc_power", int), + ("sc_sigma", float), + ("couple_lambda0", str), + ("couple_lambda1", str), + ) + ) + meta_keywords = dict((("name", str), ("description", str), ("label", str))) + other_keywords = dict((("lambdas", list),)) @property def mdp_dict(self): """Dict of key-values that can be set in a mdp file.""" - return dict(((k,v) for k,v in self.items() if k in self.mdp_keywords)) + return dict(((k, v) for k, v in self.items() if k in self.mdp_keywords)) @staticmethod def load(cfg, section): @@ -254,12 +265,14 @@ def load(cfg, section): keys.update(FEPschedule.meta_keywords) keys.update(FEPschedule.other_keywords) - cfg_get = {float: cfg.getfloat, - int: cfg.getint, - str: cfg.getstr, # literal strings, no conversion of None (which we need for the MDP!) - # CHECK: THIS IS LIKELY NOT GUARANTEED ANYMORE since getstr == get - list: cfg.getarray # numpy float array from list - } + cfg_get = { + float: cfg.getfloat, + int: cfg.getint, + str: cfg.getstr, # literal strings, no conversion of None (which we need for the MDP!) + # CHECK: THIS IS LIKELY NOT GUARANTEED ANYMORE since getstr == get + list: cfg.getarray, # numpy float array from list + } + def getter(type, section, key): value = cfg_get[type](section, key) try: @@ -269,9 +282,13 @@ def getter(type, section, key): except TypeError: pass return value + # skip any None values - return FEPschedule((key, getter(keytype, section, key)) for key,keytype in keys.items() - if getter(keytype, section, key) is not None) + return FEPschedule( + (key, getter(keytype, section, key)) + for key, keytype in keys.items() + if getter(keytype, section, key) is not None + ) def __deepcopy__(self, memo): x = FEPschedule() @@ -279,6 +296,7 @@ def __deepcopy__(self, memo): x[k] = copy.deepcopy(v) return x + class Gsolv(Journalled): r"""Simulations to calculate and analyze the solvation free energy. @@ -326,36 +344,58 @@ class Gsolv(Journalled): protocols = ["setup", "fep_run"] #: Estimators in alchemlyb - estimators = {'TI': {'extract': extract_dHdl, 'estimator': TI}, - 'BAR': {'extract': extract_u_nk, 'estimator': BAR}, - 'MBAR': {'extract': extract_u_nk, 'estimator': MBAR} - } + estimators = { + "TI": {"extract": extract_dHdl, "estimator": TI}, + "BAR": {"extract": extract_u_nk, "estimator": BAR}, + "MBAR": {"extract": extract_u_nk, "estimator": MBAR}, + } # TODO: initialize from default cfg - schedules_default = {'coulomb': - FEPschedule(name='coulomb', - description="dis-charging vdw+q --> vdw", - label='Coul', - couple_lambda0='vdw-q', couple_lambda1='vdw', - sc_alpha=0, # linear scaling for coulomb - lambdas=np.array([0.0, 0.25, 0.5, 0.75, 1.0]), # default values - ), - 'vdw': - FEPschedule(name='vdw', - description="decoupling vdw --> none", - label='VDW', - couple_lambda0='vdw', couple_lambda1='none', - sc_alpha=0.5, sc_power=1, sc_sigma=0.3, # recommended values - lambdas=np.array([0.0, 0.05, 0.1, 0.2, 0.3, - 0.4, 0.5, 0.6, 0.65, 0.7, 0.75, 0.8, - 0.85, 0.9, 0.95, 1]), # defaults - ), - } + schedules_default = { + "coulomb": FEPschedule( + name="coulomb", + description="dis-charging vdw+q --> vdw", + label="Coul", + couple_lambda0="vdw-q", + couple_lambda1="vdw", + sc_alpha=0, # linear scaling for coulomb + lambdas=np.array([0.0, 0.25, 0.5, 0.75, 1.0]), # default values + ), + "vdw": FEPschedule( + name="vdw", + description="decoupling vdw --> none", + label="VDW", + couple_lambda0="vdw", + couple_lambda1="none", + sc_alpha=0.5, + sc_power=1, + sc_sigma=0.3, # recommended values + lambdas=np.array( + [ + 0.0, + 0.05, + 0.1, + 0.2, + 0.3, + 0.4, + 0.5, + 0.6, + 0.65, + 0.7, + 0.75, + 0.8, + 0.85, + 0.9, + 0.95, + 1, + ] + ), # defaults + ), + } #: Default Gromacs *MDP* run parameter file for FEP. #: (The file is part of the package and is found with :func:`mdpow.config.get_template`.) - mdp_default = 'bar_opls.mdp' - + mdp_default = "bar_opls.mdp" def __init__(self, molecule=None, top=None, struct=None, method="BAR", **kwargs): """Set up Gsolv from input files or a equilibrium simulation. @@ -436,41 +476,49 @@ def __init__(self, molecule=None, top=None, struct=None, method="BAR", **kwargs) parameters. """ - required_args = ('molecule', 'top', 'struct') + required_args = ("molecule", "top", "struct") # should this be below somewhere? if not method in ("TI", "BAR", "MBAR"): raise ValueError("method can only be TI, BAR, or MBAR") self.method = method - filename = kwargs.pop('filename', None) - basedir = kwargs.pop('basedir', os.path.curdir) # all other dirs relative to basedir - simulation = kwargs.pop('simulation', None) - solvent = kwargs.pop('solvent', self.solvent_default) - if (None in (molecule, top, struct) and simulation is None) and filename is not None: + filename = kwargs.pop("filename", None) + basedir = kwargs.pop( + "basedir", os.path.curdir + ) # all other dirs relative to basedir + simulation = kwargs.pop("simulation", None) + solvent = kwargs.pop("solvent", self.solvent_default) + if ( + None in (molecule, top, struct) and simulation is None + ) and filename is not None: # load from pickle file self.load(filename) self.filename = filename - kwargs = {} # for super + kwargs = {} # for super else: if simulation is not None: # load data from Simulation instance self.molecule = simulation.molecule - self.top = simulation.files.processed_topology or simulation.files.topology + self.top = ( + simulation.files.processed_topology or simulation.files.topology + ) self.struct = simulation.files.MD_NPT self.ndx = simulation.files.ndx if simulation.solvent_type == solvent: self.solvent_type = simulation.solvent_type else: - errmsg = "Solvent mismatch: simulation was run for %s but Gsolv is set up for %s" % \ - (simulation.solvent_type, solvent) + errmsg = ( + "Solvent mismatch: simulation was run for %s but Gsolv is set up for %s" + % (simulation.solvent_type, solvent) + ) logger.error(errmsg) raise ValueError(errmsg) else: - self.molecule = molecule # should check that this is in top (?) + self.molecule = molecule # should check that this is in top (?) self.top = top self.struct = struct - self.ndx = kwargs.pop('ndx', None) + self.ndx = kwargs.pop("ndx", None) self.solvent_type = solvent for attr in required_args: @@ -480,54 +528,71 @@ def __init__(self, molecule=None, top=None, struct=None, method="BAR", **kwargs) # fix struct (issue with qscripts being independent from rest of code) if not os.path.exists(self.struct): # struct is not reliable as it depends on qscript so now we just try everything... - struct = gromacs.utilities.find_first(self.struct, suffices=['pdb', 'gro']) + struct = gromacs.utilities.find_first( + self.struct, suffices=["pdb", "gro"] + ) if struct is None: logger.error("Starting structure %r does not exist.", self.struct) - raise IOError(errno.ENOENT, "Starting structure not found", self.struct) + raise IOError( + errno.ENOENT, "Starting structure not found", self.struct + ) else: - logger.info("Found starting structure %r (instead of %r).", struct, self.struct) + logger.info( + "Found starting structure %r (instead of %r).", + struct, + self.struct, + ) self.struct = struct - self.Temperature = kwargs.pop('temperature', 300.0) - self.qscript = kwargs.pop('qscript', ['local.sh']) - self.deffnm = kwargs.pop('deffnm', 'md') + self.Temperature = kwargs.pop("temperature", 300.0) + self.qscript = kwargs.pop("qscript", ["local.sh"]) + self.deffnm = kwargs.pop("deffnm", "md") - self.mdp = kwargs.pop('mdp', config.get_template(self.mdp_default)) + self.mdp = kwargs.pop("mdp", config.get_template(self.mdp_default)) # schedules (deepcopy because we might modify) # For some reason 2.7 tests failed with deepcopy in 2.7 so used merge_dict instead self.schedules = config.merge_dicts(self.schedules_default, {}) - schedules = kwargs.pop('schedules', {}) + schedules = kwargs.pop("schedules", {}) self.schedules.update(schedules) self.lambdas = { - 'coulomb': kwargs.pop('lambda_coulomb', self.schedules['coulomb'].lambdas), - 'vdw': kwargs.pop('lambda_vdw', self.schedules['vdw'].lambdas), - } - self.runtime = kwargs.pop('runtime', 5000.0) # ps - self.dirname = kwargs.pop('dirname', self.dirname_default) - self.includes = list(asiterable(kwargs.pop('includes',[]))) + [config.includedir] - self.component_dirs = {'coulomb': os.path.join(self.dirname, 'Coulomb'), - 'vdw': os.path.join(self.dirname, 'VDW')} + "coulomb": kwargs.pop( + "lambda_coulomb", self.schedules["coulomb"].lambdas + ), + "vdw": kwargs.pop("lambda_vdw", self.schedules["vdw"].lambdas), + } + self.runtime = kwargs.pop("runtime", 5000.0) # ps + self.dirname = kwargs.pop("dirname", self.dirname_default) + self.includes = list(asiterable(kwargs.pop("includes", []))) + [ + config.includedir + ] + self.component_dirs = { + "coulomb": os.path.join(self.dirname, "Coulomb"), + "vdw": os.path.join(self.dirname, "VDW"), + } # for analysis - self.stride = kwargs.pop('stride', 1) - self.start = kwargs.pop('start', 0) - self.stop = kwargs.pop('stop', None) - self.SI = kwargs.pop('SI', True) + self.stride = kwargs.pop("stride", 1) + self.start = kwargs.pop("start", 0) + self.stop = kwargs.pop("stop", None) + self.SI = kwargs.pop("SI", True) # other variables #: Results from the analysis - self.results = AttributeDict(xvg=AttributeDict(), - dvdl=AttributeDict(), - DeltaA=AttributeDict(), # contains QuantityWithError - ) + self.results = AttributeDict( + xvg=AttributeDict(), + dvdl=AttributeDict(), + DeltaA=AttributeDict(), # contains QuantityWithError + ) #: Generated run scripts self.scripts = AttributeDict() # sanity checks if os.path.exists(self.dirname): - wmsg = "Directory %(dirname)r already exists --- will overwrite " \ - "existing files." % vars(self) + wmsg = ( + "Directory %(dirname)r already exists --- will overwrite " + "existing files." % vars(self) + ) warnings.warn(wmsg) logger.warning(wmsg) @@ -541,16 +606,23 @@ def __init__(self, molecule=None, top=None, struct=None, method="BAR", **kwargs) self.filename = os.path.abspath(self.filename) except (AttributeError, TypeError): # default filename if none was provided - self.filename = self.frombase(self.dirname, self.__class__.__name__+os.extsep+'fep') + self.filename = self.frombase( + self.dirname, self.__class__.__name__ + os.extsep + "fep" + ) # override pickle file for this dangerous option: must be set # on a case-by-case basis - self.permissive = kwargs.pop('permissive', False) + self.permissive = kwargs.pop("permissive", False) - logger.info("Solvation free energy calculation for molecule " - "%(molecule)s in solvent %(solvent_type)s.", vars(self)) + logger.info( + "Solvation free energy calculation for molecule " + "%(molecule)s in solvent %(solvent_type)s.", + vars(self), + ) logger.info("Base directory is %(basedir)r", vars(self)) - logger.info("Using setup directories under %(dirname)r: %(component_dirs)r", vars(self)) + logger.info( + "Using setup directories under %(dirname)r: %(component_dirs)r", vars(self) + ) logger.info("Default checkpoint file is %(filename)r", vars(self)) logger.debug("Coulomb lambdas = %(coulomb)r", self.lambdas) logger.debug("VDW lambdas = %(vdw)r", self.lambdas) @@ -585,11 +657,16 @@ def label(self, component): def tasklabel(self, component, lmbda): """Batch submission script name for a single task job.""" - return self.molecule[:3]+'_'+self.schedules[component].label+"%04d" % (1000 * lmbda) + return ( + self.molecule[:3] + + "_" + + self.schedules[component].label + + "%04d" % (1000 * lmbda) + ) def arraylabel(self, component): """Batch submission script name for a job array.""" - return self.molecule[:3]+'_'+self.schedules[component].label + return self.molecule[:3] + "_" + self.schedules[component].label def fep_dirs(self): """Generator for all simulation sub directories""" @@ -625,39 +702,46 @@ def setup(self, **kwargs): .. versionchanged:: 0.6.0 Gromacs now uses option ``-dhdl`` instead of ``-dgdl``. """ - self.journal.start('setup') + self.journal.start("setup") # -dgdl for FEP output (although that seems to have been changed to -dHdl in Gromacs 4.5.3) # NOW use -dhdl - kwargs['mdrun_opts'] = " ".join([kwargs.pop('mdrun_opts',''), '-dhdl']) - kwargs['includes'] = asiterable(kwargs.pop('includes',[])) + self.includes - kwargs['deffnm'] = self.deffnm - kwargs.setdefault('maxwarn', 1) + kwargs["mdrun_opts"] = " ".join([kwargs.pop("mdrun_opts", ""), "-dhdl"]) + kwargs["includes"] = asiterable(kwargs.pop("includes", [])) + self.includes + kwargs["deffnm"] = self.deffnm + kwargs.setdefault("maxwarn", 1) qsubargs = kwargs.copy() - qsubargs['dirname'] = self.frombase(self.dirname) + qsubargs["dirname"] = self.frombase(self.dirname) # handle templates separately (necessary for array jobs) - qscripts = qsubargs.pop('sge', None) or self.qscript - qscripts.extend(qsubargs.pop('qscript',[])) # also allow canonical 'templates' + qscripts = qsubargs.pop("sge", None) or self.qscript + qscripts.extend(qsubargs.pop("qscript", [])) # also allow canonical 'templates' # make sure that the individual batch scripts are also written - kwargs.setdefault('qscript', qscripts) + kwargs.setdefault("qscript", qscripts) for component, lambdas in self.lambdas.items(): for l in lambdas: - params = self._setup(component, l, - foreign_lambdas=lambdas, **kwargs) + params = self._setup(component, l, foreign_lambdas=lambdas, **kwargs) # generate queuing system script for array job directories = [self.wdir(component, l) for l in lambdas] - qsubargs['jobname'] = self.arraylabel(component) - qsubargs['prefix'] = self.label(component)+'_' - self.scripts[component] = gromacs.qsub.generate_submit_array(qscripts, directories, **qsubargs) - logger.info("[%s] Wrote array job scripts %r", component, self.scripts[component]) - - self.journal.completed('setup') + qsubargs["jobname"] = self.arraylabel(component) + qsubargs["prefix"] = self.label(component) + "_" + self.scripts[component] = gromacs.qsub.generate_submit_array( + qscripts, directories, **qsubargs + ) + logger.info( + "[%s] Wrote array job scripts %r", component, self.scripts[component] + ) + + self.journal.completed("setup") self.save(self.filename) - logger.info("Saved state information to %r; reload later with G = %r.", self.filename, self) + logger.info( + "Saved state information to %r; reload later with G = %r.", + self.filename, + self, + ) logger.info("Finished setting up all individual simulations. Now run them...") - params.pop('struct', None) # scrub window-specific params + params.pop("struct", None) # scrub window-specific params return params def _setup(self, component, lmbda, foreign_lambdas, **kwargs): @@ -668,36 +752,41 @@ def _setup(self, component, lmbda, foreign_lambdas, **kwargs): logger.info("Preparing %(component)s for lambda=%(lmbda)g" % vars()) wdir = self.wdir(component, lmbda) - kwargs.setdefault('couple-intramol', 'no') + kwargs.setdefault("couple-intramol", "no") ### XXX Issue 20: if an entry is None then the dict will not be updated: ### I *must* keep "none" as a legal string value - kwargs.update(self.schedules[component].mdp_dict) # sets soft core & lambda0/1 state + kwargs.update( + self.schedules[component].mdp_dict + ) # sets soft core & lambda0/1 state - if kwargs.pop('edr', True): - logger.info('Setting dhdl file to edr format') - kwargs.setdefault('separate-dhdl-file', 'no') + if kwargs.pop("edr", True): + logger.info("Setting dhdl file to edr format") + kwargs.setdefault("separate-dhdl-file", "no") else: - logger.info('Setting dhdl file to xvg format') - kwargs.setdefault('separate-dhdl-file', 'yes') + logger.info("Setting dhdl file to xvg format") + kwargs.setdefault("separate-dhdl-file", "yes") foreign_lambdas = np.asarray(foreign_lambdas) lambda_index = np.where(foreign_lambdas == lmbda)[0][0] - kwargs.update(dirname=wdir, struct=self.struct, top=self.top, - mdp=self.mdp, - ndx=self.ndx, - mainselection=None, - runtime=self.runtime, - ref_t=self.Temperature, # TODO: maybe not working yet, check _setup() - gen_temp=self.Temperature, # needed until gromacs.setup() is smarter - qname=self.tasklabel(component,lmbda), - free_energy='yes', - couple_moltype=self.molecule, - init_lambda_state=lambda_index, - fep_lambdas=foreign_lambdas, - calc_lambda_neighbors=-1, - ) + kwargs.update( + dirname=wdir, + struct=self.struct, + top=self.top, + mdp=self.mdp, + ndx=self.ndx, + mainselection=None, + runtime=self.runtime, + ref_t=self.Temperature, # TODO: maybe not working yet, check _setup() + gen_temp=self.Temperature, # needed until gromacs.setup() is smarter + qname=self.tasklabel(component, lmbda), + free_energy="yes", + couple_moltype=self.molecule, + init_lambda_state=lambda_index, + fep_lambdas=foreign_lambdas, + calc_lambda_neighbors=-1, + ) return gromacs.setup.MD(**kwargs) @@ -718,9 +807,9 @@ def dgdl_xvg(self, *args): :Raises: :exc:`IOError` with error code ENOENT if no file could be found - """ - EXTENSIONS = ('', os.path.extsep+'bz2', os.path.extsep+'gz') - root = os.path.join(*args + (self.deffnm + '.xvg',)) + """ + EXTENSIONS = ("", os.path.extsep + "bz2", os.path.extsep + "gz") + root = os.path.join(*args + (self.deffnm + ".xvg",)) for ext in EXTENSIONS: fn = root + ext if os.path.exists(fn): @@ -741,8 +830,8 @@ def dgdl_edr(self, *args): :Raises: :exc:`IOError` with error code ENOENT if no file could be found - """ - pattern = os.path.join(*args + (self.deffnm + '*.edr',)) + """ + pattern = os.path.join(*args + (self.deffnm + "*.edr",)) edrs = glob(pattern) if not edrs: logger.error("Missing dgdl.edr file %(pattern)r.", vars()) @@ -762,8 +851,8 @@ def dgdl_tpr(self, *args): :Raises: :exc:`IOError` with error code ENOENT if no file could be found - """ - fn = os.path.join(*args + (self.deffnm + '.tpr',)) + """ + fn = os.path.join(*args + (self.deffnm + ".tpr",)) if not os.path.exists(fn): logger.error("Missing TPR file %(fn)r.", vars()) raise IOError(errno.ENOENT, "Missing TPR file", fn) @@ -802,7 +891,7 @@ def convert_edr(self): total_edr = edr[0] else: total_edr = self.dgdl_total_edr(dirct) - logger.info(" {0} --> {1}".format('edrs', total_edr)) + logger.info(" {0} --> {1}".format("edrs", total_edr)) gromacs.eneconv(f=edr, o=total_edr) xvgfile = os.path.join(dirct, self.deffnm + ".xvg") # hack logger.info(" {0} --> {1}".format(total_edr, xvgfile)) @@ -829,14 +918,20 @@ def collect(self, stride=None, autosave=True, autocompress=True): # must be done before adding to results.xvg or we will not find the file later self.compress_dgdl_xvg() - logger.info("[%(dirname)s] Finding dgdl xvg files, reading with " - "stride=%(stride)d permissive=%(permissive)r." % vars(self)) + logger.info( + "[%(dirname)s] Finding dgdl xvg files, reading with " + "stride=%(stride)d permissive=%(permissive)r." % vars(self) + ) for component, lambdas in self.lambdas.items(): xvg_files = [self.dgdl_xvg(self.wdir(component, l)) for l in lambdas] - self.results.xvg[component] = (np.array(lambdas), - [XVG(xvg, permissive=self.permissive, stride=self.stride) - for xvg in xvg_files]) + self.results.xvg[component] = ( + np.array(lambdas), + [ + XVG(xvg, permissive=self.permissive, stride=self.stride) + for xvg in xvg_files + ], + ) if autosave: self.save() @@ -852,23 +947,30 @@ def compress_dgdl_xvg(self): for component, lambdas in self.lambdas.items(): xvg_files = [self.dgdl_xvg(self.wdir(component, l)) for l in lambdas] for xvg in xvg_files: - root,ext = os.path.splitext(xvg) - if ext == os.path.extsep+"xvg": + root, ext = os.path.splitext(xvg) + if ext == os.path.extsep + "xvg": fnbz2 = xvg + os.path.extsep + "bz2" - logger.info("[%s] Compressing dgdl file %r with bzip2", self.dirname, xvg) + logger.info( + "[%s] Compressing dgdl file %r with bzip2", self.dirname, xvg + ) # speed is similar to 'bzip2 -9 FILE' (using a 1 Mio buffer) # (Since GW 0.8, openany() does not take kwargs anymore so the write buffer cannot be # set anymore (buffering=1048576) so the performance might be lower in MDPOW >= 0.7.0) - with open(xvg, 'rb', buffering=1048576) as source: - with openany(fnbz2, 'wb') as target: + with open(xvg, "rb", buffering=1048576) as source: + with openany(fnbz2, "wb") as target: target.writelines(source) if os.path.exists(fnbz2) and os.path.exists(xvg): os.unlink(xvg) if not os.path.exists(fnbz2): - logger.error("[%s] Failed to compress %r --- mysterious!", self.dirname, fnbz2) + logger.error( + "[%s] Failed to compress %r --- mysterious!", + self.dirname, + fnbz2, + ) else: - logger.info("[%s] Compression complete: %r", self.dirname, fnbz2) - + logger.info( + "[%s] Compression complete: %r", self.dirname, fnbz2 + ) def contains_corrupted_xvgs(self): """Check if any of the source datafiles had reported corrupted lines. @@ -880,18 +982,22 @@ def contains_corrupted_xvgs(self): :attr:`Gsolv._corrupted` as dicts of dicts with the component as primary and the lambda as secondary key. """ + def _lencorrupted(xvg): try: return len(xvg.corrupted_lineno) except AttributeError: # backwards compatible (pre gw 0.1.10 are always ok) return 0 - except TypeError: # len(None): XVG.parse() has not been run yet - return 0 # ... so we cannot conclude that it does contain bad ones + except TypeError: # len(None): XVG.parse() has not been run yet + return 0 # ... so we cannot conclude that it does contain bad ones + corrupted = {} - self._corrupted = {} # debugging ... + self._corrupted = {} # debugging ... for component, (lambdas, xvgs) in self.results.xvg.items(): corrupted[component] = np.any([(_lencorrupted(xvg) > 0) for xvg in xvgs]) - self._corrupted[component] = dict(((l, _lencorrupted(xvg)) for l,xvg in zip(lambdas, xvgs))) + self._corrupted[component] = dict( + ((l, _lencorrupted(xvg)) for l, xvg in zip(lambdas, xvgs)) + ) return np.any([x for x in corrupted.values()]) def analyze(self, force=False, stride=None, autosave=True, ncorrel=25000): @@ -977,7 +1083,7 @@ def analyze(self, force=False, stride=None, autosave=True, ncorrel=25000): .. _p526: http://books.google.co.uk/books?id=XmyO2oRUg0cC&pg=PA526 """ stride = stride or self.stride - logger.info("Analysis stride is %s.",stride) + logger.info("Analysis stride is %s.", stride) if force or not self.has_dVdl(): try: @@ -993,36 +1099,52 @@ def analyze(self, force=False, stride=None, autosave=True, ncorrel=25000): logger.info("Analyzing stored data.") # total free energy difference at const P (all simulations are done in NPT) - GibbsFreeEnergy = QuantityWithError(0,0) + GibbsFreeEnergy = QuantityWithError(0, 0) for component, (lambdas, xvgs) in self.results.xvg.items(): - logger.info("[%s %s] Computing averages and errors for %d lambda values.", - self.molecule, component, len(lambdas)) + logger.info( + "[%s %s] Computing averages and errors for %d lambda values.", + self.molecule, + component, + len(lambdas), + ) # for TI just get the average dv/dl value (in array column 1; col 0 is the time) # (This can take a while if the XVG is now reading the array from disk first time) # Use XVG class properties: first data in column 0! Y = np.array([x.mean[0] for x in xvgs]) - stdY = np.array([x.std[0] for x in xvgs]) + stdY = np.array([x.std[0] for x in xvgs]) # compute auto correlation time and error estimate for independent samples # (this can take a while). x.array[0] == time, x.array[1] == dHdl # nstep is calculated to give ncorrel samples (or all samples if less than ncorrel are # available) - tc_data = [numkit.timeseries.tcorrel(x.array[0], x.array[1], - nstep=int(np.ceil(len(x.array[0])/float(ncorrel)))) - for x in xvgs] - DY = np.array([tc['sigma'] for tc in tc_data]) - tc = np.array([tc['tc'] for tc in tc_data]) - - self.results.dvdl[component] = {'lambdas':lambdas, 'mean':Y, 'error':DY, - 'stddev':stdY, 'tcorrel':tc} + tc_data = [ + numkit.timeseries.tcorrel( + x.array[0], + x.array[1], + nstep=int(np.ceil(len(x.array[0]) / float(ncorrel))), + ) + for x in xvgs + ] + DY = np.array([tc["sigma"] for tc in tc_data]) + tc = np.array([tc["tc"] for tc in tc_data]) + + self.results.dvdl[component] = { + "lambdas": lambdas, + "mean": Y, + "error": DY, + "stddev": stdY, + "tcorrel": tc, + } # Combined Simpson rule integration: # even="last" because dV/dl is smoother at the beginning so using trapezoidal # integration there makes less of an error (one hopes...) - a = scipy.integrate.simps(Y, x=lambdas, even='last') - da = numkit.integration.simps_error(DY, x=lambdas, even='last') + a = scipy.integrate.simps(Y, x=lambdas, even="last") + da = numkit.integration.simps_error(DY, x=lambdas, even="last") self.results.DeltaA[component] = QuantityWithError(a, da) - GibbsFreeEnergy += self.results.DeltaA[component] # error propagation is automagic! + GibbsFreeEnergy += self.results.DeltaA[ + component + ] # error propagation is automagic! # hydration free energy Delta A = -(Delta A_coul + Delta A_vdw) GibbsFreeEnergy *= -1 @@ -1034,20 +1156,24 @@ def analyze(self, force=False, stride=None, autosave=True, ncorrel=25000): self.logger_DeltaA0() return self.results.DeltaA.Gibbs - def collect_alchemlyb(self, SI=True, start=0, stop=None, stride=None, autosave=True, autocompress=True): + def collect_alchemlyb( + self, SI=True, start=0, stop=None, stride=None, autosave=True, autocompress=True + ): """Collect the data files using alchemlyb. Unlike :meth:`collect`, this method can subsample with the statistical inefficiency (parameter `SI`). """ - extract = self.estimators[self.method]['extract'] + extract = self.estimators[self.method]["extract"] if autocompress: # must be done before adding to results.xvg or we will not find the file later self.compress_dgdl_xvg() - logger.info("[%(dirname)s] Finding dgdl xvg files, reading with " - "stride=%(stride)d permissive=%(permissive)r." % vars(self)) + logger.info( + "[%(dirname)s] Finding dgdl xvg files, reading with " + "stride=%(stride)d permissive=%(permissive)r." % vars(self) + ) for component, lambdas in self.lambdas.items(): val = [] for l in lambdas: @@ -1055,21 +1181,34 @@ def collect_alchemlyb(self, SI=True, start=0, stop=None, stride=None, autosave=T xvg_df = extract(xvg_file, T=self.Temperature).iloc[start:stop:stride] full_len = len(xvg_df) if SI: - logger.info("Performing statistical inefficiency analysis for window %s %04d" % (component, 1000 * l)) + logger.info( + "Performing statistical inefficiency analysis for window %s %04d" + % (component, 1000 * l) + ) ts = _extract_dataframe(xvg_file).iloc[start:stop:stride] - ts = pd.DataFrame({'time': ts.iloc[:,0], 'dhdl': ts.iloc[:,1]}) - ts = ts.set_index('time') + ts = pd.DataFrame({"time": ts.iloc[:, 0], "dhdl": ts.iloc[:, 1]}) + ts = ts.set_index("time") # use the statistical_inefficiency function to subsample the data xvg_df = statistical_inefficiency(xvg_df, ts, conservative=True) - logger.info("The statistical inefficiency value is {:.4f}.".format(full_len/len(xvg_df)/2)) - logger.info("The data are subsampled every {:d} frames.".format(int(np.ceil(full_len/len(xvg_df)/2)))) + logger.info( + "The statistical inefficiency value is {:.4f}.".format( + full_len / len(xvg_df) / 2 + ) + ) + logger.info( + "The data are subsampled every {:d} frames.".format( + int(np.ceil(full_len / len(xvg_df) / 2)) + ) + ) val.append(xvg_df) self.results.xvg[component] = (np.array(lambdas), pd.concat(val)) if autosave: self.save() - def analyze_alchemlyb(self, SI=True, start=0, stop=None, stride=None, force=False, autosave=True): + def analyze_alchemlyb( + self, SI=True, start=0, stop=None, stride=None, force=False, autosave=True + ): """Compute the free energy from the simulation data with alchemlyb. Unlike :meth:`analyze`, the MBAR estimator is available (in @@ -1081,12 +1220,12 @@ def analyze_alchemlyb(self, SI=True, start=0, stop=None, stride=None, force=Fals start = start or self.start stop = stop or self.stop - logger.info("Analysis stride is %s.",stride) - logger.info("Analysis starts from frame %s.",start) + logger.info("Analysis stride is %s.", stride) + logger.info("Analysis starts from frame %s.", start) logger.info("Analysis stops at frame %s.", stop) - if self.method in ['TI', 'BAR', 'MBAR']: - estimator = self.estimators[self.method]['estimator'] + if self.method in ["TI", "BAR", "MBAR"]: + estimator = self.estimators[self.method]["estimator"] else: errmsg = "The method is not supported." logger.error(errmsg) @@ -1106,13 +1245,13 @@ def analyze_alchemlyb(self, SI=True, start=0, stop=None, stride=None, force=Fals logger.info("Analyzing stored data.") # total free energy difference at const P (all simulations are done in NPT) - GibbsFreeEnergy = QuantityWithError(0,0) + GibbsFreeEnergy = QuantityWithError(0, 0) for component, (lambdas, xvgs) in self.results.xvg.items(): result = estimator().fit(xvgs) - if self.method == 'BAR': - DeltaA = QuantityWithError(0,0) - a_s= np.diagonal(result.delta_f_, offset=1) + if self.method == "BAR": + DeltaA = QuantityWithError(0, 0) + a_s = np.diagonal(result.delta_f_, offset=1) da_s = np.diagonal(result.d_delta_f_, offset=1) for a, da in zip(a_s, da_s): DeltaA += QuantityWithError(a, da) @@ -1120,8 +1259,12 @@ def analyze_alchemlyb(self, SI=True, start=0, stop=None, stride=None, force=Fals else: a = result.delta_f_.loc[0.00, 1.00] da = result.d_delta_f_.loc[0.00, 1.00] - self.results.DeltaA[component] = kBT_to_kJ(QuantityWithError(a, da), self.Temperature) - GibbsFreeEnergy += self.results.DeltaA[component] # error propagation is automagic! + self.results.DeltaA[component] = kBT_to_kJ( + QuantityWithError(a, da), self.Temperature + ) + GibbsFreeEnergy += self.results.DeltaA[ + component + ] # error propagation is automagic! # hydration free energy Delta A = -(Delta A_coul + Delta A_vdw) GibbsFreeEnergy *= -1 @@ -1136,7 +1279,7 @@ def analyze_alchemlyb(self, SI=True, start=0, stop=None, stride=None, force=Fals if autosave: self.save() - def write_DeltaA0(self, filename, mode='w'): + def write_DeltaA0(self, filename, mode="w"): """Write free energy components to a file. :Arguments: @@ -1150,7 +1293,7 @@ def write_DeltaA0(self, filename, mode='w'): molecule solvent total coulomb vdw """ with open(filename, mode) as tab: - tab.write(self.summary() + '\n') + tab.write(self.summary() + "\n") def summary(self): """Return a string that summarizes the energetics. @@ -1165,21 +1308,29 @@ def summary(self): """ fmt = "%-10s %-14s %+8.2f %8.2f %+8.2f %8.2f %+8.2f %8.2f" d = self.results.DeltaA - return fmt % ((self.molecule, self.solvent_type) + \ - d.Gibbs.astuple() + d.coulomb.astuple() + \ - d.vdw.astuple()) + return fmt % ( + (self.molecule, self.solvent_type) + + d.Gibbs.astuple() + + d.coulomb.astuple() + + d.vdw.astuple() + ) def logger_DeltaA0(self): """Print the free energy contributions (errors in parentheses).""" - if not 'DeltaA' in self.results or len(self.results.DeltaA) == 0: + if not "DeltaA" in self.results or len(self.results.DeltaA) == 0: logger.info("No DeltaA free energies computed yet.") return logger.info("DeltaG0 = -(DeltaG_coul + DeltaG_vdw)") for component, energy in self.results.DeltaA.items(): - logger.info("[%s] %s solvation free energy (%s) %g (%.2f) kJ/mol", - self.molecule, self.solvent_type.capitalize(), component, - energy.value, energy.error) + logger.info( + "[%s] %s solvation free energy (%s) %g (%.2f) kJ/mol", + self.molecule, + self.solvent_type.capitalize(), + component, + energy.value, + energy.error, + ) def has_dVdl(self): """Check if dV/dl data have already been collected. @@ -1192,7 +1343,9 @@ def has_dVdl(self): return False except AttributeError: return False - return np.all(np.array([len(xvgs) for (lambdas,xvgs) in self.results.xvg.values()]) > 0) + return np.all( + np.array([len(xvgs) for (lambdas, xvgs) in self.results.xvg.values()]) > 0 + ) def plot(self, **kwargs): """Plot the TI data with error bars. @@ -1206,9 +1359,9 @@ def plot(self, **kwargs): import matplotlib import matplotlib.pyplot as plt - kwargs.setdefault('color', 'black') - kwargs.setdefault('capsize', 0) - kwargs.setdefault('elinewidth', 2) + kwargs.setdefault("color", "black") + kwargs.setdefault("capsize", 0) + kwargs.setdefault("elinewidth", 2) try: if self.results.DeltaA.Gibbs is None or len(self.results.dvdl) == 0: @@ -1221,20 +1374,32 @@ def plot(self, **kwargs): nplots = len(dvdl) fig, axs = plt.subplots(nrows=1, ncols=nplots) for i, component in enumerate(np.sort(dvdl.keys())): # stable plot order - x,y,dy = [dvdl[component][k] for k in ('lambdas', 'mean', 'error')] + x, y, dy = [dvdl[component][k] for k in ("lambdas", "mean", "error")] iplot = i ax = axs[i] energy = self.results.DeltaA[component] - label = r"$\Delta A^{\rm{%s}}_{\rm{%s}} = %.2f\pm%.2f$ kJ/mol" \ - % (component, self.solvent_type, energy.value, energy.error) + label = r"$\Delta A^{\rm{%s}}_{\rm{%s}} = %.2f\pm%.2f$ kJ/mol" % ( + component, + self.solvent_type, + energy.value, + energy.error, + ) ax.errorbar(x, y, yerr=dy, label=label, **kwargs) - ax.set_xlabel(r'$\lambda$') - ax.legend(loc='best') + ax.set_xlabel(r"$\lambda$") + ax.legend(loc="best") ax.set_xlim(-0.05, 1.05) - axs[0].set_ylabel(r'$dV/d\lambda$ in kJ/mol') - fig.suptitle(r"Free energy difference $\Delta A^{0}_{\rm{%s}}$ for %s: $%.2f\pm%.2f$ kJ/mol" % - ((self.solvent_type, self.molecule,) + self.results.DeltaA.Gibbs.astuple())) - fig.savefig('DeltaA.png') + axs[0].set_ylabel(r"$dV/d\lambda$ in kJ/mol") + fig.suptitle( + r"Free energy difference $\Delta A^{0}_{\rm{%s}}$ for %s: $%.2f\pm%.2f$ kJ/mol" + % ( + ( + self.solvent_type, + self.molecule, + ) + + self.results.DeltaA.Gibbs.astuple() + ) + ) + fig.savefig("DeltaA.png") plt.close() return fig @@ -1259,8 +1424,10 @@ def choose_script_from(scripts): with in_dir(self.dirname, create=False): for component, scripts in self.scripts.items(): - s = relpath(choose_script_from(scripts), self.dirname) # relative to dirname - cmd = ['qsub', s] + s = relpath( + choose_script_from(scripts), self.dirname + ) # relative to dirname + cmd = ["qsub", s] logger.debug("[%s] submitting locally: %s", " ".join(cmd), component) rc = call(cmd) if rc != 0: @@ -1268,7 +1435,9 @@ def choose_script_from(scripts): logger.error(errmsg) raise OSError(errmsg) - logger.info("[%r] Submitted jobs locally for %r", self.dirname, self.scripts.keys()) + logger.info( + "[%r] Submitted jobs locally for %r", self.dirname, self.scripts.keys() + ) def __repr__(self): return "%s(filename=%r)" % (self.__class__.__name__, self.filename) @@ -1276,6 +1445,7 @@ def __repr__(self): class Ghyd(Gsolv): """Sets up and analyses MD to obtain the hydration free energy of a solute.""" + solvent_default = "water" dirname_default = os.path.join(Gsolv.topdir_default, solvent_default) @@ -1292,28 +1462,50 @@ class Goct(Gsolv): part of the dV/dl curve is quite sensitive. By adding two additional points we hope to reduce the overall error on the dis-charging free energy. """ + solvent_default = "octanol" dirname_default = os.path.join(Gsolv.topdir_default, solvent_default) - schedules = {'coulomb': - FEPschedule(name='coulomb', - description="dis-charging vdw+q --> vdw", - label='Coul', - couple_lambda0='vdw-q', couple_lambda1='vdw', - sc_alpha=0, # linear scaling for coulomb - #lambdas=[0, 0.25, 0.5, 0.75, 1.0], # default - lambdas=[0, 0.125, 0.25, 0.375, 0.5, 0.75, 1.0], # +0.125, 0.375 enhanced - ), - 'vdw': - FEPschedule(name='vdw', - description="decoupling vdw --> none", - label='VDW', - couple_lambda0='vdw', couple_lambda1='none', - sc_alpha=0.5, sc_power=1, sc_sigma=0.3, # recommended values - lambdas=[0.0, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, # defaults - 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1], - ), - } + schedules = { + "coulomb": FEPschedule( + name="coulomb", + description="dis-charging vdw+q --> vdw", + label="Coul", + couple_lambda0="vdw-q", + couple_lambda1="vdw", + sc_alpha=0, # linear scaling for coulomb + # lambdas=[0, 0.25, 0.5, 0.75, 1.0], # default + lambdas=[0, 0.125, 0.25, 0.375, 0.5, 0.75, 1.0], # +0.125, 0.375 enhanced + ), + "vdw": FEPschedule( + name="vdw", + description="decoupling vdw --> none", + label="VDW", + couple_lambda0="vdw", + couple_lambda1="none", + sc_alpha=0.5, + sc_power=1, + sc_sigma=0.3, # recommended values + lambdas=[ + 0.0, + 0.05, + 0.1, + 0.2, + 0.3, + 0.4, + 0.5, + 0.6, # defaults + 0.65, + 0.7, + 0.75, + 0.8, + 0.85, + 0.9, + 0.95, + 1, + ], + ), + } class Gwoct(Goct): @@ -1323,13 +1515,14 @@ class Gwoct(Goct): part of the dV/dl curve is quite sensitive. By adding two additional points we hope to reduce the overall error on the dis-charging free energy. """ + solvent_default = "wetoctanol" dirname_default = os.path.join(Gsolv.topdir_default, solvent_default) class Gtol(Gsolv): - """Sets up and analyses MD to obtain the solvation free energy of a solute in toluene. - """ + """Sets up and analyses MD to obtain the solvation free energy of a solute in toluene.""" + solvent_default = "toluene" dirname_default = os.path.join(Gsolv.topdir_default, solvent_default) @@ -1388,10 +1581,13 @@ def p_transfer(G1, G2, **kwargs): """ - kwargs.setdefault('force', False) - estimator = kwargs.pop('estimator', 'alchemlyb') - if not estimator in ('mdpow', 'alchemlyb'): - errmsg = "estimator = %r is not supported, must be 'mdpow' or 'alchemlyb'" % estimator + kwargs.setdefault("force", False) + estimator = kwargs.pop("estimator", "alchemlyb") + if not estimator in ("mdpow", "alchemlyb"): + errmsg = ( + "estimator = %r is not supported, must be 'mdpow' or 'alchemlyb'" + % estimator + ) logger.error(errmsg) raise ValueError(errmsg) @@ -1400,40 +1596,49 @@ def p_transfer(G1, G2, **kwargs): if G1.Temperature != G2.Temperature: raise ValueError("The two simulations were done at different temperatures.") - logger.info("[%s] transfer free energy %s --> %s calculation", - G1.molecule, G1.solvent_type, G2.solvent_type) + logger.info( + "[%s] transfer free energy %s --> %s calculation", + G1.molecule, + G1.solvent_type, + G2.solvent_type, + ) for G in (G1, G2): G_kwargs = kwargs.copy() # for fep files generated with old code which doesn't have these attributes - if not hasattr(G, 'start'): - G.start = G_kwargs.pop('start', 0) - if not hasattr(G, 'stop'): - G.stop = G_kwargs.pop('stop', None) - if not hasattr(G, 'SI'): - G_kwargs.setdefault('SI', True) + if not hasattr(G, "start"): + G.start = G_kwargs.pop("start", 0) + if not hasattr(G, "stop"): + G.stop = G_kwargs.pop("stop", None) + if not hasattr(G, "SI"): + G_kwargs.setdefault("SI", True) else: - G_kwargs.setdefault('SI', G.SI) + G_kwargs.setdefault("SI", G.SI) # for this version. use the method given instead of the one in the input cfg file - G.method = G_kwargs.pop('method', 'MBAR') - if estimator == 'mdpow': + G.method = G_kwargs.pop("method", "MBAR") + if estimator == "mdpow": if G.method != "TI": - errmsg = "Method %s is not implemented in MDPOW, use estimator='alchemlyb'" % G.method + errmsg = ( + "Method %s is not implemented in MDPOW, use estimator='alchemlyb'" + % G.method + ) logger.error(errmsg) raise ValueError(errmsg) logger.info("The solvent is %s .", G.solvent_type) - if kwargs['force'] or 'Gibbs' not in G.results.DeltaA: + if kwargs["force"] or "Gibbs" not in G.results.DeltaA: # write out the settings when the analysis is performed logger.info("Estimator is %s.", estimator) logger.info("Free energy calculation method is %s.", G.method) - if estimator == 'mdpow': - G_kwargs.pop('SI', None) # G.analyze() does not know SI + if estimator == "mdpow": + G_kwargs.pop("SI", None) # G.analyze() does not know SI G.analyze(**G_kwargs) - elif estimator == 'alchemlyb': - logger.info("Statistical inefficiency analysis will %s be performed." % - ("" if G_kwargs['SI'] else "not")) + elif estimator == "alchemlyb": + logger.info( + "Statistical inefficiency analysis will %s be performed." + % ("" if G_kwargs["SI"] else "not") + ) G.analyze_alchemlyb(**G_kwargs) else: logger.info("Using already calculated free energy DeltaA") @@ -1451,18 +1656,25 @@ def p_transfer(G1, G2, **kwargs): # water -> cyclohexane: P_cw # water -> toluene: P_tw coefficient = "P_{0}{1}".format( - G2.solvent_type.lower()[0], G1.solvent_type.lower()[0]) + G2.solvent_type.lower()[0], G1.solvent_type.lower()[0] + ) logger.info("[%s] Values at T = %g K", molecule, G1.Temperature) - logger.info("[%s] Free energy of transfer %s --> %s: %.3f (%.3f) kJ/mol", - molecule, - G1.solvent_type, G2.solvent_type, - transferFE.value, transferFE.error) - logger.info("[%s] log %s: %.3f (%.3f)", - molecule, coefficient, logPow.value, logPow.error) + logger.info( + "[%s] Free energy of transfer %s --> %s: %.3f (%.3f) kJ/mol", + molecule, + G1.solvent_type, + G2.solvent_type, + transferFE.value, + transferFE.error, + ) + logger.info( + "[%s] log %s: %.3f (%.3f)", molecule, coefficient, logPow.value, logPow.error + ) return transferFE, logPow + def pOW(G1, G2, **kwargs): """Compute water-octanol partition coefficient from two :class:`Gsolv` objects. @@ -1503,11 +1715,13 @@ def pOW(G1, G2, **kwargs): args = (G2, G1) else: msg = "For pOW need water and octanol simulations but instead got {0} and {1}".format( - G1.solvent_type, G2.solvent_type) + G1.solvent_type, G2.solvent_type + ) logger.error(msg) raise ValueError(msg) return p_transfer(*args, **kwargs) + def pCW(G1, G2, **kwargs): """Compute water-cyclohexane partition coefficient from two :class:`Gsolv` objects. @@ -1548,11 +1762,13 @@ def pCW(G1, G2, **kwargs): args = (G2, G1) else: msg = "For pCW need water and cyclohexane simulations but instead got {0} and {1}".format( - G1.solvent_type, G2.solvent_type) + G1.solvent_type, G2.solvent_type + ) logger.error(msg) raise ValueError(msg) return p_transfer(*args, **kwargs) + def pTW(G1, G2, **kwargs): """Compute water-toluene partition coefficient from two :class:`Gsolv` objects. @@ -1593,7 +1809,8 @@ def pTW(G1, G2, **kwargs): args = (G2, G1) else: msg = "For pTW need water and toluene simulations but instead got {0} and {1}".format( - G1.solvent_type, G2.solvent_type) + G1.solvent_type, G2.solvent_type + ) logger.error(msg) raise ValueError(msg) - return p_transfer(*args, **kwargs) \ No newline at end of file + return p_transfer(*args, **kwargs) diff --git a/mdpow/filelock.py b/mdpow/filelock.py index f01dc0fc..948b2a96 100644 --- a/mdpow/filelock.py +++ b/mdpow/filelock.py @@ -30,18 +30,20 @@ import time import errno + class FileLockException(Exception): pass + class FileLock(object): - """ A file locking mechanism that has context-manager support so - you can use it in a with statement. This should be relatively cross - compatible as it doesn't rely on msvcrt or fcntl for the locking. + """A file locking mechanism that has context-manager support so + you can use it in a with statement. This should be relatively cross + compatible as it doesn't rely on msvcrt or fcntl for the locking. """ - def __init__(self, file_name, timeout=10, delay=.05): - """ Prepare the file locker. Specify the file to lock and optionally - the maximum timeout and the delay between each attempt to lock. + def __init__(self, file_name, timeout=10, delay=0.05): + """Prepare the file locker. Specify the file to lock and optionally + the maximum timeout and the delay between each attempt to lock. """ self.is_locked = False self.lockfile = os.path.join(os.getcwd(), "%s.lock" % file_name) @@ -49,17 +51,16 @@ def __init__(self, file_name, timeout=10, delay=.05): self.timeout = timeout self.delay = delay - def acquire(self): - """ Acquire the lock, if possible. If the lock is in use, it check again - every `wait` seconds. It does this until it either gets the lock or - exceeds `timeout` number of seconds, in which case it throws - an exception. + """Acquire the lock, if possible. If the lock is in use, it check again + every `wait` seconds. It does this until it either gets the lock or + exceeds `timeout` number of seconds, in which case it throws + an exception. """ start_time = time.time() while True: try: - self.fd = os.open(self.lockfile, os.O_CREAT|os.O_EXCL|os.O_RDWR) + self.fd = os.open(self.lockfile, os.O_CREAT | os.O_EXCL | os.O_RDWR) break except OSError as e: if e.errno != errno.EEXIST: @@ -69,37 +70,33 @@ def acquire(self): time.sleep(self.delay) self.is_locked = True - def release(self): - """ Get rid of the lock by deleting the lockfile. - When working in a `with` statement, this gets automatically - called at the end. + """Get rid of the lock by deleting the lockfile. + When working in a `with` statement, this gets automatically + called at the end. """ if self.is_locked: os.close(self.fd) os.unlink(self.lockfile) self.is_locked = False - def __enter__(self): - """ Activated when used in the with statement. - Should automatically acquire a lock to be used in the with block. + """Activated when used in the with statement. + Should automatically acquire a lock to be used in the with block. """ if not self.is_locked: self.acquire() return self - def __exit__(self, type, value, traceback): - """ Activated at the end of the with statement. - It automatically releases the lock if it isn't locked. + """Activated at the end of the with statement. + It automatically releases the lock if it isn't locked. """ if self.is_locked: self.release() - def __del__(self): - """ Make sure that the FileLock instance doesn't leave a lockfile - lying around. + """Make sure that the FileLock instance doesn't leave a lockfile + lying around. """ self.release() diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index 7ad9ebe3..348944da 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -58,6 +58,7 @@ from collections import defaultdict import logging + logger = logging.getLogger("mdpow.forecefields") #: Default force field. At the moment, OPLS-AA, CHARMM/CGENFF, and AMBER/GAFF @@ -65,13 +66,13 @@ #: default here as this behavior is not tested. DEFAULT_FORCEFIELD = "OPLS-AA" -#------------------------------------------------------------ +# ------------------------------------------------------------ # Gromacs water models -#------------------------------------------------------------ +# ------------------------------------------------------------ #: See the file ``top/oplsaa.ff/watermodels.dat`` for a description of #: available water models that are bundled with MDPOW. -GMX_WATERMODELS_DAT=""" +GMX_WATERMODELS_DAT = """ tip4p TIP4P TIP 4-point, recommended tip3p TIP3P TIP 3-point tip5p TIP5P TIP 5-point @@ -82,14 +83,25 @@ tip4pew TIP4PEW TIP 4-point modified for use with Ewald techniques (TIP4PEW) """ + class GromacsSolventModel(object): """Data for a solvent model in Gromacs.""" - def __init__(self, identifier, name=None, itp=None, coordinates=None, - description=None, forcefield="OPLS-AA"): + + def __init__( + self, + identifier, + name=None, + itp=None, + coordinates=None, + description=None, + forcefield="OPLS-AA", + ): self.identifier = identifier self.name = name if name is not None else str(identifier).upper() - self.itp = itp if itp is not None else self.guess_filename('itp') - self.coordinates = coordinates if coordinates is not None else self.guess_filename('gro') + self.itp = itp if itp is not None else self.guess_filename("itp") + self.coordinates = ( + coordinates if coordinates is not None else self.guess_filename("gro") + ) self.description = description self.forcefield = forcefield @@ -98,35 +110,44 @@ def guess_filename(self, extension): return self.identifier.lower() + os.extsep + str(extension) def __repr__(self): - return "<{0[name]} water: identifier={0[identifier]}, ff={0[forcefield]}>".format(vars(self)) + return ( + "<{0[name]} water: identifier={0[identifier]}, ff={0[forcefield]}>".format( + vars(self) + ) + ) + #: For some water models we cannot derive the filename for the equilibrated box #: so we supply them explicitly. SPECIAL_WATER_COORDINATE_FILES = defaultdict( lambda: None, - spc='spc216.gro', - spce='spc216.gro', - tip3p='spc216.gro', - m24='spc216.gro', - tip4pd='tip4p.gro', - tip4pew='tip4p.gro', + spc="spc216.gro", + spce="spc216.gro", + tip3p="spc216.gro", + m24="spc216.gro", + tip4pd="tip4p.gro", + tip4pew="tip4p.gro", ) + def _create_water_models(watermodelsdat): models = {} - for line in GMX_WATERMODELS_DAT.split('\n'): + for line in GMX_WATERMODELS_DAT.split("\n"): line = line.strip() - if not line or line.startswith('#'): + if not line or line.startswith("#"): continue fields = line.split() identifier, name = fields[:2] description = " ".join(fields[2:]) models[identifier] = GromacsSolventModel( - identifier, name=name, + identifier, + name=name, coordinates=SPECIAL_WATER_COORDINATE_FILES[identifier], - description=description) + description=description, + ) return models + #: Use the default water model unless another water model is chosen in the #: :ref:`run input file ` file by setting the #: ``setup.watermodel`` parameter. @@ -145,6 +166,7 @@ def _create_water_models(watermodelsdat): #: For OPLS-AA the following ones are available. GROMACS_WATER_MODELS = _create_water_models(GMX_WATERMODELS_DAT) + def get_water_model(watermodel=DEFAULT_WATER_MODEL): """Return a :class:`GromacsSolventModel` corresponding to identifier *watermodel*""" @@ -152,63 +174,84 @@ def get_water_model(watermodel=DEFAULT_WATER_MODEL): return GROMACS_WATER_MODELS[watermodel] except KeyError: msg = "{0} is not a valid water model: choose one from {1}".format( - watermodel, ", ".join(GROMACS_WATER_MODELS.keys())) + watermodel, ", ".join(GROMACS_WATER_MODELS.keys()) + ) logger.error(msg) raise ValueError(msg) + #: Other solvents (not water, see :data:`GROMACS_WATER_MODELS` for those). -new_octanol = '''Zangi R (2018) Refinement of the OPLSAA force-field +new_octanol = """Zangi R (2018) Refinement of the OPLSAA force-field for liquid alcohols.; ACS Omega 3(12):18089-18099. - doi: 10.1021/acsomega.8b03132''' + doi: 10.1021/acsomega.8b03132""" OPLS_SOLVENT_MODELS = { - 'octanol': GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct.gro"), - 'octanolnew': GromacsSolventModel( - identifier="octanol", itp="1octnew.itp", coordinates="1oct.gro", - description=new_octanol), - 'cyclohexane': GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo.gro"), - 'wetoctanol': GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet.gro"), - 'wetoctanolnew': GromacsSolventModel( - identifier="wetoctanol", itp="1octwetnew.itp", coordinates="1octwet.gro", - description=new_octanol), - 'toluene': GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_oplsaa.gro"), - } + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct.gro" + ), + "octanolnew": GromacsSolventModel( + identifier="octanol", + itp="1octnew.itp", + coordinates="1oct.gro", + description=new_octanol, + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet.gro" + ), + "wetoctanolnew": GromacsSolventModel( + identifier="wetoctanol", + itp="1octwetnew.itp", + coordinates="1octwet.gro", + description=new_octanol, + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_oplsaa.gro" + ), +} CHARMM_SOLVENT_MODELS = { - 'octanol': GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct_charmm.gro"), - 'wetoctanol': GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_charmm.gro"), - 'cyclohexane': GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_charmm.gro"), - 'toluene': GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_charmm.gro"), - } + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct_charmm.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_charmm.gro" + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_charmm.gro" + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_charmm.gro" + ), +} AMBER_SOLVENT_MODELS = { - 'octanol': GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct_amber.gro"), - 'wetoctanol': GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_amber.gro"), - 'cyclohexane': GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_amber.gro"), - 'toluene': GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_amber.gro"), - } + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct_amber.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_amber.gro" + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_amber.gro" + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_amber.gro" + ), +} #: Solvents available in GROMACS; the keys of the dictionary #: are the forcefields. GROMACS_SOLVENT_MODELS = { - 'OPLS-AA': OPLS_SOLVENT_MODELS, - 'CHARMM': CHARMM_SOLVENT_MODELS, - 'AMBER': AMBER_SOLVENT_MODELS, - } + "OPLS-AA": OPLS_SOLVENT_MODELS, + "CHARMM": CHARMM_SOLVENT_MODELS, + "AMBER": AMBER_SOLVENT_MODELS, +} -def get_solvent_identifier(solvent_type, model=None, forcefield='OPLS-AA'): + +def get_solvent_identifier(solvent_type, model=None, forcefield="OPLS-AA"): """Get the identifier for a solvent model. The identifier is needed to access a water model (i.e., a @@ -232,9 +275,9 @@ def get_solvent_identifier(solvent_type, model=None, forcefield='OPLS-AA'): :Returns: Either an identifier or ``None`` """ - + if solvent_type == "water": - identifier = model if not model in (None, 'water') else DEFAULT_WATER_MODEL + identifier = model if not model in (None, "water") else DEFAULT_WATER_MODEL return identifier if identifier in GROMACS_WATER_MODELS else None if model not in GROMACS_SOLVENT_MODELS[forcefield]: if solvent_type in GROMACS_SOLVENT_MODELS[forcefield]: @@ -244,7 +287,7 @@ def get_solvent_identifier(solvent_type, model=None, forcefield='OPLS-AA'): return model -def get_solvent_model(identifier, forcefield='OPLS-AA'): +def get_solvent_model(identifier, forcefield="OPLS-AA"): """Return a :class:`GromacsSolventModel` corresponding to identifier *identifier*. If identifier is "water" then the :data:`DEFAULT_WATER_MODEL` is assumed. @@ -263,19 +306,20 @@ def get_solvent_model(identifier, forcefield='OPLS-AA'): raise ValueError(msg) -def get_ff_paths(forcefield='OPLS-AA'): +def get_ff_paths(forcefield="OPLS-AA"): """Return a :list: containing the forcefield directory, paths of ions and default watermodel itp files. """ - + settings = { - 'OPLS-AA': ['oplsaa.ff/', 'oplsaa.ff/ions_opls.itp', - 'oplsaa.ff/tip4p.itp'], - 'AMBER': ['amber99sb.ff/', 'amber99sb.ff/ions.itp', - 'amber99sb.ff/tip3p.itp'], - 'CHARMM': ['charmm36-mar2019.ff/', 'charmm36-mar2019.ff/ions.itp', - 'charmm36-mar2019.ff/tip3p.itp'], - } + "OPLS-AA": ["oplsaa.ff/", "oplsaa.ff/ions_opls.itp", "oplsaa.ff/tip4p.itp"], + "AMBER": ["amber99sb.ff/", "amber99sb.ff/ions.itp", "amber99sb.ff/tip3p.itp"], + "CHARMM": [ + "charmm36-mar2019.ff/", + "charmm36-mar2019.ff/ions.itp", + "charmm36-mar2019.ff/tip3p.itp", + ], + } try: return settings[forcefield] except KeyError: @@ -286,10 +330,14 @@ def get_ff_paths(forcefield='OPLS-AA'): def get_top_template(identifier): """Return the topology file template suitable for the solvent model.""" - - templates = {'water': 'system.top', 'octanol': 'system.top', - 'cyclohexane': 'system.top', 'wetoctanol': 'system_octwet.top', - 'toluene': 'system.top',} + + templates = { + "water": "system.top", + "octanol": "system.top", + "cyclohexane": "system.top", + "wetoctanol": "system_octwet.top", + "toluene": "system.top", + } try: return templates[identifier] except KeyError: diff --git a/mdpow/log.py b/mdpow/log.py index f2727293..fbe0b31d 100644 --- a/mdpow/log.py +++ b/mdpow/log.py @@ -26,6 +26,7 @@ import logging + def create(logname, logfile): """Create a top level logger. @@ -38,7 +39,9 @@ def create(logname, logfile): logger.setLevel(logging.DEBUG) logfile = logging.FileHandler(logfile) - logfile_formatter = logging.Formatter('%(asctime)s %(name)-12s %(levelname)-8s %(message)s') + logfile_formatter = logging.Formatter( + "%(asctime)s %(name)-12s %(levelname)-8s %(message)s" + ) logfile.setFormatter(logfile_formatter) logger.addHandler(logfile) @@ -46,12 +49,13 @@ def create(logname, logfile): console = logging.StreamHandler() console.setLevel(logging.INFO) # set a format which is simpler for console use - formatter = logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s') + formatter = logging.Formatter("%(name)-12s: %(levelname)-8s %(message)s") console.setFormatter(formatter) logger.addHandler(console) return logger + def clear_handlers(logger): """clean out handlers in the library top level logger @@ -59,5 +63,3 @@ def clear_handlers(logger): """ for h in logger.handlers: logger.removeHandler(h) - - diff --git a/mdpow/restart.py b/mdpow/restart.py index 02d55f6e..2b2e362a 100644 --- a/mdpow/restart.py +++ b/mdpow/restart.py @@ -26,16 +26,20 @@ import os import logging -logger = logging.getLogger('mdpow.checkpoint') + +logger = logging.getLogger("mdpow.checkpoint") + def checkpoint(name, sim, filename): """Execute the :meth:`Journalled.save` method and log the event.""" logger.info("checkpoint: %(name)s", vars()) sim.save(filename) + class JournalSequenceError(Exception): """Raised when a stage is started without another one having been completed.""" + class Journal(object): """Class that keeps track of the stage in a protocol. @@ -69,6 +73,7 @@ class Journal(object): # raises JournalSequenceError """ + def __init__(self, stages): """Initialise the journal that keeps track of stages. @@ -92,8 +97,10 @@ def current(self): @current.setter def current(self, stage): if not stage in self.stages: - raise ValueError("Can only assign a registered stage from %r, not %r" % - (self.stages, stage)) + raise ValueError( + "Can only assign a registered stage from %r, not %r" + % (self.stages, stage) + ) self.__current = stage @current.deleter @@ -108,7 +115,9 @@ def incomplete(self): @incomplete.setter def incomplete(self, stage): if not stage in self.stages: - raise ValueError("can only assign a registered stage from %(stages)r" % vars(self)) + raise ValueError( + "can only assign a registered stage from %(stages)r" % vars(self) + ) self.__incomplete = stage @incomplete.deleter @@ -126,15 +135,19 @@ def history(self): def completed(self, stage): """Record completed stage and reset :attr:`Journal.current`""" - assert stage == self.current, "Program logic error: can only complete the current stage" + assert ( + stage == self.current + ), "Program logic error: can only complete the current stage" self.__history.append(self.current) del self.current def start(self, stage): """Record that *stage* is starting.""" if self.current is not None: - errmsg = "Cannot start stage %s because previously started stage %s " \ + errmsg = ( + "Cannot start stage %s because previously started stage %s " "has not been completed." % (stage, self.current) + ) logger.error(errmsg) raise JournalSequenceError(errmsg) self.current = stage @@ -155,12 +168,14 @@ def clear(self): def __repr__(self): return "%s(%r)" % (self.__class__.__name__, self.stages) + class Journalled(object): """A base class providing methods for journalling and restarts. It installs an instance of :class:`Journal` in the attribute :attr:`Journalled.journal` if it does not exist already. """ + #: Class-attribute that contains the names of computation protocols #: supported by the class. These are either method names or dummy names, #: whose logic is provided by an external callback function. @@ -199,7 +214,9 @@ def get_protocol(self, protocol): """ if protocol not in self.protocols: - raise ValueError("%r: protocol must be one of %r" % (protocol, self.protocols)) + raise ValueError( + "%r: protocol must be one of %r" % (protocol, self.protocols) + ) try: return self.__getattribute__(protocol) except AttributeError: @@ -216,6 +233,7 @@ def dummy_protocol(*args, **kwargs): if success: self.journal.completed(protocol) return success + return dummy_protocol def save(self, filename=None): @@ -237,7 +255,7 @@ def save(self, filename=None): raise ValueError(errmsg) else: self.filename = os.path.abspath(filename) - with open(self.filename, 'wb') as f: + with open(self.filename, "wb") as f: pickle.dump(self, f) logger.debug("Instance pickled to %(filename)r" % vars(self)) @@ -264,12 +282,12 @@ def load(self, filename=None): # Do not remove this code when dropping Py 2.7 support as it is needed to # be able to read old data files with Python 3 MDPOW. - with open(filename, 'rb') as f: + with open(filename, "rb") as f: try: instance = pickle.load(f) except UnicodeDecodeError: logger.debug("Reading old Python 2 Pickle file %(filename)r" % vars()) - instance = pickle.load(f, encoding='latin1') + instance = pickle.load(f, encoding="latin1") self.__dict__.update(instance.__dict__) logger.debug("Instance loaded from %(filename)r" % vars()) diff --git a/mdpow/run.py b/mdpow/run.py index 4738634f..44469626 100644 --- a/mdpow/run.py +++ b/mdpow/run.py @@ -44,14 +44,14 @@ import gromacs.run import gromacs.exceptions -from .config import (get_configuration, set_gromacsoutput, - NoSectionError) +from .config import get_configuration, set_gromacsoutput, NoSectionError from . import equil from . import fep from .restart import checkpoint import logging -logger = logging.getLogger('mdpow.run') + +logger = logging.getLogger("mdpow.run") def setupMD(S, protocol, cfg): @@ -63,37 +63,48 @@ def setupMD(S, protocol, cfg): maxwarn = 0 simulation_protocol = S.get_protocol(protocol) - params = simulation_protocol(runtime=cfg.getfloat(protocol, "runtime"), - qscript=cfg.getlist(protocol, "qscript"), - maxwarn=maxwarn, - ) + params = simulation_protocol( + runtime=cfg.getfloat(protocol, "runtime"), + qscript=cfg.getlist(protocol, "qscript"), + maxwarn=maxwarn, + ) return params + def get_mdp_files(cfg, protocols): """Get file names of MDP files from *cfg* for all *protocols*""" mdpfiles = {} for protocol in protocols: try: - mdp = cfg.findfile(protocol, 'mdp') + mdp = cfg.findfile(protocol, "mdp") except NoSectionError: # skip anything for which we do not define sections, such as # the dummy run protocols mdp = None except ValueError: # But it is a problem if we can't find a file! - logger.critical("Failed to find custom MDP file %r for protocol [%s]", - cfg.get(protocol, 'mdp'), protocol) + logger.critical( + "Failed to find custom MDP file %r for protocol [%s]", + cfg.get(protocol, "mdp"), + protocol, + ) raise else: if mdp is None: # Should not happen... let's continue and wait for hard-coded defaults - logger.warning("No 'mdp' config file entry for protocol [%s]---check input files! " - "Using package defaults.", protocol) + logger.warning( + "No 'mdp' config file entry for protocol [%s]---check input files! " + "Using package defaults.", + protocol, + ) if mdp: mdpfiles[protocol] = mdp - logger.debug("%(protocol)s: Using MDP file %(mdp)r from config file", vars()) + logger.debug( + "%(protocol)s: Using MDP file %(mdp)r from config file", vars() + ) return mdpfiles + def runMD_or_exit(S, protocol, params, cfg, exit_on_error=True, **kwargs): """run simulation @@ -129,15 +140,17 @@ def runMD_or_exit(S, protocol, params, cfg, exit_on_error=True, **kwargs): raise ValueError("supply dirname as a keyword argument") simulation_done = False if cfg.getboolean(protocol, "runlocal"): - logger.info("Running %s (%s.log) ... stand by.", protocol, params['deffnm']) + logger.info("Running %s (%s.log) ... stand by.", protocol, params["deffnm"]) logger.info("Run directory: %(dirname)s", vars()) mdrun = gromacs.run.MDrunner( - dirname=dirname, deffnm=params['deffnm'], - v=cfg.getboolean('mdrun','verbose'), - stepout=cfg.getint('mdrun','stepout'), - nice=cfg.getint('mdrun','nice'), - nt=cfg.get('mdrun','maxthreads'), - cpi=True) + dirname=dirname, + deffnm=params["deffnm"], + v=cfg.getboolean("mdrun", "verbose"), + stepout=cfg.getint("mdrun", "stepout"), + nice=cfg.getint("mdrun", "nice"), + nt=cfg.get("mdrun", "maxthreads"), + cpi=True, + ) simulation_done = mdrun.run_check() if not simulation_done: # should probably stop @@ -146,12 +159,13 @@ def runMD_or_exit(S, protocol, params, cfg, exit_on_error=True, **kwargs): sys.exit(1) else: raise gromacs.exceptions.GromacsError( - f"Failed {protocol}, investigate manually.") + f"Failed {protocol}, investigate manually." + ) else: # must check if the simulation was run externally - logfile = os.path.join(dirname, params['deffnm']+os.extsep+"log") + logfile = os.path.join(dirname, params["deffnm"] + os.extsep + "log") logger.debug("Checking logfile %r if simulation has been completed.", logfile) - simulation_done = gromacs.run.check_mdrun_success(logfile) ### broken?? + simulation_done = gromacs.run.check_mdrun_success(logfile) ### broken?? if simulation_done is None: logger.info("Now go and run %(protocol)s in directory %(dirname)r.", vars()) if exit_on_error: @@ -159,12 +173,16 @@ def runMD_or_exit(S, protocol, params, cfg, exit_on_error=True, **kwargs): else: return simulation_done elif simulation_done is False: - logger.warning("Simulation %(protocol)s in directory %(dirname)r is incomplete (log=%(logfile)s).", vars()) + logger.warning( + "Simulation %(protocol)s in directory %(dirname)r is incomplete (log=%(logfile)s).", + vars(), + ) if exit_on_error: sys.exit(1) else: raise gromacs.exceptions.MissingDataError( - f"Simulation {protocol} in directory {dirname} is incomplete (log={logfile}).") + f"Simulation {protocol} in directory {dirname} is incomplete (log={logfile})." + ) logger.info("Simulation %(protocol)s seems complete (log=%(logfile)s)", vars()) return simulation_done @@ -178,19 +196,20 @@ def equilibrium_simulation(cfg, solvent, **kwargs): (``runlocal``), :program:`mdrun` is executed at various stages, and hence this process can take a while. """ - deffnm = kwargs.pop('deffnm', "md") + deffnm = kwargs.pop("deffnm", "md") Simulations = { - 'water': equil.WaterSimulation, - 'octanol': equil.OctanolSimulation, - 'wetoctanol': equil.WetOctanolSimulation, - 'cyclohexane':equil.CyclohexaneSimulation, - 'toluene': equil.TolueneSimulation, - } + "water": equil.WaterSimulation, + "octanol": equil.OctanolSimulation, + "wetoctanol": equil.WetOctanolSimulation, + "cyclohexane": equil.CyclohexaneSimulation, + "toluene": equil.TolueneSimulation, + } try: Simulation = Simulations[solvent] except KeyError: - raise ValueError("solvent must be one of {0}".format( - ", ".join(Simulations.keys()))) + raise ValueError( + "solvent must be one of {0}".format(", ".join(Simulations.keys())) + ) # generate a canonical path under dirname topdir = kwargs.get("dirname", None) @@ -208,18 +227,17 @@ def equilibrium_simulation(cfg, solvent, **kwargs): # custom mdp files mdpfiles = get_mdp_files(cfg, Simulation.protocols) try: - distance = cfg.get('setup', 'distance') + distance = cfg.get("setup", "distance") except KeyError: - distance = None # if no distance is specified, None = default + distance = None # if no distance is specified, None = default try: - boxtype = cfg.get('setup', 'boxtype') + boxtype = cfg.get("setup", "boxtype") except KeyError: - boxtype = None # if no distance is specified, None = default - + boxtype = None # if no distance is specified, None = default solventmodel = None try: - solventmodel = cfg.get('setup', 'solventmodel') + solventmodel = cfg.get("setup", "solventmodel") logger.info("Selected solvent model: {0}".format(solventmodel)) except KeyError: solventmodel = None @@ -228,22 +246,28 @@ def equilibrium_simulation(cfg, solvent, **kwargs): # parameterization included and hence there is no mechanism to # choose between different models. - S = Simulation(molecule=cfg.get("setup", "molecule"), - forcefield=cfg.get("setup", "forcefield"), - dirname=dirname, deffnm=deffnm, mdp=mdpfiles, - distance=distance, - solventmodel=solventmodel) + S = Simulation( + molecule=cfg.get("setup", "molecule"), + forcefield=cfg.get("setup", "forcefield"), + dirname=dirname, + deffnm=deffnm, + mdp=mdpfiles, + distance=distance, + solventmodel=solventmodel, + ) if S.journal.has_not_completed("energy_minimize"): maxwarn = cfg.getint("setup", "maxwarn") or None prm = cfg.get("setup", "prm") or None - maxthreads = cfg.get('mdrun', 'maxthreads') or None + maxthreads = cfg.get("mdrun", "maxthreads") or None S.topology(itp=cfg.getpath("setup", "itp"), prm=prm) - S.solvate(struct=cfg.getpath("setup", "structure"), - bt=cfg.get("setup", "boxtype"), - maxwarn=maxwarn) - S.energy_minimize(maxwarn=maxwarn, mdrun_args={'nt': maxthreads}) - checkpoint('energy_minize', S, savefilename) + S.solvate( + struct=cfg.getpath("setup", "structure"), + bt=cfg.get("setup", "boxtype"), + maxwarn=maxwarn, + ) + S.energy_minimize(maxwarn=maxwarn, mdrun_args={"nt": maxthreads}) + checkpoint("energy_minize", S, savefilename) else: logger.info("Fast-forwarding: setup + energy_minimize done") @@ -251,12 +275,14 @@ def equilibrium_simulation(cfg, solvent, **kwargs): params = setupMD(S, "MD_relaxed", cfg) checkpoint("MD_relaxed", S, savefilename) else: - params = {'deffnm': deffnm} + params = {"deffnm": deffnm} logger.info("Fast-forwarding: MD_relaxed (setup) done") if S.journal.has_not_completed("MD_relaxed_run"): wrapper = S.get_protocol("MD_relaxed_run") - success = wrapper(runMD_or_exit, S, "MD_relaxed", params, cfg) # note: MD_relaxed! + success = wrapper( + runMD_or_exit, S, "MD_relaxed", params, cfg + ) # note: MD_relaxed! checkpoint("MD_relaxed_run", S, savefilename) else: logger.info("Fast-forwarding: MD_relaxed (run) done") @@ -269,13 +295,15 @@ def equilibrium_simulation(cfg, solvent, **kwargs): if S.journal.has_not_completed("MD_NPT_run"): wrapper = S.get_protocol("MD_NPT_run") - success = wrapper(runMD_or_exit, S, "MD_NPT", params, cfg) # note: MD_NPT + success = wrapper(runMD_or_exit, S, "MD_NPT", params, cfg) # note: MD_NPT checkpoint("MD_NPT_run", S, savefilename) else: logger.info("Fast-forwarding: MD_NPT (run) done") - logger.info("Equilibrium simulation phase complete, use %(savefilename)r to continue.", - vars()) + logger.info( + "Equilibrium simulation phase complete, use %(savefilename)r to continue.", + vars(), + ) return savefilename @@ -290,27 +318,29 @@ def fep_simulation(cfg, solvent, **kwargs): recommended to use ``runlocal = False`` in the run input file and submit all window simulations to a cluster. """ - exit_on_error = kwargs.pop('exit_on_error', True) - deffnm = kwargs.pop('deffnm', "md") + exit_on_error = kwargs.pop("exit_on_error", True) + deffnm = kwargs.pop("deffnm", "md") EquilSimulations = { - 'water': equil.WaterSimulation, - 'octanol': equil.OctanolSimulation, - 'wetoctanol': equil.WetOctanolSimulation, - 'cyclohexane': equil.CyclohexaneSimulation, - 'toluene': equil.TolueneSimulation, - } + "water": equil.WaterSimulation, + "octanol": equil.OctanolSimulation, + "wetoctanol": equil.WetOctanolSimulation, + "cyclohexane": equil.CyclohexaneSimulation, + "toluene": equil.TolueneSimulation, + } Simulations = { - 'water': fep.Ghyd, - 'octanol': fep.Goct, - 'wetoctanol': fep.Gwoct, - 'cyclohexane': fep.Gcyclo, - 'toluene': fep.Gtol, - } + "water": fep.Ghyd, + "octanol": fep.Goct, + "wetoctanol": fep.Gwoct, + "cyclohexane": fep.Gcyclo, + "toluene": fep.Gtol, + } try: EquilSimulation = EquilSimulations[solvent] Simulation = Simulations[solvent] except KeyError: - raise ValueError("solvent must be 'water', 'octanol', 'wetoctanol', 'cyclohexane' or 'toluene'") + raise ValueError( + "solvent must be 'water', 'octanol', 'wetoctanol', 'cyclohexane' or 'toluene'" + ) # generate a canonical path under dirname topdir = kwargs.get("dirname", None) if topdir is None: @@ -320,15 +350,19 @@ def fep_simulation(cfg, solvent, **kwargs): # Gsolv ... should be a static method or something else I can use before # the class is instantiated. Note that the pickle files live under dirname # and NOT topdir (bit of an historic inconsistency) - savefilename = os.path.join(dirname, Simulation.__name__ + os.extsep + 'fep') + savefilename = os.path.join(dirname, Simulation.__name__ + os.extsep + "fep") # need pickle files for the equilibrium simulation ... another nasty guess: equil_savefilename = os.path.join(topdir, "%(solvent)s.simulation" % vars()) try: equil_S = EquilSimulation(filename=equil_savefilename) except IOError as err: if err.errno == errno.ENOENT: - logger.critical("Missing the equilibrium simulation %(equil_savefilename)r.", vars()) - logger.critical("Run `mdpow-equilibrium -S %s %s' first!", solvent, "RUNINPUT.cfg") + logger.critical( + "Missing the equilibrium simulation %(equil_savefilename)r.", vars() + ) + logger.critical( + "Run `mdpow-equilibrium -S %s %s' first!", solvent, "RUNINPUT.cfg" + ) raise # output to screen or hidden? @@ -347,33 +381,44 @@ def fep_simulation(cfg, solvent, **kwargs): logger.debug("Using [FEP] MDP file %r from config file", mdp) # lambda schedules can be read from [FEP_schedule_*] sections - schedules = {'coulomb': fep.FEPschedule.load(cfg, "FEP_schedule_Coulomb"), - 'vdw': fep.FEPschedule.load(cfg, "FEP_schedule_VDW"), - } + schedules = { + "coulomb": fep.FEPschedule.load(cfg, "FEP_schedule_Coulomb"), + "vdw": fep.FEPschedule.load(cfg, "FEP_schedule_VDW"), + } logger.debug("Loaded FEP schedules %r from config file", schedules.keys()) # Note that we set basedir=topdir (and *not* dirname=dirname!)...FEP is a bit convoluted - S = Simulation(simulation=equil_S, runtime=cfg.getfloat("FEP", "runtime"), - basedir=topdir, deffnm=deffnm, mdp=mdp, schedules=schedules, - method=method) + S = Simulation( + simulation=equil_S, + runtime=cfg.getfloat("FEP", "runtime"), + basedir=topdir, + deffnm=deffnm, + mdp=mdp, + schedules=schedules, + method=method, + ) if S.journal.has_not_completed("setup"): - params = S.setup(qscript=cfg.getlist("FEP", "qscript"), - maxwarn=cfg.getint("FEP", "maxwarn")) + params = S.setup( + qscript=cfg.getlist("FEP", "qscript"), maxwarn=cfg.getint("FEP", "maxwarn") + ) checkpoint("setup", S, savefilename) else: - params = {'deffnm': deffnm} + params = {"deffnm": deffnm} logger.info("Fast-forwarding: FEP setup done") if S.journal.has_not_completed("fep_run"): + def run_all_FEPS(): for wdir in S.fep_dirs(): runMD_or_exit(S, "FEP", params, cfg, dirname=wdir, dgdl=True) + wrapper = S.get_protocol("fep_run") wrapper(run_all_FEPS) checkpoint("fep_run", S, savefilename) else: logger.info("Fast-forwarding: fep (run) done") - logger.info("FEP simulation phase complete, use %(savefilename)r to continue.", - vars()) + logger.info( + "FEP simulation phase complete, use %(savefilename)r to continue.", vars() + ) return savefilename diff --git a/mdpow/tests/__init__.py b/mdpow/tests/__init__.py index df6a7e6a..a59ab5ed 100644 --- a/mdpow/tests/__init__.py +++ b/mdpow/tests/__init__.py @@ -4,7 +4,7 @@ from pkg_resources import resource_filename -RESOURCES = py.path.local(resource_filename(__name__, 'testing_resources')) +RESOURCES = py.path.local(resource_filename(__name__, "testing_resources")) MANIFEST = RESOURCES / "manifest.yml" diff --git a/mdpow/tests/tempdir.py b/mdpow/tests/tempdir.py index 3e865d58..28c5c943 100644 --- a/mdpow/tests/tempdir.py +++ b/mdpow/tests/tempdir.py @@ -28,11 +28,11 @@ class TempDir(object): - """ class for temporary directories -creates a (named) directory which is deleted after use. -All files created within the directory are destroyed -Might not work on windows when the files are still opened -""" + """class for temporary directories + creates a (named) directory which is deleted after use. + All files created within the directory are destroyed + Might not work on windows when the files are still opened""" + def __init__(self, suffix="", prefix="tmp", basedir=None): self.name = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=basedir) @@ -57,13 +57,15 @@ def dissolve(self): def __str__(self): if self.name: - return "temporary directory at: {}".format(self.name,) + return "temporary directory at: {}".format( + self.name, + ) else: return "dissolved temporary directory" class in_tempdir(object): - """Create a temporary directory and change to it. """ + """Create a temporary directory and change to it.""" def __init__(self, *args, **kwargs): self.tmpdir = TempDir(*args, **kwargs) @@ -82,10 +84,13 @@ def run_in_tempdir(*args, **kwargs): """Make a function execute in a new tempdir. Any time the function is called, a new tempdir is created and destroyed. """ + def change_dird(fnc): @wraps(fnc) def wrapper(*funcargs, **funckwargs): with in_tempdir(*args, **kwargs): return fnc(*funcargs, **funckwargs) + return wrapper + return change_dird diff --git a/mdpow/tests/test_Gsolv.py b/mdpow/tests/test_Gsolv.py index bd9e603c..6fda59ec 100644 --- a/mdpow/tests/test_Gsolv.py +++ b/mdpow/tests/test_Gsolv.py @@ -9,19 +9,21 @@ from . import RESOURCES -class Test_Gsolv_manual(object): +class Test_Gsolv_manual(object): def setup_method(self): self.tmpdir = td.TempDir() - self.m = pybol.Manifest(str(RESOURCES / 'manifest.yml')) - self.m.assemble('md_npt',self.tmpdir.name) - simulation_filename = os.path.join(self.tmpdir.name,'benzene', - 'water.simulation') - self.S = equil.Simulation(filename = simulation_filename) - - self.S.make_paths_relative(prefix=os.path.join( - self.tmpdir.name,'benzene', 'Equilibrium', 'water')) - self.S.dirs.includes = os.path.join(self.tmpdir.name, 'top') + self.m = pybol.Manifest(str(RESOURCES / "manifest.yml")) + self.m.assemble("md_npt", self.tmpdir.name) + simulation_filename = os.path.join( + self.tmpdir.name, "benzene", "water.simulation" + ) + self.S = equil.Simulation(filename=simulation_filename) + + self.S.make_paths_relative( + prefix=os.path.join(self.tmpdir.name, "benzene", "Equilibrium", "water") + ) + self.S.dirs.includes = os.path.join(self.tmpdir.name, "top") self.S.save() def teardown_method(self): @@ -30,19 +32,18 @@ def teardown_method(self): def _setup(self, **kwargs): mdp = config.get_template("bar_opls.mdp") with in_dir(self.tmpdir.name, create=False): - self.Gsolv = fep.Gsolv(simulation=self.S, molecule='BNZ', - mdp=mdp ,**kwargs) + self.Gsolv = fep.Gsolv(simulation=self.S, molecule="BNZ", mdp=mdp, **kwargs) self.Gsolv.setup(maxwarn=1) def test_default_setup(self): self._setup() def test_list_foreign_lambdas(self): - lambda_coulomb = [0,0.5,1.0] - lambda_vdw = [0,0.2,1.0] + lambda_coulomb = [0, 0.5, 1.0] + lambda_vdw = [0, 0.2, 1.0] self._setup(lambda_coulomb=lambda_coulomb, lambda_vdw=lambda_vdw) def test_array_foreign_lambdas(self): - lambda_coulomb = np.array([0,0.5,1.0]) - lambda_vdw = np.array([0,0.2,1.0]) + lambda_coulomb = np.array([0, 0.5, 1.0]) + lambda_vdw = np.array([0, 0.2, 1.0]) self._setup(lambda_coulomb=lambda_coulomb, lambda_vdw=lambda_vdw) diff --git a/mdpow/tests/test_analysis.py b/mdpow/tests/test_analysis.py index bf242919..d4b21e22 100644 --- a/mdpow/tests/test_analysis.py +++ b/mdpow/tests/test_analysis.py @@ -17,6 +17,7 @@ MANIFEST = RESOURCES.join("manifest.yml") + def fix_manifest(topdir): """Create a temporary manifest with a custom `path`. @@ -46,7 +47,7 @@ def fix_manifest(topdir): manifest = yaml.safe_load(MANIFEST.open()) # simple heuristic: last element of the recorded manifest::path is the name # of the states directory, typically 'states' (from .../testing_resources/states) - manifest['path'] = RESOURCES.join(os.path.basename(manifest['path'])).strpath + manifest["path"] = RESOURCES.join(os.path.basename(manifest["path"])).strpath new_manifest = topdir.join("local_manifest.yml") yaml.dump(manifest, stream=new_manifest.open("w")) return new_manifest @@ -54,13 +55,15 @@ def fix_manifest(topdir): # session scope if read-only use + @pytest.fixture(scope="function") def fep_benzene_directory(tmpdir_factory): - topdir = tmpdir_factory.mktemp('analysis') + topdir = tmpdir_factory.mktemp("analysis") m = pybol.Manifest(fix_manifest(topdir).strpath) - m.assemble('FEP', topdir.strpath) + m.assemble("FEP", topdir.strpath) return topdir.join("benzene") + class TestAnalyze(object): def get_Gsolv(self, pth): gsolv = pth.join("FEP", "water", "Gsolv.fep") @@ -82,15 +85,17 @@ def assert_DeltaA(G): # - June 2023: in CI, >= 3.8 results differ from reference values (although # locally no changes are obvious) after ~4 decimals for unknown reasons. DeltaA = G.results.DeltaA - assert_array_almost_equal(DeltaA.Gibbs.astuple(), - (-3.7217472974883794, 2.3144288928034911), - decimal=3) - assert_array_almost_equal(DeltaA.coulomb.astuple(), - (8.3346255170099575, 0.73620918517131495), - decimal=3) - assert_array_almost_equal(DeltaA.vdw.astuple(), - (-4.6128782195215781, 2.1942144688960972), - decimal=3) + assert_array_almost_equal( + DeltaA.Gibbs.astuple(), (-3.7217472974883794, 2.3144288928034911), decimal=3 + ) + assert_array_almost_equal( + DeltaA.coulomb.astuple(), + (8.3346255170099575, 0.73620918517131495), + decimal=3, + ) + assert_array_almost_equal( + DeltaA.vdw.astuple(), (-4.6128782195215781, 2.1942144688960972), decimal=3 + ) def test_convert_edr(self, fep_benzene_directory): G = self.get_Gsolv(fep_benzene_directory) @@ -98,11 +103,13 @@ def test_convert_edr(self, fep_benzene_directory): with pytest.warns(numkit.LowAccuracyWarning): G.analyze(force=True, autosave=False) except IOError as err: - raise AssertionError("Failed to auto-convert edr to xvg: {0}: {1}".format( - err.strerror, err.filename)) + raise AssertionError( + "Failed to auto-convert edr to xvg: {0}: {1}".format( + err.strerror, err.filename + ) + ) self.assert_DeltaA(G) - def test_TI(self, fep_benzene_directory): G = self.get_Gsolv(fep_benzene_directory) # ensure conversion EDR to XVG.bz2; if the fixture is session scoped @@ -114,6 +121,9 @@ def test_TI(self, fep_benzene_directory): with pytest.warns(numkit.LowAccuracyWarning): G.analyze(force=True, autosave=False) except IOError as err: - raise AssertionError("Failed to convert edr to xvg: {0}: {1}".format( - err.strerror, err.filename)) + raise AssertionError( + "Failed to convert edr to xvg: {0}: {1}".format( + err.strerror, err.filename + ) + ) self.assert_DeltaA(G) diff --git a/mdpow/tests/test_analysis_alchemlyb.py b/mdpow/tests/test_analysis_alchemlyb.py index 2452b6bc..9dbb0f1f 100644 --- a/mdpow/tests/test_analysis_alchemlyb.py +++ b/mdpow/tests/test_analysis_alchemlyb.py @@ -15,6 +15,7 @@ MANIFEST = RESOURCES.join("manifest.yml") + def fix_manifest(topdir): """Create a temporary manifest with a custom `path`. @@ -44,7 +45,7 @@ def fix_manifest(topdir): manifest = yaml.safe_load(MANIFEST.open()) # simple heuristic: last element of the recorded manifest::path is the name # of the states directory, typically 'states' (from .../testing_resources/states) - manifest['path'] = RESOURCES.join(os.path.basename(manifest['path'])).strpath + manifest["path"] = RESOURCES.join(os.path.basename(manifest["path"])).strpath new_manifest = topdir.join("local_manifest.yml") yaml.dump(manifest, stream=new_manifest.open("w")) return new_manifest @@ -52,13 +53,15 @@ def fix_manifest(topdir): # session scope if read-only use + @pytest.fixture(scope="function") def fep_benzene_directory(tmpdir_factory): - topdir = tmpdir_factory.mktemp('analysis') + topdir = tmpdir_factory.mktemp("analysis") m = pybol.Manifest(fix_manifest(topdir).strpath) - m.assemble('FEP', topdir.strpath) + m.assemble("FEP", topdir.strpath) return topdir.join("benzene") + class TestAnalyze(object): def get_Gsolv(self, pth): gsolv = pth.join("FEP", "water", "Gsolv.fep") @@ -70,25 +73,26 @@ def get_Gsolv(self, pth): G.filename = gsolv.strpath return G - @pytest.mark.parametrize('method, Gibbs, coulomb, vdw', [ - ('TI', - (-3.901068, 0.550272), - (8.417035, 0.22289), - (-4.515967, 0.50311)), - ('BAR', - (-4.091241, 0.385413), - (8.339705, 0.166802), - (-4.248463, 0.347449)), - ('MBAR', - (-6.793117, 0.475149), - (8.241836, 0.219235), - (-1.448719, 0.421548)) - ]) - - @pytest.mark.xfail(pandas.__version__.startswith("1.3.0"), - reason="bug in pandas 1.3.0 see alchemistry/alchemlyb#147") - def test_estimator_alchemlyb(self, fep_benzene_directory, method, - Gibbs, coulomb, vdw): + @pytest.mark.parametrize( + "method, Gibbs, coulomb, vdw", + [ + ("TI", (-3.901068, 0.550272), (8.417035, 0.22289), (-4.515967, 0.50311)), + ("BAR", (-4.091241, 0.385413), (8.339705, 0.166802), (-4.248463, 0.347449)), + ( + "MBAR", + (-6.793117, 0.475149), + (8.241836, 0.219235), + (-1.448719, 0.421548), + ), + ], + ) + @pytest.mark.xfail( + pandas.__version__.startswith("1.3.0"), + reason="bug in pandas 1.3.0 see alchemistry/alchemlyb#147", + ) + def test_estimator_alchemlyb( + self, fep_benzene_directory, method, Gibbs, coulomb, vdw + ): G = self.get_Gsolv(fep_benzene_directory) G.method = method G.start = 0 @@ -101,42 +105,58 @@ def test_estimator_alchemlyb(self, fep_benzene_directory, method, try: G.analyze_alchemlyb(force=True, autosave=False, SI=False) except IOError as err: - raise AssertionError("Failed to convert edr to xvg: {0}: {1}".format( - err.strerror, err.filename)) + raise AssertionError( + "Failed to convert edr to xvg: {0}: {1}".format( + err.strerror, err.filename + ) + ) DeltaA = G.results.DeltaA - assert_array_almost_equal(DeltaA.Gibbs.astuple(), Gibbs, - decimal=5) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") - assert_array_almost_equal(DeltaA.coulomb.astuple(), coulomb, - decimal=5) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") - assert_array_almost_equal(DeltaA.vdw.astuple(), vdw, - decimal=5) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") - - @pytest.mark.xfail(pandas.__version__.startswith("1.3.0"), - reason="bug in pandas 1.3.0 see alchemistry/alchemlyb#147") + assert_array_almost_equal( + DeltaA.Gibbs.astuple(), Gibbs, decimal=5 + ) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") + assert_array_almost_equal( + DeltaA.coulomb.astuple(), coulomb, decimal=5 + ) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") + assert_array_almost_equal( + DeltaA.vdw.astuple(), vdw, decimal=5 + ) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") + + @pytest.mark.xfail( + pandas.__version__.startswith("1.3.0"), + reason="bug in pandas 1.3.0 see alchemistry/alchemlyb#147", + ) def test_SI(self, fep_benzene_directory): G = self.get_Gsolv(fep_benzene_directory) - G.method = 'TI' + G.method = "TI" G.start = 0 G.stop = None G.convert_edr() try: G.analyze_alchemlyb(force=True, SI=True, autosave=False) except IOError as err: - raise AssertionError("Failed to convert edr to xvg: {0}: {1}".format( - err.strerror, err.filename)) + raise AssertionError( + "Failed to convert edr to xvg: {0}: {1}".format( + err.strerror, err.filename + ) + ) DeltaA = G.results.DeltaA - assert_array_almost_equal(DeltaA.Gibbs.astuple(), (-2.908885, 2.175976), - decimal=5) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") - assert_array_almost_equal(DeltaA.coulomb.astuple(), (7.755779, 0.531481), - decimal=5) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") - assert_array_almost_equal(DeltaA.vdw.astuple(), (-4.846894, 2.110071), - decimal=5) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") - - @pytest.mark.xfail(pandas.__version__.startswith("1.3.0"), - reason="bug in pandas 1.3.0 see alchemistry/alchemlyb#147") + assert_array_almost_equal( + DeltaA.Gibbs.astuple(), (-2.908885, 2.175976), decimal=5 + ) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") + assert_array_almost_equal( + DeltaA.coulomb.astuple(), (7.755779, 0.531481), decimal=5 + ) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") + assert_array_almost_equal( + DeltaA.vdw.astuple(), (-4.846894, 2.110071), decimal=5 + ) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") + + @pytest.mark.xfail( + pandas.__version__.startswith("1.3.0"), + reason="bug in pandas 1.3.0 see alchemistry/alchemlyb#147", + ) def test_start_stop_stride(self, fep_benzene_directory): G = self.get_Gsolv(fep_benzene_directory) - G.method = 'TI' + G.method = "TI" G.start = 10 G.stride = 2 G.stop = 200 @@ -144,12 +164,18 @@ def test_start_stop_stride(self, fep_benzene_directory): try: G.analyze_alchemlyb(force=True, autosave=False, SI=False) except IOError as err: - raise AssertionError("Failed to convert edr to xvg: {0}: {1}".format( - err.strerror, err.filename)) + raise AssertionError( + "Failed to convert edr to xvg: {0}: {1}".format( + err.strerror, err.filename + ) + ) DeltaA = G.results.DeltaA - assert_array_almost_equal(DeltaA.Gibbs.astuple(), (-3.318109, 0.905128), - decimal=5) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") - assert_array_almost_equal(DeltaA.coulomb.astuple(), (8.146806, 0.348866), - decimal=5) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") - assert_array_almost_equal(DeltaA.vdw.astuple(), (-4.828696, 0.835195), - decimal=5) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") + assert_array_almost_equal( + DeltaA.Gibbs.astuple(), (-3.318109, 0.905128), decimal=5 + ) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") + assert_array_almost_equal( + DeltaA.coulomb.astuple(), (8.146806, 0.348866), decimal=5 + ) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") + assert_array_almost_equal( + DeltaA.vdw.astuple(), (-4.828696, 0.835195), decimal=5 + ) # with more recent versions of pandas/alchemlyb/numpy the original values are only reproduced to 5 decimals, see PR #166") diff --git a/mdpow/tests/test_automated_dihedral_analysis.py b/mdpow/tests/test_automated_dihedral_analysis.py index b5f70139..0bc1850f 100644 --- a/mdpow/tests/test_automated_dihedral_analysis.py +++ b/mdpow/tests/test_automated_dihedral_analysis.py @@ -18,20 +18,21 @@ from pkg_resources import resource_filename from mdpow.workflows import dihedrals -RESOURCES = pathlib.PurePath(resource_filename(__name__, 'testing_resources')) +RESOURCES = pathlib.PurePath(resource_filename(__name__, "testing_resources")) MANIFEST = RESOURCES / "manifest.yml" resname = "UNK" molname = "SM25" + @pytest.fixture -def molname_workflows_directory(tmp_path, molname='SM25'): +def molname_workflows_directory(tmp_path, molname="SM25"): m = pybol.Manifest(str(MANIFEST)) - m.assemble('workflows', tmp_path) + m.assemble("workflows", tmp_path) return tmp_path / molname -class TestAutomatedDihedralAnalysis(object): +class TestAutomatedDihedralAnalysis(object): @pytest.fixture def SM25_tmp_dir(self, molname_workflows_directory): dirname = molname_workflows_directory @@ -50,7 +51,9 @@ def atom_indices(self, mol_sol_data): # testing optional user input of alternate SMARTS string # for automated dihedral atom group selection - atom_group_indices_alt = dihedrals.get_atom_indices(mol=mol, SMARTS='[!$(*#*)&!D1]-!@[!$(*#*)&!D1]') + atom_group_indices_alt = dihedrals.get_atom_indices( + mol=mol, SMARTS="[!$(*#*)&!D1]-!@[!$(*#*)&!D1]" + ) return atom_group_indices, atom_group_indices_alt # fixture output, tuple: # atom_indices[0]=atom_group_indices @@ -67,15 +70,17 @@ def bond_indices(self, mol_sol_data, atom_indices): def dihedral_groups(self, mol_sol_data, atom_indices): _, solute = mol_sol_data atom_index, _ = atom_indices - dihedral_groups = dihedrals.get_dihedral_groups(solute=solute, atom_indices=atom_index) + dihedral_groups = dihedrals.get_dihedral_groups( + solute=solute, atom_indices=atom_index + ) return dihedral_groups @pytest.fixture def dihedral_data(self, SM25_tmp_dir, atom_indices): atom_group_indices, _ = atom_indices - df = dihedrals.dihedral_groups_ensemble(atom_indices=atom_group_indices, - dirname=SM25_tmp_dir, - solvents=('water',)) + df = dihedrals.dihedral_groups_ensemble( + atom_indices=atom_group_indices, dirname=SM25_tmp_dir, solvents=("water",) + ) df_aug = dihedrals.periodic_angle_padding(df) return df, df_aug # fixture output, tuple: @@ -84,58 +89,129 @@ def dihedral_data(self, SM25_tmp_dir, atom_indices): # tuple-tuples of dihedral atom group indices # collected using mdpow.workflows.dihedrals.SMARTS_DEFAULT - check_atom_group_indices = ((0, 1, 2, 3),(0, 1, 12, 13),(1, 2, 3, 11),(1, 2, 3, 10), - (1, 2, 3, 4),(1, 12, 13, 14),(2, 3, 4, 5),(2, 3, 4, 9), - (2, 1, 12, 13),(3, 2, 1, 12),(5, 4, 3, 11),(5, 4, 3, 10), - (9, 4, 3, 11),(9, 4, 3, 10),(12, 13, 14, 15),(12, 13, 14, 19)) + check_atom_group_indices = ( + (0, 1, 2, 3), + (0, 1, 12, 13), + (1, 2, 3, 11), + (1, 2, 3, 10), + (1, 2, 3, 4), + (1, 12, 13, 14), + (2, 3, 4, 5), + (2, 3, 4, 9), + (2, 1, 12, 13), + (3, 2, 1, 12), + (5, 4, 3, 11), + (5, 4, 3, 10), + (9, 4, 3, 11), + (9, 4, 3, 10), + (12, 13, 14, 15), + (12, 13, 14, 19), + ) # tuple-tuples of dihedral atom group indices # collected using alternate SMARTS input (explicitly defined) # see: fixture - atom_indices().atom_group_indices_alt check_atom_group_indices_alt = ((1, 2), (1, 12), (2, 3), (3, 4), (12, 13), (13, 14)) - check_atom_name_index_pairs = {'O1-C2-N3-S4': (0, 1, 2, 3), - 'O1-C2-C13-C14': (0, 1, 12, 13), - 'C2-N3-S4-O12': (1, 2, 3, 11), - 'C2-N3-S4-O11': (1, 2, 3, 10), - 'C2-N3-S4-C5': (1, 2, 3, 4), - 'C2-C13-C14-C15': (1, 12, 13, 14), - 'N3-S4-C5-C6': (2, 3, 4, 5), - 'N3-S4-C5-C10': (2, 3, 4, 9), - 'N3-C2-C13-C14': (2, 1, 12, 13), - 'S4-N3-C2-C13': (3, 2, 1, 12), - 'C6-C5-S4-O12': (5, 4, 3, 11), - 'C6-C5-S4-O11': (5, 4, 3, 10), - 'C10-C5-S4-O12': (9, 4, 3, 11), - 'C10-C5-S4-O11': (9, 4, 3, 10), - 'C13-C14-C15-C16': (12, 13, 14, 15), - 'C13-C14-C15-C20': (12, 13, 14, 19)} - - check_groups = [np.array(['O1', 'C2', 'N3', 'S4'], dtype=object), - np.array(['O1', 'C2', 'C13', 'C14'], dtype=object), - np.array(['C2', 'N3', 'S4', 'O12'], dtype=object), - np.array(['C2', 'N3', 'S4', 'O11'], dtype=object), - np.array(['C2', 'N3', 'S4', 'C5'], dtype=object), - np.array(['C2', 'C13', 'C14', 'C15'], dtype=object), - np.array(['N3', 'S4', 'C5', 'C6'], dtype=object), - np.array(['N3', 'S4', 'C5', 'C10'], dtype=object), - np.array(['N3', 'C2', 'C13', 'C14'], dtype=object), - np.array(['S4', 'N3', 'C2', 'C13'], dtype=object), - np.array(['C6', 'C5', 'S4', 'O12'], dtype=object), - np.array(['C6', 'C5', 'S4', 'O11'], dtype=object), - np.array(['C10', 'C5', 'S4', 'O12'], dtype=object), - np.array(['C10', 'C5', 'S4', 'O11'], dtype=object), - np.array(['C13', 'C14', 'C15', 'C16'], dtype=object), - np.array(['C13', 'C14', 'C15', 'C20'], dtype=object)] - - universe_solute_atom_names = np.array(['O1', 'C2', 'N3', 'S4', 'C5', 'C6', 'C7', 'C8', - 'C9', 'C10', 'O11', 'O12', 'C13', 'C14', 'C15', - 'C16', 'C17', 'C18', 'C19', 'C20', 'H21', 'H22', - 'H23', 'H24', 'H25', 'H26', 'H27', 'H28', 'H29', - 'H30', 'H31', 'H32', 'H33', 'H34', 'H35'], dtype=object) - - check_hydrogens = np.array(['H21', 'H22', 'H23', 'H24', 'H25', 'H26', 'H27', 'H28', - 'H29', 'H30', 'H31', 'H32', 'H33', 'H34', 'H35'], dtype=object) + check_atom_name_index_pairs = { + "O1-C2-N3-S4": (0, 1, 2, 3), + "O1-C2-C13-C14": (0, 1, 12, 13), + "C2-N3-S4-O12": (1, 2, 3, 11), + "C2-N3-S4-O11": (1, 2, 3, 10), + "C2-N3-S4-C5": (1, 2, 3, 4), + "C2-C13-C14-C15": (1, 12, 13, 14), + "N3-S4-C5-C6": (2, 3, 4, 5), + "N3-S4-C5-C10": (2, 3, 4, 9), + "N3-C2-C13-C14": (2, 1, 12, 13), + "S4-N3-C2-C13": (3, 2, 1, 12), + "C6-C5-S4-O12": (5, 4, 3, 11), + "C6-C5-S4-O11": (5, 4, 3, 10), + "C10-C5-S4-O12": (9, 4, 3, 11), + "C10-C5-S4-O11": (9, 4, 3, 10), + "C13-C14-C15-C16": (12, 13, 14, 15), + "C13-C14-C15-C20": (12, 13, 14, 19), + } + + check_groups = [ + np.array(["O1", "C2", "N3", "S4"], dtype=object), + np.array(["O1", "C2", "C13", "C14"], dtype=object), + np.array(["C2", "N3", "S4", "O12"], dtype=object), + np.array(["C2", "N3", "S4", "O11"], dtype=object), + np.array(["C2", "N3", "S4", "C5"], dtype=object), + np.array(["C2", "C13", "C14", "C15"], dtype=object), + np.array(["N3", "S4", "C5", "C6"], dtype=object), + np.array(["N3", "S4", "C5", "C10"], dtype=object), + np.array(["N3", "C2", "C13", "C14"], dtype=object), + np.array(["S4", "N3", "C2", "C13"], dtype=object), + np.array(["C6", "C5", "S4", "O12"], dtype=object), + np.array(["C6", "C5", "S4", "O11"], dtype=object), + np.array(["C10", "C5", "S4", "O12"], dtype=object), + np.array(["C10", "C5", "S4", "O11"], dtype=object), + np.array(["C13", "C14", "C15", "C16"], dtype=object), + np.array(["C13", "C14", "C15", "C20"], dtype=object), + ] + + universe_solute_atom_names = np.array( + [ + "O1", + "C2", + "N3", + "S4", + "C5", + "C6", + "C7", + "C8", + "C9", + "C10", + "O11", + "O12", + "C13", + "C14", + "C15", + "C16", + "C17", + "C18", + "C19", + "C20", + "H21", + "H22", + "H23", + "H24", + "H25", + "H26", + "H27", + "H28", + "H29", + "H30", + "H31", + "H32", + "H33", + "H34", + "H35", + ], + dtype=object, + ) + + check_hydrogens = np.array( + [ + "H21", + "H22", + "H23", + "H24", + "H25", + "H26", + "H27", + "H28", + "H29", + "H30", + "H31", + "H32", + "H33", + "H34", + "H35", + ], + dtype=object, + ) # pre 'angle padding' - scipy.stats for # dihedral atom group: O1-C2-N3-S4 @@ -156,7 +232,7 @@ def dihedral_data(self, SM25_tmp_dir, atom_indices): def test_build_universe(self, SM25_tmp_dir): u = dihedrals.build_universe(dirname=SM25_tmp_dir) - solute = u.select_atoms('resname UNK') + solute = u.select_atoms("resname UNK") solute_names = solute.atoms.names assert solute_names.all() == self.universe_solute_atom_names.all() @@ -164,7 +240,6 @@ def test_build_universe(self, SM25_tmp_dir): # between RDKIT versions; issue raised (#239) to identify and # resolve exact package/version responsible def test_dihedral_indices(self, atom_indices): - atom_group_indices = atom_indices[0] assert set(atom_group_indices) == set(self.check_atom_group_indices) @@ -188,14 +263,17 @@ def test_dihedral_groups(self, dihedral_groups): # bond indices are determined by atom indices and are subsequently self-consistent # dihedral group names are determined by the MDAnalysis solute object from RDKit-derived atom indices # this test checks if indexing schemes for RDKit and MDAnalysis are consistent - def test_RDKit_MDAnalysis_atom_index_consistency(self, atom_indices, bond_indices, dihedral_groups): + def test_RDKit_MDAnalysis_atom_index_consistency( + self, atom_indices, bond_indices, dihedral_groups + ): atom_index, _ = atom_indices bond_index = bond_indices groups = dihedral_groups - name_index_pairs = dihedrals.get_paired_indices(atom_indices=atom_index, bond_indices=bond_index, - dihedral_groups=groups) - + name_index_pairs = dihedrals.get_paired_indices( + atom_indices=atom_index, bond_indices=bond_index, dihedral_groups=groups + ) + atom_name_index_pairs = {} for key in name_index_pairs.keys(): @@ -205,14 +283,13 @@ def test_RDKit_MDAnalysis_atom_index_consistency(self, atom_indices, bond_indice # Possible ordering issue (#239) def test_dihedral_groups_ensemble(self, dihedral_data): - df, _ = dihedral_data - dh1_result = df.loc[df['selection'] == 'O1-C2-N3-S4']['dihedral'] + dh1_result = df.loc[df["selection"] == "O1-C2-N3-S4"]["dihedral"] dh1_mean = circmean(dh1_result, high=180, low=-180) dh1_var = circvar(dh1_result, high=180, low=-180) - dh2_result = df.loc[df['selection'] == 'C13-C14-C15-C20']['dihedral'] + dh2_result = df.loc[df["selection"] == "C13-C14-C15-C20"]["dihedral"] dh2_mean = circmean(dh2_result, high=180, low=-180) dh2_var = circvar(dh2_result, high=180, low=-180) @@ -225,22 +302,32 @@ def test_dihedral_groups_ensemble(self, dihedral_data): def test_save_df(self, dihedral_data, SM25_tmp_dir): df, _ = dihedral_data - dihedrals.save_df(df=df, df_save_dir=SM25_tmp_dir, resname='UNK', molname='SM25') - assert (SM25_tmp_dir / 'SM25' / 'SM25_full_df.csv.bz2').exists(), 'Compressed csv file not saved' + dihedrals.save_df( + df=df, df_save_dir=SM25_tmp_dir, resname="UNK", molname="SM25" + ) + assert ( + SM25_tmp_dir / "SM25" / "SM25_full_df.csv.bz2" + ).exists(), "Compressed csv file not saved" def test_save_df_info(self, dihedral_data, SM25_tmp_dir, caplog): df, _ = dihedral_data caplog.clear() - caplog.set_level(logging.INFO, logger='mdpow.workflows.dihedrals') - dihedrals.save_df(df=df, df_save_dir=SM25_tmp_dir, resname='UNK', molname='SM25') - assert f'Results DataFrame saved as {SM25_tmp_dir}/SM25/SM25_full_df.csv.bz2' in caplog.text, 'Save location not logged or returned' + caplog.set_level(logging.INFO, logger="mdpow.workflows.dihedrals") + dihedrals.save_df( + df=df, df_save_dir=SM25_tmp_dir, resname="UNK", molname="SM25" + ) + assert ( + f"Results DataFrame saved as {SM25_tmp_dir}/SM25/SM25_full_df.csv.bz2" + in caplog.text + ), "Save location not logged or returned" # Possible ordering issue (#239) def test_periodic_angle(self, dihedral_data): - _, df_aug = dihedral_data - aug_dh2_result = df_aug.loc[df_aug['selection'] == 'C13-C14-C15-C20']['dihedral'] + aug_dh2_result = df_aug.loc[df_aug["selection"] == "C13-C14-C15-C20"][ + "dihedral" + ] aug_dh2_mean = circmean(aug_dh2_result, high=180, low=-180) aug_dh2_var = circvar(aug_dh2_result, high=180, low=-180) @@ -252,47 +339,76 @@ def test_periodic_angle(self, dihedral_data): # Tests using similar instances of the automated analyses # will use module or class-scoped fixtures, pending #235 def test_save_fig(self, SM25_tmp_dir): - dihedrals.automated_dihedral_analysis(dirname=SM25_tmp_dir, figdir=SM25_tmp_dir, - resname=resname, molname='SM25', - solvents=('water',)) - assert (SM25_tmp_dir / 'SM25' / 'SM25_C10-C5-S4-O11_violins.pdf').exists(), 'PDF file not generated' + dihedrals.automated_dihedral_analysis( + dirname=SM25_tmp_dir, + figdir=SM25_tmp_dir, + resname=resname, + molname="SM25", + solvents=("water",), + ) + assert ( + SM25_tmp_dir / "SM25" / "SM25_C10-C5-S4-O11_violins.pdf" + ).exists(), "PDF file not generated" # Possible ordering issue (#239) # Tests using similar instances of the automated analyses # will use module or class-scoped fixtures, pending #235 def test_save_fig_info(self, SM25_tmp_dir, caplog): caplog.clear() - caplog.set_level(logging.INFO, logger='mdpow.workflows.dihedrals') - dihedrals.automated_dihedral_analysis(dirname=SM25_tmp_dir, figdir=SM25_tmp_dir, - resname=resname, molname='SM25', - solvents=('water',)) - assert f'Figure saved as {SM25_tmp_dir}/SM25/SM25_C10-C5-S4-O11_violins.pdf' in caplog.text, 'PDF file not saved' + caplog.set_level(logging.INFO, logger="mdpow.workflows.dihedrals") + dihedrals.automated_dihedral_analysis( + dirname=SM25_tmp_dir, + figdir=SM25_tmp_dir, + resname=resname, + molname="SM25", + solvents=("water",), + ) + assert ( + f"Figure saved as {SM25_tmp_dir}/SM25/SM25_C10-C5-S4-O11_violins.pdf" + in caplog.text + ), "PDF file not saved" # Tests using similar instances of the automated analyses # will use module or class-scoped fixtures, pending #235 def test_DataFrame_input(self, SM25_tmp_dir, dihedral_data): df, _ = dihedral_data - dihedrals.automated_dihedral_analysis(dirname=SM25_tmp_dir, figdir=SM25_tmp_dir, - resname=resname, molname=molname, - solvents=('water',), dataframe=df) - assert (SM25_tmp_dir / 'SM25' / 'SM25_C10-C5-S4-O11_violins.pdf').exists(), 'PDF file not generated' + dihedrals.automated_dihedral_analysis( + dirname=SM25_tmp_dir, + figdir=SM25_tmp_dir, + resname=resname, + molname=molname, + solvents=("water",), + dataframe=df, + ) + assert ( + SM25_tmp_dir / "SM25" / "SM25_C10-C5-S4-O11_violins.pdf" + ).exists(), "PDF file not generated" # Tests using similar instances of the automated analyses # will use module or class-scoped fixtures, pending #235 def test_DataFrame_input_info(self, SM25_tmp_dir, dihedral_data, caplog): caplog.clear() - caplog.set_level(logging.INFO, logger='mdpow.workflows.dihedrals') + caplog.set_level(logging.INFO, logger="mdpow.workflows.dihedrals") df, _ = dihedral_data - dihedrals.automated_dihedral_analysis(dirname=SM25_tmp_dir, figdir=SM25_tmp_dir, - resname=resname, molname=molname, - solvents=('water',), dataframe=df) - assert 'Proceeding with results DataFrame provided.' in caplog.text, 'No dataframe provided or dataframe not recognized' + dihedrals.automated_dihedral_analysis( + dirname=SM25_tmp_dir, + figdir=SM25_tmp_dir, + resname=resname, + molname=molname, + solvents=("water",), + dataframe=df, + ) + assert ( + "Proceeding with results DataFrame provided." in caplog.text + ), "No dataframe provided or dataframe not recognized" # testing resources only contain analyses with single solvent input def test_single_solvent(self, dihedral_data): df, _ = dihedral_data # all analysis data in one violin plot - g = dihedrals.dihedral_violins(df=df, width=0.9, solvents=('water',), plot_title='test') + g = dihedrals.dihedral_violins( + df=df, width=0.9, solvents=("water",), plot_title="test" + ) # number of solvents in DataFrame used to generate plot - number_of_solvents = g.data['solvent'].nunique() - assert number_of_solvents == 1 \ No newline at end of file + number_of_solvents = g.data["solvent"].nunique() + assert number_of_solvents == 1 diff --git a/mdpow/tests/test_config.py b/mdpow/tests/test_config.py index 4a34dd25..a3646539 100644 --- a/mdpow/tests/test_config.py +++ b/mdpow/tests/test_config.py @@ -7,33 +7,39 @@ import mdpow.config + @pytest.fixture def cfg(): # default bundled config return mdpow.config.get_configuration() + @pytest.fixture def minicfg(): s = StringIO("setup:\n name: 'Alice'\n gromacsoutput: False\n") yield s s.close() + class TestConfigurationParser: def test_get_NoSectionError(self): cfg = mdpow.config.POWConfigParser() - with pytest.raises(mdpow.config.NoSectionError, - match="Config file has no section Jabberwocky"): - cfg.get('Jabberwocky', 'elump') + with pytest.raises( + mdpow.config.NoSectionError, match="Config file has no section Jabberwocky" + ): + cfg.get("Jabberwocky", "elump") def test_get_NoOptionWarning_gives_None(self, cfg): - with pytest.warns(mdpow.config.NoOptionWarning, - match="Config file section FEP contains no " - "option Jabberwocky. Using 'None'."): + with pytest.warns( + mdpow.config.NoOptionWarning, + match="Config file section FEP contains no " + "option Jabberwocky. Using 'None'.", + ): item = cfg.get("FEP", "Jabberwocky") assert item is None def test_get(self, cfg): - item = cfg.get("setup","solventmodel") + item = cfg.get("setup", "solventmodel") assert isinstance(item, str) assert item == "tip4p" @@ -42,7 +48,7 @@ def test_get_None(self, cfg): assert item is None def test_getstr(self, cfg): - args = "setup","solventmodel" + args = "setup", "solventmodel" item = cfg.getstr(*args) assert isinstance(item, str) assert item == "tip4p" @@ -75,7 +81,7 @@ def test_getfloat(self, cfg): def test_getpath(self, cfg): pth = "~/mirrors/jbwck.itp" - cfg.conf['setup']['itp'] = pth + cfg.conf["setup"]["itp"] = pth item = cfg.getpath("setup", "itp") @@ -99,7 +105,7 @@ def test_getlist(self, cfg): item = cfg.getlist("FEP_schedule_Coulomb", "lambdas") assert isinstance(item, list) - assert item == ['0', '0.25', '0.5', '0.75', '1.0'] + assert item == ["0", "0.25", "0.5", "0.75", "1.0"] def test_getlist_empty(self, cfg): # get an option with None for this test diff --git a/mdpow/tests/test_dihedral.py b/mdpow/tests/test_dihedral.py index a8a0b7ee..0a48a62f 100644 --- a/mdpow/tests/test_dihedral.py +++ b/mdpow/tests/test_dihedral.py @@ -19,7 +19,7 @@ from pkg_resources import resource_filename -RESOURCES = py.path.local(resource_filename(__name__, 'testing_resources')) +RESOURCES = py.path.local(resource_filename(__name__, "testing_resources")) MANIFEST = RESOURCES.join("manifest.yml") @@ -31,49 +31,55 @@ class TestDihedral(object): def setup_method(self): self.tmpdir = td.TempDir() - self.m = pybol.Manifest(str(RESOURCES / 'manifest.yml')) - self.m.assemble('example_FEP', self.tmpdir.name) - self.Ens = Ensemble(dirname=self.tmpdir.name, solvents=['water']) + self.m = pybol.Manifest(str(RESOURCES / "manifest.yml")) + self.m.assemble("example_FEP", self.tmpdir.name) + self.Ens = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) def teardown_method(self): self.tmpdir.dissolve() def test_dataframe(self): - dh1 = self.Ens.select_atoms('name C4', 'name C17', 'name S2', 'name N3') + dh1 = self.Ens.select_atoms("name C4", "name C17", "name S2", "name N3") dh_run = DihedralAnalysis([dh1]).run(start=0, stop=4, step=1) results = dh_run.results - assert results['selection'][0] == 'C4-C17-S2-N3' - for s in results['solvent']: - assert s == 'water' - for i in results['interaction'][:12]: - assert i == 'Coulomb' + assert results["selection"][0] == "C4-C17-S2-N3" + for s in results["solvent"]: + assert s == "water" + for i in results["interaction"][:12]: + assert i == "Coulomb" def test_selection_error(self): - dh1 = self.Ens.select_atoms('name C17', 'name S2', 'name N3') + dh1 = self.Ens.select_atoms("name C17", "name S2", "name N3") with pytest.raises(SelectionError): dh_run = DihedralAnalysis([dh1]).run(start=0, stop=4, step=1) def test_results_recursive1(self): - dh1 = self.Ens.select_atoms('name C11', 'name C10', 'name C9', 'name C4') - dh2 = self.Ens.select_atoms('name C11', 'name C10', 'name C9', 'name C4') + dh1 = self.Ens.select_atoms("name C11", "name C10", "name C9", "name C4") + dh2 = self.Ens.select_atoms("name C11", "name C10", "name C9", "name C4") dh_run1 = DihedralAnalysis([dh1]).run(start=0, stop=4, step=1) dh_run2 = DihedralAnalysis([dh2]).run(start=0, stop=4, step=1) - assert len(dh_run1.results['dihedral']) == len(dh_run2.results['dihedral']) - for i in range(len(dh_run1.results['dihedral'])): - assert dh_run1.results['dihedral'][i] == dh_run2.results['dihedral'][i] + assert len(dh_run1.results["dihedral"]) == len(dh_run2.results["dihedral"]) + for i in range(len(dh_run1.results["dihedral"])): + assert dh_run1.results["dihedral"][i] == dh_run2.results["dihedral"][i] - @pytest.mark.skipif(sys.version_info < (3, 8), reason="scipy circvar gives wrong answers") + @pytest.mark.skipif( + sys.version_info < (3, 8), reason="scipy circvar gives wrong answers" + ) def test_results_recursive2(self): - dh1 = self.Ens.select_atoms('name C11', 'name C10', 'name C9', 'name C4') - dh2 = self.Ens.select_atoms('name C8', 'name C4', 'name C9', 'name C10') + dh1 = self.Ens.select_atoms("name C11", "name C10", "name C9", "name C4") + dh2 = self.Ens.select_atoms("name C8", "name C4", "name C9", "name C10") dh_run = DihedralAnalysis([dh1, dh2]).run(start=0, stop=4, step=1) - dh1_result = dh_run.results.loc[dh_run.results['selection'] == 'C11-C10-C9-C4']['dihedral'] - dh2_result = dh_run.results.loc[dh_run.results['selection'] == 'C8-C4-C9-C10']['dihedral'] + dh1_result = dh_run.results.loc[dh_run.results["selection"] == "C11-C10-C9-C4"][ + "dihedral" + ] + dh2_result = dh_run.results.loc[dh_run.results["selection"] == "C8-C4-C9-C10"][ + "dihedral" + ] dh1_mean = circmean(dh1_result, high=180, low=-180) dh2_mean = circmean(dh2_result, high=180, low=-180) @@ -86,15 +92,15 @@ def test_results_recursive2(self): assert_almost_equal(dh2_var, self.DG491011_var, 6) def test_ValueError_different_ensemble(self): - other = Ensemble(dirname=self.tmpdir.name, solvents=['water']) - dh1 = self.Ens.select_atoms('name C11', 'name C10', 'name C9', 'name C4') - dh2 = other.select_atoms('name C8', 'name C4', 'name C9', 'name C10') - with pytest.raises(ValueError, - match='Dihedral selections from different Ensembles, '): + other = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) + dh1 = self.Ens.select_atoms("name C11", "name C10", "name C9", "name C4") + dh2 = other.select_atoms("name C8", "name C4", "name C9", "name C10") + with pytest.raises( + ValueError, match="Dihedral selections from different Ensembles, " + ): DihedralAnalysis([dh1, dh2]) def test_single_universe(self): - dh = self.Ens.select_atoms('name C4', 'name C17', 'name S2', 'name N3') + dh = self.Ens.select_atoms("name C4", "name C17", "name S2", "name N3") with pytest.raises(NotImplementedError): - DihedralAnalysis([dh])._single_universe() diff --git a/mdpow/tests/test_ensemble.py b/mdpow/tests/test_ensemble.py index d6e95fde..75c7bb39 100644 --- a/mdpow/tests/test_ensemble.py +++ b/mdpow/tests/test_ensemble.py @@ -21,110 +21,120 @@ from pkg_resources import resource_filename -RESOURCES = py.path.local(resource_filename(__name__, 'testing_resources')) +RESOURCES = py.path.local(resource_filename(__name__, "testing_resources")) MANIFEST = RESOURCES.join("manifest.yml") -ensemble_keys = [('water', 'Coulomb', '0000'), - ('water', 'Coulomb', '0500'), - ('water', 'Coulomb', '1000'), - ('water', 'VDW', '0000'), - ('water', 'VDW', '0250'), - ('water', 'VDW', '0500'), - ('water', 'VDW', '1000')] +ensemble_keys = [ + ("water", "Coulomb", "0000"), + ("water", "Coulomb", "0500"), + ("water", "Coulomb", "1000"), + ("water", "VDW", "0000"), + ("water", "VDW", "0250"), + ("water", "VDW", "0500"), + ("water", "VDW", "1000"), +] class TestEnsemble(object): def setup_method(self): self.tmpdir = td.TempDir() - self.m = pybol.Manifest(str(RESOURCES / 'manifest.yml')) - self.m.assemble('example_FEP', self.tmpdir.name) + self.m = pybol.Manifest(str(RESOURCES / "manifest.yml")) + self.m.assemble("example_FEP", self.tmpdir.name) def teardown_method(self): self.tmpdir.dissolve() def test_build_ensemble(self): # Octanol will be added later - Sim = Ensemble(dirname=self.tmpdir.name, solvents=['water']) + Sim = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) diff = set(Sim.keys()) ^ set(ensemble_keys) assert not diff def test_kwargs(self): - l_dir = os.path.abspath(os.path.join(self.tmpdir.name, 'FEP', 'md.gro')) - bnz = Ensemble(dirname=self.tmpdir.name, solvents=['water'], topology_paths={'water': l_dir}) + l_dir = os.path.abspath(os.path.join(self.tmpdir.name, "FEP", "md.gro")) + bnz = Ensemble( + dirname=self.tmpdir.name, + solvents=["water"], + topology_paths={"water": l_dir}, + ) diff = set(bnz.keys()) ^ set(ensemble_keys) assert not diff def test_add_remove_systems(self): with in_dir(self.tmpdir.name, create=False): bnz = Ensemble() - l_dir = os.path.join(os.curdir, 'FEP', 'water', 'Coulomb', '0000') - top_dir = os.path.join(l_dir, 'md.gro') - trj_dir = os.path.join(l_dir, 'md_red.xtc') + l_dir = os.path.join(os.curdir, "FEP", "water", "Coulomb", "0000") + top_dir = os.path.join(l_dir, "md.gro") + trj_dir = os.path.join(l_dir, "md_red.xtc") U = mda.Universe(top_dir, trj_dir) - bnz.add_system(('water', 'Coulomb', '0000'), U) - assert bnz.keys() == [('water', 'Coulomb', '0000')] + bnz.add_system(("water", "Coulomb", "0000"), U) + assert bnz.keys() == [("water", "Coulomb", "0000")] assert bnz._num_systems == 1 assert bnz.__repr__() == "" assert len(bnz) == 1 - bnz.pop(('water', 'Coulomb', '0000')) + bnz.pop(("water", "Coulomb", "0000")) assert bnz._num_systems == 0 assert len(bnz) == 0 def test_select_atoms(self): - Sim = Ensemble(dirname=self.tmpdir.name, solvents=['water']) - solute = Sim.select_atoms('not resname SOL') + Sim = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) + solute = Sim.select_atoms("not resname SOL") assert len(solute) == 7 for k in solute.keys(): assert len(solute[k]) == 42 def test_select_systems(self): - Sim = Ensemble(dirname=self.tmpdir.name, solvents=['water']) - Sel1 = Sim.select_systems(keys=[('water', 'Coulomb', '0000'), - ('water', 'VDW', '0500')]) - assert Sel1.keys() == [('water', 'Coulomb', '0000'), - ('water', 'VDW', '0500')] - Sel2 = Sim.select_systems(solvents=['water'], interactions=['Coulomb'], - lambdas=['0000', '1000']) - assert Sel2.keys() == [('water', 'Coulomb', '0000'), - ('water', 'Coulomb', '1000')] - Sel3 = Sim.select_systems(solvents=['water'], interactions=['VDW'], - lambda_range=[0, 1]) + Sim = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) + Sel1 = Sim.select_systems( + keys=[("water", "Coulomb", "0000"), ("water", "VDW", "0500")] + ) + assert Sel1.keys() == [("water", "Coulomb", "0000"), ("water", "VDW", "0500")] + Sel2 = Sim.select_systems( + solvents=["water"], interactions=["Coulomb"], lambdas=["0000", "1000"] + ) + assert Sel2.keys() == [ + ("water", "Coulomb", "0000"), + ("water", "Coulomb", "1000"), + ] + Sel3 = Sim.select_systems( + solvents=["water"], interactions=["VDW"], lambda_range=[0, 1] + ) diff = set(Sel3.keys()) ^ set(ensemble_keys[3:]) assert not diff def test_ensemble_ag_methods(self): - Solv_system = Ensemble(dirname=self.tmpdir.name, solvents=['water']) - Sol1 = Solv_system.select_atoms('resname SOL') - Sol2 = Sol1.select_atoms('resid 2') + Solv_system = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) + Sol1 = Solv_system.select_atoms("resname SOL") + Sol2 = Sol1.select_atoms("resid 2") Sol2_pos = Sol2.positions() assert len(Sol2_pos) > 0 for k in Sol2_pos: assert np.shape(Sol2_pos[k]) == (3, 3) assert not Sol1 == Sol2 assert isinstance(Sol2, EnsembleAtomGroup) - assert Sol2 == Sol1.select_atoms('resid 2') + assert Sol2 == Sol1.select_atoms("resid 2") assert ensemble_keys.sort() == Sol1.ensemble.keys().sort() - Sol1._groups.pop(('water', 'Coulomb', '0000')) + Sol1._groups.pop(("water", "Coulomb", "0000")) Sol1._keys = Sol1._groups.keys() assert not Sol1 == Sol2 - pos2 = Sol2.positions(keys=[('water', 'Coulomb', '0000')]) - assert np.shape(pos2[('water', 'Coulomb', '0000')]) == (3, 3) + pos2 = Sol2.positions(keys=[("water", "Coulomb", "0000")]) + assert np.shape(pos2[("water", "Coulomb", "0000")]) == (3, 3) def test_ensemble_init_exception(self): with pytest.raises(FileNotFoundError): - Ens = Ensemble(dirname='foo') + Ens = Ensemble(dirname="foo") def test_ensemble_build_exceptions(self): with pytest.raises(NoDataError): - ens = Ensemble(self.tmpdir.name, solvents=['test_solv']) + ens = Ensemble(self.tmpdir.name, solvents=["test_solv"]) def test_ensemble_selection_error(self): - ens = Ensemble(dirname=self.tmpdir.name, solvents=['water']) - sel1 = ens.select_atoms('resid 1') + ens = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) + sel1 = ens.select_atoms("resid 1") with pytest.raises(SelectionError): - ens.select_atoms('foo') + ens.select_atoms("foo") with pytest.raises(SelectionError): - sel1.select_atoms('foo') + sel1.select_atoms("foo") def test_ensemble_analysis(self): class TestAnalysis(EnsembleAnalysis): @@ -140,12 +150,12 @@ def _single_universe(self): self.key_list.append(self._key) def _single_frame(self): - assert len(self._system.select_atoms('not resname SOL')) == 42 + assert len(self._system.select_atoms("not resname SOL")) == 42 def _conclude_universe(self): assert self.n_frames == self.stop - Sim = Ensemble(dirname=self.tmpdir.name, solvents=['water']) + Sim = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) TestRun = TestAnalysis(Sim).run(start=0, step=1, stop=10) assert Sim.keys() == TestRun.key_list @@ -159,7 +169,7 @@ def __init__(self, test_ensemble): def _single_universe(self): pass - Sim = Ensemble(dirname=self.tmpdir.name, solvents=['water']) + Sim = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) TestRun = TestAnalysis(Sim) with pytest.raises(NotImplementedError): @@ -175,21 +185,21 @@ def __init__(self, test_ensemble): def _single_frame(self): pass - Sim = Ensemble(dirname=self.tmpdir.name, solvents=['water']) + Sim = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) TestRun = TestAnalysis(Sim) with pytest.raises(NotImplementedError): TestRun._single_universe() def test_value_error(self): - ens = Ensemble(dirname=self.tmpdir.name, solvents=['water']) + ens = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) copy_ens = Ensemble() copy_ens._ensemble_dir = self.tmpdir.name for k in ens.keys(): copy_ens.add_system(k, ens[k]) - dh1 = ens.select_atoms('name C4 or name C17 or name S2 or name N3') - dh2 = copy_ens.select_atoms('name C4 or name C17 or name S2 or name N3') - dh3 = ens.select_atoms('name C4 or name C17 or name S2 or name N3') - dh4 = ens.select_atoms('name C4 or name C17 or name S2 or name N3') + dh1 = ens.select_atoms("name C4 or name C17 or name S2 or name N3") + dh2 = copy_ens.select_atoms("name C4 or name C17 or name S2 or name N3") + dh3 = ens.select_atoms("name C4 or name C17 or name S2 or name N3") + dh4 = ens.select_atoms("name C4 or name C17 or name S2 or name N3") with pytest.raises(ValueError): dh_run = DihedralAnalysis([dh1, dh2, dh4, dh3]).run(start=0, stop=4, step=1) diff --git a/mdpow/tests/test_equilibration_script.py b/mdpow/tests/test_equilibration_script.py index 5b9c4cb9..c0b5f752 100644 --- a/mdpow/tests/test_equilibration_script.py +++ b/mdpow/tests/test_equilibration_script.py @@ -10,36 +10,52 @@ from . import RESOURCES + class TestEquilibriumScript(object): def setup_method(self): self.tmpdir = td.TempDir() self.old_path = os.getcwd() self.resources = RESOURCES - m = pybol.Manifest(str(self.resources / 'manifest.yml')) - m.assemble('base', self.tmpdir.name) + m = pybol.Manifest(str(self.resources / "manifest.yml")) + m.assemble("base", self.tmpdir.name) def teardown_method(self): self.tmpdir.dissolve() def _run_equil(self, solvent, dirname): - cfg = get_configuration('runinput.yml') + cfg = get_configuration("runinput.yml") self.S = equilibrium_simulation(cfg, solvent, dirname=dirname) def test_basic_run(self): with in_dir(self.tmpdir.name, create=False): try: - self._run_equil('water','benzene/') + self._run_equil("water", "benzene/") self._new_structures() except Exception as err: - raise AssertionError('Equilibration simulations failed with exception:\n{0}'.format(str(err))) + raise AssertionError( + "Equilibration simulations failed with exception:\n{0}".format( + str(err) + ) + ) def _new_structures(self): assert os.path.exists( - os.path.join(self.tmpdir.name, - 'benzene', 'Equilibrium', 'water', 'em', 'em.pdb')) + os.path.join( + self.tmpdir.name, "benzene", "Equilibrium", "water", "em", "em.pdb" + ) + ) assert os.path.exists( - os.path.join(self.tmpdir.name, - 'benzene', 'Equilibrium', 'water', 'solvation', 'solvated.gro')) + os.path.join( + self.tmpdir.name, + "benzene", + "Equilibrium", + "water", + "solvation", + "solvated.gro", + ) + ) assert os.path.exists( - os.path.join(self.tmpdir.name, - 'benzene', 'Equilibrium', 'water', 'MD_NPT', 'md.gro')) + os.path.join( + self.tmpdir.name, "benzene", "Equilibrium", "water", "MD_NPT", "md.gro" + ) + ) diff --git a/mdpow/tests/test_fep.py b/mdpow/tests/test_fep.py index 6bda9432..d9447ac3 100644 --- a/mdpow/tests/test_fep.py +++ b/mdpow/tests/test_fep.py @@ -10,46 +10,72 @@ import mdpow.config import mdpow.fep + def test_molar_to_nm3(): assert_almost_equal(mdpow.fep.molar_to_nm3(1.5), 0.9033212684) assert_almost_equal(mdpow.fep.molar_to_nm3(55.5), 33.42288693449999) + def test_bar_to_kJmolnm3(): assert_almost_equal(mdpow.fep.bar_to_kJmolnm3(1.0), 0.0602214179) + def test_kcal_to_kJ(): assert_almost_equal(mdpow.fep.kcal_to_kJ(10.0), 41.84) + def test_kJ_to_kcal(): assert_almost_equal(mdpow.fep.kJ_to_kcal(41.84), 10.0) + def test_kBT_to_kJ(): - ref = constants.N_A*constants.k*1e-3 + ref = constants.N_A * constants.k * 1e-3 assert_almost_equal(mdpow.fep.kBT_to_kJ(1, 1), ref) + class TestFEPschedule(object): reference = { - 'VDW': - {'couple_lambda0': 'vdw', - 'couple_lambda1': 'none', - 'description': 'decoupling vdw --> none', - 'label': 'VDW', - 'lambdas': np.array([ 0. , 0.05, 0.1 , 0.2 , 0.3 , 0.4 , 0.5 , 0.6 , 0.65, - 0.7 , 0.75, 0.8 , 0.85, 0.9 , 0.95, 1. ]), - 'name': 'vdw', - 'sc_alpha': 0.5, - 'sc_power': 1, - 'sc_sigma': 0.3}, - 'Coulomb': - {'couple_lambda0': 'vdw-q', - 'couple_lambda1': 'vdw', - 'description': 'dis-charging vdw+q --> vdw', - 'label': 'Coul', - 'lambdas': np.array([ 0. , 0.25, 0.5 , 0.75, 1. ]), - 'name': 'Coulomb', - 'sc_alpha': 0, - 'sc_power': 1, - 'sc_sigma': 0.3} + "VDW": { + "couple_lambda0": "vdw", + "couple_lambda1": "none", + "description": "decoupling vdw --> none", + "label": "VDW", + "lambdas": np.array( + [ + 0.0, + 0.05, + 0.1, + 0.2, + 0.3, + 0.4, + 0.5, + 0.6, + 0.65, + 0.7, + 0.75, + 0.8, + 0.85, + 0.9, + 0.95, + 1.0, + ] + ), + "name": "vdw", + "sc_alpha": 0.5, + "sc_power": 1, + "sc_sigma": 0.3, + }, + "Coulomb": { + "couple_lambda0": "vdw-q", + "couple_lambda1": "vdw", + "description": "dis-charging vdw+q --> vdw", + "label": "Coul", + "lambdas": np.array([0.0, 0.25, 0.5, 0.75, 1.0]), + "name": "Coulomb", + "sc_alpha": 0, + "sc_power": 1, + "sc_sigma": 0.3, + }, } @pytest.fixture @@ -58,14 +84,14 @@ def cfg(self): return mdpow.config.get_configuration() def test_VDW(self, cfg): - return self._test_schedule(cfg, 'VDW') + return self._test_schedule(cfg, "VDW") def test_Coulomb(self, cfg): - return self._test_schedule(cfg, 'Coulomb') + return self._test_schedule(cfg, "Coulomb") - @pytest.mark.parametrize('component', ['VDW', 'Coulomb']) + @pytest.mark.parametrize("component", ["VDW", "Coulomb"]) def test_copy(self, cfg, component): - section = 'FEP_schedule_{0}'.format(component) + section = "FEP_schedule_{0}".format(component) schedule = deepcopy(mdpow.fep.FEPschedule.load(cfg, section)) reference = self.reference[component] @@ -77,30 +103,39 @@ def test_copy(self, cfg, component): for k in schedule.keys(): if k == "lambdas": - assert_array_almost_equal(schedule[k], reference[k], - err_msg="FEP schedule {0} mismatch".format(k)) + assert_array_almost_equal( + schedule[k], + reference[k], + err_msg="FEP schedule {0} mismatch".format(k), + ) else: - assert schedule[k] == reference[k], \ - "mismatch between loaded FEP schedule entry {0} and reference".format(k) + assert ( + schedule[k] == reference[k] + ), "mismatch between loaded FEP schedule entry {0} and reference".format( + k + ) - @pytest.mark.parametrize('component', ['VDW', 'Coulomb']) + @pytest.mark.parametrize("component", ["VDW", "Coulomb"]) def test_write(self, cfg, component, tmp_path): filename = tmp_path / "cfg.yaml" cfg.write(filename) new_cfg = mdpow.config.get_configuration(filename) assert new_cfg.conf == cfg.conf - @pytest.mark.parametrize("x,ref", [ - ("test", False), - ([1, 1, 2, 3], True), - ({1, 2, 3}, True), - (None, False), - ]) + @pytest.mark.parametrize( + "x,ref", + [ + ("test", False), + ([1, 1, 2, 3], True), + ({1, 2, 3}, True), + (None, False), + ], + ) def test_iterable(self, x, ref): assert mdpow.config.iterable(x) == ref def _test_schedule(self, cfg, component): - section = 'FEP_schedule_{0}'.format(component) + section = "FEP_schedule_{0}".format(component) schedule = mdpow.fep.FEPschedule.load(cfg, section) reference = self.reference[component] @@ -112,20 +147,26 @@ def _test_schedule(self, cfg, component): for k in schedule.keys(): if k == "lambdas": - assert_array_almost_equal(schedule[k], reference[k], - err_msg="FEP schedule {0} mismatch".format(k)) + assert_array_almost_equal( + schedule[k], + reference[k], + err_msg="FEP schedule {0} mismatch".format(k), + ) else: - assert schedule[k] == reference[k], \ - "mismatch between loaded FEP schedule entry {0} and reference".format(k) + assert ( + schedule[k] == reference[k] + ), "mismatch between loaded FEP schedule entry {0} and reference".format( + k + ) def test_skip_empty_entries(self, cfg, section="FEP_schedule_Coulomb"): # remove some entries - del cfg.conf[section]['name'] # string - del cfg.conf[section]['lambdas'] # array + del cfg.conf[section]["name"] # string + del cfg.conf[section]["lambdas"] # array with pytest.warns(mdpow.config.NoOptionWarning): schedule = mdpow.fep.FEPschedule.load(cfg, section) - assert schedule['label'] == "Coul" - assert schedule['sc_power'] == 1 - assert 'name' not in schedule - assert 'lambdas' not in schedule + assert schedule["label"] == "Coul" + assert schedule["sc_power"] == 1 + assert "name" not in schedule + assert "lambdas" not in schedule diff --git a/mdpow/tests/test_fep_analysis.py b/mdpow/tests/test_fep_analysis.py index 8619e54e..e9bf3981 100644 --- a/mdpow/tests/test_fep_analysis.py +++ b/mdpow/tests/test_fep_analysis.py @@ -8,14 +8,16 @@ from . import STATES + @pytest.fixture def FEP_dir(tmpdir): - name = STATES['FEP'].basename # a py.path.local - fepdir = tmpdir.join(name) # a py.path.local - shutil.copytree(STATES['FEP'].strpath, fepdir.strpath) + name = STATES["FEP"].basename # a py.path.local + fepdir = tmpdir.join(name) # a py.path.local + shutil.copytree(STATES["FEP"].strpath, fepdir.strpath) assert os.path.isdir(fepdir.strpath) return fepdir + def setup_Ghyd(fepdir): basedir = fepdir.join("benzene") gsolv = basedir.join("FEP", "water", "Gsolv.fep") @@ -30,25 +32,31 @@ def setup_Ghyd(fepdir): def Ghyd(FEP_dir): return setup_Ghyd(FEP_dir) + @pytest.fixture def Ghyd_other(FEP_dir): return setup_Ghyd(FEP_dir) + def test_load_Ghyd(Ghyd): assert isinstance(Ghyd, mdpow.fep.Ghyd) -@pytest.mark.parametrize("kwargs", ( - {}, - {'SI': True, 'estimator': 'alchemlyb', 'method': 'TI'}, - {'SI': False, 'estimator': 'alchemlyb', 'method': 'MBAR', 'force': False}, - {'SI': False, 'estimator': 'mdpow', 'method': 'TI', 'force': True}, + +@pytest.mark.parametrize( + "kwargs", + ( + {}, + {"SI": True, "estimator": "alchemlyb", "method": "TI"}, + {"SI": False, "estimator": "alchemlyb", "method": "MBAR", "force": False}, + {"SI": False, "estimator": "mdpow", "method": "TI", "force": True}, ), - ids=["defaults", - "SI=True, estimator='alchemlyb', method='TI'", - "SI=False, estimator='alchemlyb', method='MBAR', force=False", - "SI=False, estimator='mdpow', method='TI', force=True", - ] - ) + ids=[ + "defaults", + "SI=True, estimator='alchemlyb', method='TI'", + "SI=False, estimator='alchemlyb', method='MBAR', force=False", + "SI=False, estimator='mdpow', method='TI', force=True", + ], +) def test_p_transfer(Ghyd, Ghyd_other, kwargs): """Test transfer water <-> water with same data.""" G1 = Ghyd @@ -59,13 +67,16 @@ def test_p_transfer(Ghyd, Ghyd_other, kwargs): assert transferFE == pytest.approx(0.0) assert logPow == pytest.approx(0.0) + def test_p_transfer_wrong_method(Ghyd, Ghyd_other): """Test transfer water <-> water with same data.""" G1 = Ghyd G2 = Ghyd_other - with pytest.raises(ValueError, - match="Method MBAR is not implemented in MDPOW, use estimator='alchemlyb'"): + with pytest.raises( + ValueError, + match="Method MBAR is not implemented in MDPOW, use estimator='alchemlyb'", + ): mdpow.fep.p_transfer(G1, G2, estimator="mdpow", method="MBAR") @@ -73,10 +84,12 @@ def test_pOW_error(Ghyd, Ghyd_other): with pytest.raises(ValueError): mdpow.fep.pOW(Ghyd, Ghyd_other) + def test_pCW_error(Ghyd, Ghyd_other): with pytest.raises(ValueError): mdpow.fep.pCW(Ghyd, Ghyd_other) + def test_pTW_error(Ghyd, Ghyd_other): with pytest.raises(ValueError): mdpow.fep.pTW(Ghyd, Ghyd_other) diff --git a/mdpow/tests/test_fep_script.py b/mdpow/tests/test_fep_script.py index f7e001f8..ff4c29b5 100644 --- a/mdpow/tests/test_fep_script.py +++ b/mdpow/tests/test_fep_script.py @@ -13,27 +13,30 @@ from . import RESOURCES + class TestFEPScript(object): def setup_method(self): self.tmpdir = td.TempDir() self.old_path = os.getcwd() self.resources = RESOURCES - self.m = pybol.Manifest(str(self.resources / 'manifest.yml')) - self.m.assemble('md_npt', self.tmpdir.name) + self.m = pybol.Manifest(str(self.resources / "manifest.yml")) + self.m.assemble("md_npt", self.tmpdir.name) - S = Simulation(filename=os.path.join( - self.tmpdir.name, 'benzene', 'water.simulation')) - S.make_paths_relative(prefix=os.path.join( - self.tmpdir.name,'benzene', 'Equilibrium', 'water')) - S.dirs.includes = os.path.join(self.tmpdir.name, 'top') + S = Simulation( + filename=os.path.join(self.tmpdir.name, "benzene", "water.simulation") + ) + S.make_paths_relative( + prefix=os.path.join(self.tmpdir.name, "benzene", "Equilibrium", "water") + ) + S.dirs.includes = os.path.join(self.tmpdir.name, "top") S.save() def teardown_method(self): self.tmpdir.dissolve() def _run_fep(self, solvent, dirname): - cfg = get_configuration('runinput.yml') - if gromacs.release.startswith('4'): + cfg = get_configuration("runinput.yml") + if gromacs.release.startswith("4"): # For GROMACS 4.6.5 explicitly enable the group neighbor # scheme by creating a copy of the MDP file in the current # directory with MDP cutoff-scheme option changed. The local @@ -41,15 +44,19 @@ def _run_fep(self, solvent, dirname): # in the templates. fep_mdp_name = cfg.get("FEP", "mdp") mdp = mdpow.config.get_template(fep_mdp_name) - gromacs.cbook.edit_mdp(mdp, - new_mdp=os.path.join(os.getcwd(), fep_mdp_name), - cutoff_scheme="group") - self.savefilename = fep_simulation(cfg, solvent, dirname=dirname, exit_on_error=False) + gromacs.cbook.edit_mdp( + mdp, + new_mdp=os.path.join(os.getcwd(), fep_mdp_name), + cutoff_scheme="group", + ) + self.savefilename = fep_simulation( + cfg, solvent, dirname=dirname, exit_on_error=False + ) def test_default_run(self, capsys): with gromacs.utilities.in_dir(self.tmpdir.name, create=False): try: - self._run_fep('water', 'benzene/') + self._run_fep("water", "benzene/") except Exception as err: # check if log file contains # 'There are 2 perturbed non-bonded pair interactions beyond the pair-list cutoff' @@ -58,12 +65,22 @@ def test_default_run(self, capsys): # internal problems.) captured = capsys.readouterr() for line in captured: - if "perturbed non-bonded pair interactions beyond the pair-list cutoff'" in line: - pytest.xfail("Stochastic test failure (perturbed non-bonded beyond cutoff). " - "Still works as expected, see #175.") + if ( + "perturbed non-bonded pair interactions beyond the pair-list cutoff'" + in line + ): + pytest.xfail( + "Stochastic test failure (perturbed non-bonded beyond cutoff). " + "Still works as expected, see #175." + ) break else: - raise AssertionError('FEP simulations failed with exception:\n{0}'.format(str(err))) + raise AssertionError( + "FEP simulations failed with exception:\n{0}".format(str(err)) + ) - assert os.path.exists(os.path.join(self.tmpdir.name, - 'benzene', 'FEP', 'water', 'VDW', '0000', 'md.edr')) + assert os.path.exists( + os.path.join( + self.tmpdir.name, "benzene", "FEP", "water", "VDW", "0000", "md.edr" + ) + ) diff --git a/mdpow/tests/test_filelock.py b/mdpow/tests/test_filelock.py index 1cbed583..a337cdae 100644 --- a/mdpow/tests/test_filelock.py +++ b/mdpow/tests/test_filelock.py @@ -4,6 +4,7 @@ from mdpow import filelock + def test_FileLock_acquire(tmpdir, filename="test.txt"): with tmpdir.as_cwd(): with filelock.FileLock(filename, timeout=2) as lock: @@ -11,6 +12,7 @@ def test_FileLock_acquire(tmpdir, filename="test.txt"): f.write("Humpty Dumpty sat on a wall") assert os.path.exists(filename) + def test_FileLock_lock(filename="test.txt"): with filelock.FileLock(filename, timeout=2) as lock: with pytest.raises(filelock.FileLockException): diff --git a/mdpow/tests/test_forcefields.py b/mdpow/tests/test_forcefields.py index 5e95be83..bc5c3112 100644 --- a/mdpow/tests/test_forcefields.py +++ b/mdpow/tests/test_forcefields.py @@ -6,8 +6,9 @@ import mdpow.forcefields # currently supported -WATERMODELS = ('tip4p', 'tip3p', 'tip5p', 'spc', 'spce', 'm24', 'tip4pd') -SOLVENTMODELS = ('water', 'cyclohexane', 'octanol', 'toluene') +WATERMODELS = ("tip4p", "tip3p", "tip5p", "spc", "spce", "m24", "tip4pd") +SOLVENTMODELS = ("water", "cyclohexane", "octanol", "toluene") + class TestIncludedForcefiels(object): @staticmethod @@ -18,35 +19,40 @@ def test_default_forcefield(): def test_oplsaa_itp(): assert "ffoplsaa.itp" in mdpow.config.topfiles assert mdpow.config.topfiles["ffoplsaa.itp"].endswith( - os.path.join('mdpow', 'top', 'ffoplsaa.itp')) + os.path.join("mdpow", "top", "ffoplsaa.itp") + ) @staticmethod def test_oplsaa_ff(): assert "oplsaa.ff" in mdpow.config.topfiles assert mdpow.config.topfiles["oplsaa.ff"].endswith( - os.path.join('mdpow', 'top', 'oplsaa.ff')) + os.path.join("mdpow", "top", "oplsaa.ff") + ) + class TestIncludedSolvents(object): solvents = { - 'tip4p': { - 'tip4p.itp': os.path.join('mdpow', 'top', 'oplsaa.ff', 'tip4p.itp'), - 'tip4p.gro': os.path.join('mdpow', 'top', 'tip4p.gro') + "tip4p": { + "tip4p.itp": os.path.join("mdpow", "top", "oplsaa.ff", "tip4p.itp"), + "tip4p.gro": os.path.join("mdpow", "top", "tip4p.gro"), }, - 'octanol': { - '1oct.gro': os.path.join('mdpow', 'top', '1oct.gro'), - '1oct.itp': os.path.join('mdpow', 'top', 'oplsaa.ff', '1oct.itp'), + "octanol": { + "1oct.gro": os.path.join("mdpow", "top", "1oct.gro"), + "1oct.itp": os.path.join("mdpow", "top", "oplsaa.ff", "1oct.itp"), }, - 'cyclohexane': { - '1cyclo.gro': os.path.join('mdpow', 'top', '1cyclo.gro'), - '1cyclo.itp': os.path.join('mdpow', 'top', 'oplsaa.ff', '1cyclo.itp') + "cyclohexane": { + "1cyclo.gro": os.path.join("mdpow", "top", "1cyclo.gro"), + "1cyclo.itp": os.path.join("mdpow", "top", "oplsaa.ff", "1cyclo.itp"), }, - 'toluene': { - '1tol_oplsaa.gro': os.path.join('mdpow', 'top', '1tol_oplsaa.gro'), - '1tol.itp': os.path.join('mdpow', 'top', 'oplsaa.ff', '1tol.itp') + "toluene": { + "1tol_oplsaa.gro": os.path.join("mdpow", "top", "1tol_oplsaa.gro"), + "1tol.itp": os.path.join("mdpow", "top", "oplsaa.ff", "1tol.itp"), }, } - @pytest.mark.parametrize("solvent_name", ["tip4p", "octanol", "cyclohexane", "toluene"]) + @pytest.mark.parametrize( + "solvent_name", ["tip4p", "octanol", "cyclohexane", "toluene"] + ) def test_solvent(self, solvent_name): solvent = self.solvents[solvent_name] for filename, path in solvent.items(): @@ -60,12 +66,14 @@ def test_default_water_model(): assert mdpow.forcefields.DEFAULT_WATER_MODEL == "tip4p" def test_watermodelsdat(self): - included_watermodels = open(mdpow.config.topfiles['watermodels.dat']).read() - for line, ref in zip(self._simple_line_parser(mdpow.forcefields.GMX_WATERMODELS_DAT), - self._simple_line_parser(included_watermodels)): + included_watermodels = open(mdpow.config.topfiles["watermodels.dat"]).read() + for line, ref in zip( + self._simple_line_parser(mdpow.forcefields.GMX_WATERMODELS_DAT), + self._simple_line_parser(included_watermodels), + ): assert line.strip() == ref.strip() - @pytest.mark.parametrize('identifier', WATERMODELS) + @pytest.mark.parametrize("identifier", WATERMODELS) def test_gromacs_water_models(self, identifier): models = mdpow.forcefields.GROMACS_WATER_MODELS @@ -75,33 +83,37 @@ def test_gromacs_water_models(self, identifier): assert model.itp in mdpow.config.topfiles assert model.coordinates in mdpow.config.topfiles - @staticmethod def _simple_line_parser(string): - for line in string.split('\n'): + for line in string.split("\n"): line = line.strip() - if not line or line.startswith('#'): + if not line or line.startswith("#"): continue yield line @staticmethod def test_get_water_model(): model = mdpow.forcefields.DEFAULT_WATER_MODEL - assert (mdpow.forcefields.get_water_model(model) is - mdpow.forcefields.GROMACS_WATER_MODELS[model]) + assert ( + mdpow.forcefields.get_water_model(model) + is mdpow.forcefields.GROMACS_WATER_MODELS[model] + ) @staticmethod def test_get_water_model_ValueError(): with pytest.raises(ValueError): mdpow.forcefields.get_water_model("The Jabberwock is an imaginary beast.") + class TestSolventModels(object): @staticmethod def test_get_solvent_default_water(): model = "water" defaultmodel = mdpow.forcefields.DEFAULT_WATER_MODEL - assert (mdpow.forcefields.get_solvent_model(model) is - mdpow.forcefields.GROMACS_WATER_MODELS[defaultmodel]) + assert ( + mdpow.forcefields.get_solvent_model(model) + is mdpow.forcefields.GROMACS_WATER_MODELS[defaultmodel] + ) @staticmethod def test_get_solvent_model_ValueError(): @@ -110,46 +122,57 @@ def test_get_solvent_model_ValueError(): @staticmethod def test_get_solvent_cyclohexane(): - model = 'cyclohexane' - forcefield = 'OPLS-AA' - assert (mdpow.forcefields.get_solvent_model(model) is - mdpow.forcefields.GROMACS_SOLVENT_MODELS[forcefield][model]) - - @pytest.mark.parametrize("forcefield", ['OPLS-AA', 'CHARMM', 'AMBER']) + model = "cyclohexane" + forcefield = "OPLS-AA" + assert ( + mdpow.forcefields.get_solvent_model(model) + is mdpow.forcefields.GROMACS_SOLVENT_MODELS[forcefield][model] + ) + + @pytest.mark.parametrize("forcefield", ["OPLS-AA", "CHARMM", "AMBER"]) def test_get_solvent_octanol(self, forcefield): - model = 'octanol' - assert (mdpow.forcefields.get_solvent_model(model, forcefield=forcefield) is - mdpow.forcefields.GROMACS_SOLVENT_MODELS[forcefield][model]) + model = "octanol" + assert ( + mdpow.forcefields.get_solvent_model(model, forcefield=forcefield) + is mdpow.forcefields.GROMACS_SOLVENT_MODELS[forcefield][model] + ) - @pytest.mark.parametrize("forcefield", ['OPLS-AA', 'CHARMM', 'AMBER']) + @pytest.mark.parametrize("forcefield", ["OPLS-AA", "CHARMM", "AMBER"]) def test_get_solvent_wetoctanol(self, forcefield): - model = 'wetoctanol' - assert (mdpow.forcefields.get_solvent_model(model, forcefield=forcefield) is - mdpow.forcefields.GROMACS_SOLVENT_MODELS[forcefield][model]) + model = "wetoctanol" + assert ( + mdpow.forcefields.get_solvent_model(model, forcefield=forcefield) + is mdpow.forcefields.GROMACS_SOLVENT_MODELS[forcefield][model] + ) - @pytest.mark.parametrize("forcefield", ['OPLS-AA', 'CHARMM', 'AMBER']) + @pytest.mark.parametrize("forcefield", ["OPLS-AA", "CHARMM", "AMBER"]) def test_get_solvent_toluene(self, forcefield): - model = 'toluene' - assert (mdpow.forcefields.get_solvent_model(model, forcefield=forcefield) is - mdpow.forcefields.GROMACS_SOLVENT_MODELS[forcefield][model]) + model = "toluene" + assert ( + mdpow.forcefields.get_solvent_model(model, forcefield=forcefield) + is mdpow.forcefields.GROMACS_SOLVENT_MODELS[forcefield][model] + ) @staticmethod def test_get_solvent_identifier_default_is_water(): - assert (mdpow.forcefields.get_solvent_identifier('water') is - mdpow.forcefields.DEFAULT_WATER_MODEL) + assert ( + mdpow.forcefields.get_solvent_identifier("water") + is mdpow.forcefields.DEFAULT_WATER_MODEL + ) @pytest.mark.parametrize("model", WATERMODELS) def test_get_solvent_identifier_water(self, model): - assert mdpow.forcefields.get_solvent_identifier('water', model=model) is model + assert mdpow.forcefields.get_solvent_identifier("water", model=model) is model - @pytest.mark.parametrize('solvent', - [model for model in SOLVENTMODELS if model != "water"]) - @pytest.mark.parametrize('model', [None, "Jabberwock model"]) + @pytest.mark.parametrize( + "solvent", [model for model in SOLVENTMODELS if model != "water"] + ) + @pytest.mark.parametrize("model", [None, "Jabberwock model"]) def test_get_solvent_identifier_solvents(self, solvent, model): # The model="Jabberwock model" checks that "model" is properly ignored. assert mdpow.forcefields.get_solvent_identifier(solvent, model=model) is solvent @staticmethod def test_get_solvent_identifier_None(): - assert mdpow.forcefields.get_solvent_identifier('water', model="foobar") is None - assert mdpow.forcefields.get_solvent_identifier('benzene') is None + assert mdpow.forcefields.get_solvent_identifier("water", model="foobar") is None + assert mdpow.forcefields.get_solvent_identifier("benzene") is None diff --git a/mdpow/tests/test_run.py b/mdpow/tests/test_run.py index 8c97d0d4..d774d31b 100644 --- a/mdpow/tests/test_run.py +++ b/mdpow/tests/test_run.py @@ -16,29 +16,33 @@ def cfg(): return mdpow.config.get_configuration() -@pytest.mark.parametrize("protocols", [["energy_minimize"], - ["MD_relaxed"], - ["MD_NPT", "FEP"], - ]) +@pytest.mark.parametrize( + "protocols", + [ + ["energy_minimize"], + ["MD_relaxed"], + ["MD_NPT", "FEP"], + ], +) def test_get_mdp_files(cfg, protocols): mdpfiles = mdpow.run.get_mdp_files(cfg, protocols) assert len(mdpfiles) == len(protocols) assert set(mdpfiles.keys()) == set(protocols) assert all([mdp.endswith(".mdp") for mdp in mdpfiles.values()]) -@pytest.mark.parametrize("protocols", [["FEP"], - ["Jabberwocky", "Mad Hatter"] - ]) + +@pytest.mark.parametrize("protocols", [["FEP"], ["Jabberwocky", "Mad Hatter"]]) def test_get_mdp_files_None(cfg, protocols): # modify cfg - del cfg.conf['FEP']['mdp'] + del cfg.conf["FEP"]["mdp"] with pytest.warns(mdpow.config.NoOptionWarning): mdpfiles = mdpow.run.get_mdp_files(cfg, ["FEP"]) assert mdpfiles == {} + def test_get_mdp_files_ValueError(cfg): # modify cfg with a non-existant file - cfg.conf['FEP']['mdp'] = "smoke_and_mirror.mdp" + cfg.conf["FEP"]["mdp"] = "smoke_and_mirror.mdp" with pytest.raises(ValueError): mdpow.run.get_mdp_files(cfg, ["MD_NPT", "FEP"]) @@ -47,12 +51,15 @@ def test_get_mdp_files_ValueError(cfg): # and methods that would return failures, so that we don't have to # actually run simulations. + @pytest.fixture def MDrunner_failure(monkeypatch): # mock gromacs.run.MDrunner: pretend that the simulation failed def mock_run_check(*args, **kwargs): return False - monkeypatch.setattr(gromacs.run.MDrunner, 'run_check', mock_run_check) + + monkeypatch.setattr(gromacs.run.MDrunner, "run_check", mock_run_check) + # mock gromacs.run.check_mdrun_success(logfile) @pytest.fixture @@ -60,7 +67,9 @@ def check_mdrun_success_failure(monkeypatch): # pretend simulation has not completed as indicated by log file def mock_check_mdrun_success(arg): return False - monkeypatch.setattr(gromacs.run, 'check_mdrun_success', mock_check_mdrun_success) + + monkeypatch.setattr(gromacs.run, "check_mdrun_success", mock_check_mdrun_success) + @pytest.fixture def check_mdrun_success_none(monkeypatch): @@ -68,54 +77,71 @@ def check_mdrun_success_none(monkeypatch): # check and check_mdrun_success() returns None def mock_check_mdrun_success(arg): return None - monkeypatch.setattr(gromacs.run, 'check_mdrun_success', mock_check_mdrun_success) - -@pytest.mark.parametrize("runlocal,exception", - [(True, gromacs.exceptions.GromacsError), - (False, gromacs.exceptions.MissingDataError)]) -def test_runMD_or_exit_exceptions(runlocal, exception, cfg, MDrunner_failure, check_mdrun_success_failure, - monkeypatch, tmpdir): - params = {'deffnm': 'md'} + monkeypatch.setattr(gromacs.run, "check_mdrun_success", mock_check_mdrun_success) + + +@pytest.mark.parametrize( + "runlocal,exception", + [ + (True, gromacs.exceptions.GromacsError), + (False, gromacs.exceptions.MissingDataError), + ], +) +def test_runMD_or_exit_exceptions( + runlocal, + exception, + cfg, + MDrunner_failure, + check_mdrun_success_failure, + monkeypatch, + tmpdir, +): + params = {"deffnm": "md"} S = {} def mock_getboolean(*args): return runlocal + monkeypatch.setattr(cfg, "getboolean", mock_getboolean) with pytest.raises(exception): - mdpow.run.runMD_or_exit(S, "FEP", params, cfg, - dirname=str(tmpdir), - exit_on_error=False) + mdpow.run.runMD_or_exit( + S, "FEP", params, cfg, dirname=str(tmpdir), exit_on_error=False + ) + def test_runMD_or_exit_None(cfg, check_mdrun_success_none, monkeypatch, tmpdir): # special case where runlocal=False and no simulation has been run # so there's no logfile to check and check_mdrun_success() returns # None - params = {'deffnm': 'md'} + params = {"deffnm": "md"} S = {} def mock_getboolean(*args): return False + monkeypatch.setattr(cfg, "getboolean", mock_getboolean) - return_value = mdpow.run.runMD_or_exit(S, "FEP", params, cfg, - dirname=str(tmpdir), - exit_on_error=False) + return_value = mdpow.run.runMD_or_exit( + S, "FEP", params, cfg, dirname=str(tmpdir), exit_on_error=False + ) assert return_value is None @pytest.mark.parametrize("runlocal", [True, False]) -def test_runMD_or_exit_SysExit(runlocal, cfg, MDrunner_failure, check_mdrun_success_failure, - monkeypatch, tmpdir): - params = {'deffnm': 'md'} +def test_runMD_or_exit_SysExit( + runlocal, cfg, MDrunner_failure, check_mdrun_success_failure, monkeypatch, tmpdir +): + params = {"deffnm": "md"} S = {} def mock_getboolean(*args): return runlocal + monkeypatch.setattr(cfg, "getboolean", mock_getboolean) with pytest.raises(SystemExit): - mdpow.run.runMD_or_exit(S, "FEP", params, cfg, - dirname=str(tmpdir), - exit_on_error=True) + mdpow.run.runMD_or_exit( + S, "FEP", params, cfg, dirname=str(tmpdir), exit_on_error=True + ) diff --git a/mdpow/tests/test_runinput.py b/mdpow/tests/test_runinput.py index dc416279..cbf4db9e 100644 --- a/mdpow/tests/test_runinput.py +++ b/mdpow/tests/test_runinput.py @@ -7,98 +7,85 @@ from mdpow import config + class TestAlteredConfig(object): params_altered = { - 'DEFAULT': - { - 'qscripts':'custom.sh' - }, - 'setup': - { - 'name': 'custom_name', - 'molecule': 'some_molecule_ident', - 'itp': 'some_molecules_itp', - 'structure': 'some_molecules_structure', - 'watermodel': 'spce', - 'maxwarn': 2, - 'distance': None, # default (not in this input file) - 'boxtype': 'dodecahedron', # default (not in this input file) - 'gromacsoutput': True, - }, - 'energy_minimize': - { - 'mdp': 'custom_emin.mdp' - }, - 'MD_relaxed': - { - 'qscript': 'MD_relaxed.sge', - 'runtime': 10, - 'runlocal': False, - 'mdp': 'MD_relaxed_NPT_opls.mdp' - }, - 'MD_NPT': - { - 'qscript': 'MD_NPT.sge', - 'runtime': 10000, - 'runlocal': True, - 'mdp': 'MD_NPT_opls.mdp', - }, - 'FEP': - { - 'method': 'TI', - 'qscript': 'FEP.sge', - 'runtime': 1000, - 'runlocal': True, - 'maxwarn': 3, - 'mdp': 'fep_custom_opls.mdp' - }, - 'FEP_schedule_Coulomb': - { - 'name': 'Coul', - 'description': 'transition_1', - 'label': 'coulomb', - 'couple_lambda0': 'vdw', - 'couple_lambda1': 'vdw-q', - 'sc_alpha': 0.2, - 'sc_power': 2, - 'sc_sigma': 0.6, - 'lambdas': np.array([ 0 , 0.1 , 0.2 , 0.3 , 0.4 , 0.5 , 0.6 , 0.7 , 0.8 , 0.9 , 1. ]) - }, - 'FEP_schedule_VDW': - { - 'name': 'VANDERWAALS', - 'description': 'transition_2', - 'label': 'vanderwaals', - 'couple_lambda0': 'none', - 'couple_lambda1': 'vdw', - 'sc_alpha': 0, - 'sc_power': 3, - 'sc_sigma': 0.1, - 'lambdas': np.array([ 0.0 , 0.25 , 0.50 , 0.75 , 1 ]) - }, - 'mdrun': - { - 'stepout': 12000, - 'verbose': False, - 'nice': 12, - 'maxthreads': 1 - } + "DEFAULT": {"qscripts": "custom.sh"}, + "setup": { + "name": "custom_name", + "molecule": "some_molecule_ident", + "itp": "some_molecules_itp", + "structure": "some_molecules_structure", + "watermodel": "spce", + "maxwarn": 2, + "distance": None, # default (not in this input file) + "boxtype": "dodecahedron", # default (not in this input file) + "gromacsoutput": True, + }, + "energy_minimize": {"mdp": "custom_emin.mdp"}, + "MD_relaxed": { + "qscript": "MD_relaxed.sge", + "runtime": 10, + "runlocal": False, + "mdp": "MD_relaxed_NPT_opls.mdp", + }, + "MD_NPT": { + "qscript": "MD_NPT.sge", + "runtime": 10000, + "runlocal": True, + "mdp": "MD_NPT_opls.mdp", + }, + "FEP": { + "method": "TI", + "qscript": "FEP.sge", + "runtime": 1000, + "runlocal": True, + "maxwarn": 3, + "mdp": "fep_custom_opls.mdp", + }, + "FEP_schedule_Coulomb": { + "name": "Coul", + "description": "transition_1", + "label": "coulomb", + "couple_lambda0": "vdw", + "couple_lambda1": "vdw-q", + "sc_alpha": 0.2, + "sc_power": 2, + "sc_sigma": 0.6, + "lambdas": np.array([0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]), + }, + "FEP_schedule_VDW": { + "name": "VANDERWAALS", + "description": "transition_2", + "label": "vanderwaals", + "couple_lambda0": "none", + "couple_lambda1": "vdw", + "sc_alpha": 0, + "sc_power": 3, + "sc_sigma": 0.1, + "lambdas": np.array([0.0, 0.25, 0.50, 0.75, 1]), + }, + "mdrun": {"stepout": 12000, "verbose": False, "nice": 12, "maxthreads": 1}, } @pytest.fixture def cfg(self): - return config.get_configuration(str(CONFIGURATIONS / 'altered_runinput.yml')) + return config.get_configuration(str(CONFIGURATIONS / "altered_runinput.yml")) def _test_section(self, cfg, section): section_dict = self.params_altered[section] for k in section_dict.keys(): - if k == 'lambdas': - parsed = np.array([float(x.strip()) for x in cfg.get(section,k).split(",")]) - assert_array_almost_equal(parsed, section_dict[k], - err_msg="mismatch in lambdas") + if k == "lambdas": + parsed = np.array( + [float(x.strip()) for x in cfg.get(section, k).split(",")] + ) + assert_array_almost_equal( + parsed, section_dict[k], err_msg="mismatch in lambdas" + ) else: - assert cfg.get(section,k) == section_dict[k], \ - "mismatch in {}:{}".format(section,k) + assert ( + cfg.get(section, k) == section_dict[k] + ), "mismatch in {}:{}".format(section, k) def test_DEFAULT(self, cfg): return self._test_section(cfg, "DEFAULT") diff --git a/mdpow/tests/test_solv_shell.py b/mdpow/tests/test_solv_shell.py index ac79ef13..0f020c98 100644 --- a/mdpow/tests/test_solv_shell.py +++ b/mdpow/tests/test_solv_shell.py @@ -18,40 +18,47 @@ from . import RESOURCES, MANIFEST + class TestSolvShell(object): def setup_method(self): self.tmpdir = td.TempDir() - self.m = pybol.Manifest(str(RESOURCES / 'manifest.yml')) - self.m.assemble('example_FEP', self.tmpdir.name) - self.ens = Ensemble(dirname=self.tmpdir.name, solvents=['water']) - self.solute = self.ens.select_atoms('not resname SOL') - self.solvent = self.ens.select_atoms('resname SOL and name OW') + self.m = pybol.Manifest(str(RESOURCES / "manifest.yml")) + self.m.assemble("example_FEP", self.tmpdir.name) + self.ens = Ensemble(dirname=self.tmpdir.name, solvents=["water"]) + self.solute = self.ens.select_atoms("not resname SOL") + self.solvent = self.ens.select_atoms("resname SOL and name OW") def teardown_method(self): self.tmpdir.dissolve() def test_dataframe(self): - solv = SolvationAnalysis(self.solute, self.solvent, [1.2]).run(start=0, stop=4, step=1) + solv = SolvationAnalysis(self.solute, self.solvent, [1.2]).run( + start=0, stop=4, step=1 + ) assert isinstance(solv.results, pd.DataFrame) - for d in solv.results['distance']: + for d in solv.results["distance"]: assert d == 1.2 - for s in solv.results['solvent']: - assert s == 'water' - for i in solv.results['interaction'][:12]: - assert i == 'Coulomb' + for s in solv.results["solvent"]: + assert s == "water" + for i in solv.results["interaction"][:12]: + assert i == "Coulomb" - @pytest.fixture(scope='class') + @pytest.fixture(scope="class") def solvation_analysis_list_results(self): self.setup_method() # Won't have solute and solvent without this - return SolvationAnalysis(self.solute, self.solvent, [2, 10]).run(start=0, stop=4, step=1) + return SolvationAnalysis(self.solute, self.solvent, [2, 10]).run( + start=0, stop=4, step=1 + ) - @pytest.mark.parametrize("d,ref_mean,ref_std", [(2, 1.10714285,2.07604166), - (10, 5306.89285714, 129.16720594)]) + @pytest.mark.parametrize( + "d,ref_mean,ref_std", + [(2, 1.10714285, 2.07604166), (10, 5306.89285714, 129.16720594)], + ) def test_selection(self, solvation_analysis_list_results, d, ref_mean, ref_std): results = solvation_analysis_list_results.results - mean = np.mean(results.loc[results['distance'] == d]['N_solvent']) - std = np.std(results.loc[results['distance'] == d]['N_solvent']) + mean = np.mean(results.loc[results["distance"] == d]["N_solvent"]) + std = np.std(results.loc[results["distance"] == d]["N_solvent"]) assert mean == pytest.approx(ref_mean) assert std == pytest.approx(ref_std) diff --git a/mdpow/tests/test_solvation.py b/mdpow/tests/test_solvation.py index d1d0c9e4..d2d75404 100644 --- a/mdpow/tests/test_solvation.py +++ b/mdpow/tests/test_solvation.py @@ -10,58 +10,67 @@ from . import RESOURCES -sims = {"water" : equil.WaterSimulation, - "octanol" : equil.OctanolSimulation, - "cyclohexane" : equil.CyclohexaneSimulation, - "wetoctanol" : equil.WetOctanolSimulation, - "toluene": equil.TolueneSimulation, - } - -test_file = {"OPLS-AA": 'benzene.itp', - "CHARMM": 'benzene_charmm.itp', - "AMBER": 'benzene_amber.itp', - } +sims = { + "water": equil.WaterSimulation, + "octanol": equil.OctanolSimulation, + "cyclohexane": equil.CyclohexaneSimulation, + "wetoctanol": equil.WetOctanolSimulation, + "toluene": equil.TolueneSimulation, +} + +test_file = { + "OPLS-AA": "benzene.itp", + "CHARMM": "benzene_charmm.itp", + "AMBER": "benzene_amber.itp", +} + @pytest.fixture def setup(tmpdir): - newdir = tmpdir.mkdir('resources') - files = ['benzene.pdb', 'benzene.itp', - 'benzene_charmm.itp', 'benzene_amber.itp'] + newdir = tmpdir.mkdir("resources") + files = ["benzene.pdb", "benzene.itp", "benzene_charmm.itp", "benzene_amber.itp"] for f in files: - orig = RESOURCES / 'molecules' / 'benzene' / f + orig = RESOURCES / "molecules" / "benzene" / f shutil.copy(orig, newdir.dirname) return newdir.dirname -def solvation(setup, solvent, ff='OPLS-AA'): + +def solvation(setup, solvent, ff="OPLS-AA"): itp = test_file[ff] with in_dir(setup, create=False): try: - S = sims[solvent](molecule='BNZ', forcefield=ff) + S = sims[solvent](molecule="BNZ", forcefield=ff) S.topology(itp=itp) - S.solvate(struct='benzene.pdb') + S.solvate(struct="benzene.pdb") except Exception: - raise AssertionError('Solvation failed.') + raise AssertionError("Solvation failed.") + -@pytest.mark.parametrize("ff", ['OPLS-AA', 'CHARMM', 'AMBER']) +@pytest.mark.parametrize("ff", ["OPLS-AA", "CHARMM", "AMBER"]) def test_solvation_water(setup, ff): solvation(setup, "water", ff) -@pytest.mark.parametrize("ff", ['OPLS-AA', 'CHARMM', 'AMBER']) + +@pytest.mark.parametrize("ff", ["OPLS-AA", "CHARMM", "AMBER"]) def test_solvation_octanol(setup, ff): solvation(setup, "octanol", ff) + def test_solvation_cyclohexane(setup): solvation(setup, "cyclohexane") -@pytest.mark.parametrize("ff", ['OPLS-AA', 'AMBER']) + +@pytest.mark.parametrize("ff", ["OPLS-AA", "AMBER"]) def test_solvation_toluene(setup, ff): solvation(setup, "toluene", ff) -@pytest.mark.xfail(gromacs.release.startswith('4') - or gromacs.release.startswith('5') - or gromacs.release.startswith('2016'), - reason="GROMACS < 2018 cannot easily work with mixed solvents " - "(see issue #111)") -@pytest.mark.parametrize("ff", ['OPLS-AA', 'CHARMM', 'AMBER']) + +@pytest.mark.xfail( + gromacs.release.startswith("4") + or gromacs.release.startswith("5") + or gromacs.release.startswith("2016"), + reason="GROMACS < 2018 cannot easily work with mixed solvents " "(see issue #111)", +) +@pytest.mark.parametrize("ff", ["OPLS-AA", "CHARMM", "AMBER"]) def test_solvation_wetoctanol(setup, ff): solvation(setup, "wetoctanol", ff) diff --git a/mdpow/tests/test_version.py b/mdpow/tests/test_version.py index 187f27d4..28968abd 100644 --- a/mdpow/tests/test_version.py +++ b/mdpow/tests/test_version.py @@ -2,16 +2,17 @@ import mdpow + @pytest.fixture(scope="module") def version(): return mdpow.__version__ + def test_version_string(version): assert isinstance(version, str) + def test_version(version): # generic non-empty check because versioneer can provide different # answers depending on VCS status assert version - - diff --git a/mdpow/tests/test_workflows_base.py b/mdpow/tests/test_workflows_base.py index 665e58d3..d46e1080 100644 --- a/mdpow/tests/test_workflows_base.py +++ b/mdpow/tests/test_workflows_base.py @@ -16,10 +16,11 @@ from pkg_resources import resource_filename from mdpow.workflows import base + @pytest.fixture def molname_workflows_directory(tmp_path): m = pybol.Manifest(str(MANIFEST)) - m.assemble('workflows', tmp_path) + m.assemble("workflows", tmp_path) return tmp_path @@ -32,30 +33,38 @@ def universe(request): u.add_TopologyAttr("masses", masses) return u -@pytest.mark.parametrize("universe,elements", - [ - [ - (np.array([12.011, 14.007, 0, 12.011, 35.45, 12.011]), - np.array(["C", "Nx", "DUMMY", "C0S", "Cl123", "C0U"])), - np.array(['C', 'N', 'DUMMY', 'C', 'CL', 'C']) - ], - [ - (np.array([12.011, 14.007, 0, 35.45]), - np.array(["C", "Nx", "DUMMY", "Cl123"])), - np.array(['C', 'N', 'DUMMY', 'CL']) - ], - [ - (np.array([15.999, 0, 40.08, 40.08, 40.08, 24.305, 132.9]), - np.array(["OW", "MW", "C0", "CAL", "CA2+", "MG2+", "CES"])), - np.array(['O', 'DUMMY', 'CA', 'CA', 'CA', 'MG', 'CS']) - ], - [ - (np.array([16, 1e-6, 40.085, 133]), - np.array(["OW", "MW", "CA2+", "CES"])), - np.array(['O', 'DUMMY', 'CA', 'CS']) - ], - ], - indirect=["universe"]) + +@pytest.mark.parametrize( + "universe,elements", + [ + [ + ( + np.array([12.011, 14.007, 0, 12.011, 35.45, 12.011]), + np.array(["C", "Nx", "DUMMY", "C0S", "Cl123", "C0U"]), + ), + np.array(["C", "N", "DUMMY", "C", "CL", "C"]), + ], + [ + ( + np.array([12.011, 14.007, 0, 35.45]), + np.array(["C", "Nx", "DUMMY", "Cl123"]), + ), + np.array(["C", "N", "DUMMY", "CL"]), + ], + [ + ( + np.array([15.999, 0, 40.08, 40.08, 40.08, 24.305, 132.9]), + np.array(["OW", "MW", "C0", "CAL", "CA2+", "MG2+", "CES"]), + ), + np.array(["O", "DUMMY", "CA", "CA", "CA", "MG", "CS"]), + ], + [ + (np.array([16, 1e-6, 40.085, 133]), np.array(["OW", "MW", "CA2+", "CES"])), + np.array(["O", "DUMMY", "CA", "CS"]), + ], + ], + indirect=["universe"], +) def test_guess_elements(universe, elements): u = universe guessed_elements = base.guess_elements(u.atoms) @@ -63,7 +72,6 @@ def test_guess_elements(universe, elements): assert_equal(guessed_elements, elements) - class TestWorkflowsBase(object): @pytest.fixture def SM_tmp_dir(self, molname_workflows_directory): @@ -72,14 +80,13 @@ def SM_tmp_dir(self, molname_workflows_directory): @pytest.fixture def csv_input_data(self): - csv_path = STATES['workflows'] / 'project_paths.csv' + csv_path = STATES["workflows"] / "project_paths.csv" csv_df = pd.read_csv(csv_path).reset_index(drop=True) return csv_path, csv_df @pytest.fixture def test_df_data(self): - test_dict = {'molecule' : ['SM25', 'SM26'], - 'resname' : ['SM25', 'SM26']} + test_dict = {"molecule": ["SM25", "SM26"], "resname": ["SM25", "SM26"]} test_df = pd.DataFrame(test_dict).reset_index(drop=True) return test_df @@ -92,10 +99,10 @@ def test_project_paths(self, test_df_data, project_paths_data): test_df = test_df_data project_paths = project_paths_data - assert project_paths['molecule'][0] == test_df['molecule'][0] - assert project_paths['molecule'][1] == test_df['molecule'][1] - assert project_paths['resname'][0] == test_df['resname'][0] - assert project_paths['resname'][1] == test_df['resname'][1] + assert project_paths["molecule"][0] == test_df["molecule"][0] + assert project_paths["molecule"][1] == test_df["molecule"][1] + assert project_paths["resname"][0] == test_df["resname"][0] + assert project_paths["resname"][1] == test_df["resname"][1] def test_project_paths_csv_input(self, csv_input_data): csv_path, csv_df = csv_input_data @@ -105,39 +112,51 @@ def test_project_paths_csv_input(self, csv_input_data): def test_dihedral_analysis_figdir_requirement(self, project_paths_data, caplog): caplog.clear() - caplog.set_level(logging.ERROR, logger='mdpow.workflows.base') + caplog.set_level(logging.ERROR, logger="mdpow.workflows.base") project_paths = project_paths_data # change resname to match topology (every SAMPL7 resname is 'UNK') # only necessary for this dataset, not necessary for normal use - project_paths['resname'] = 'UNK' - - with pytest.raises(AssertionError, - match="figdir MUST be set, even though it is a kwarg. Will be changed with #244"): + project_paths["resname"] = "UNK" - base.automated_project_analysis(project_paths, solvents=('water',), - ensemble_analysis='DihedralAnalysis') + with pytest.raises( + AssertionError, + match="figdir MUST be set, even though it is a kwarg. Will be changed with #244", + ): + base.automated_project_analysis( + project_paths, solvents=("water",), ensemble_analysis="DihedralAnalysis" + ) - assert 'all analyses completed' in caplog.text, ('automated_dihedral_analysis ' - 'did not iteratively run to completion for the provided project') + assert "all analyses completed" in caplog.text, ( + "automated_dihedral_analysis " + "did not iteratively run to completion for the provided project" + ) def test_automated_project_analysis_KeyError(self, project_paths_data, caplog): caplog.clear() - caplog.set_level(logging.ERROR, logger='mdpow.workflows.base') + caplog.set_level(logging.ERROR, logger="mdpow.workflows.base") project_paths = project_paths_data # change resname to match topology (every SAMPL7 resname is 'UNK') # only necessary for this dataset, not necessary for normal use - project_paths['resname'] = 'UNK' + project_paths["resname"] = "UNK" # test error output when raised - with pytest.raises(KeyError, - match="Invalid ensemble_analysis 'DarthVaderAnalysis'. " - "An EnsembleAnalysis type that corresponds to an existing " - "automated workflow module must be input as a kwarg. ex: " - "ensemble_analysis='DihedralAnalysis'"): - base.automated_project_analysis(project_paths, ensemble_analysis='DarthVaderAnalysis', solvents=('water',)) + with pytest.raises( + KeyError, + match="Invalid ensemble_analysis 'DarthVaderAnalysis'. " + "An EnsembleAnalysis type that corresponds to an existing " + "automated workflow module must be input as a kwarg. ex: " + "ensemble_analysis='DihedralAnalysis'", + ): + base.automated_project_analysis( + project_paths, + ensemble_analysis="DarthVaderAnalysis", + solvents=("water",), + ) # test logger error recording - assert "'DarthVaderAnalysis' is an invalid selection" in caplog.text, ('did not catch incorrect ' - 'key specification for workflows.registry that results in KeyError') + assert "'DarthVaderAnalysis' is an invalid selection" in caplog.text, ( + "did not catch incorrect " + "key specification for workflows.registry that results in KeyError" + ) diff --git a/mdpow/tests/test_workflows_registry.py b/mdpow/tests/test_workflows_registry.py index a1f7b708..50143818 100644 --- a/mdpow/tests/test_workflows_registry.py +++ b/mdpow/tests/test_workflows_registry.py @@ -2,5 +2,6 @@ from mdpow.workflows import registry + def test_registry(): - assert list(registry.registry.keys()) == ['DihedralAnalysis'] + assert list(registry.registry.keys()) == ["DihedralAnalysis"] diff --git a/mdpow/workflows/base.py b/mdpow/workflows/base.py index 8f4ef2e6..93ddb561 100644 --- a/mdpow/workflows/base.py +++ b/mdpow/workflows/base.py @@ -29,123 +29,126 @@ import pandas as pd from MDAnalysis.topology import guessers, tables -logger = logging.getLogger('mdpow.workflows.base') +logger = logging.getLogger("mdpow.workflows.base") + def project_paths(parent_directory=None, csv=None, csv_save_dir=None): """Takes a top directory containing MDPOW projects and determines - the molname, resname, and path, of each MDPOW project within. + the molname, resname, and path, of each MDPOW project within. - Optionally takes a .csv file containing `molname`, `resname`, and - `paths`, in that order. + Optionally takes a .csv file containing `molname`, `resname`, and + `paths`, in that order. - :keywords: + :keywords: - *parent_directory* - the path for the location of the top directory - under which the subdirectories of MDPOW simulation - data exist, additionally creates a 'project_paths.csv' file - for user manipulation of metadata and for future reference + *parent_directory* + the path for the location of the top directory + under which the subdirectories of MDPOW simulation + data exist, additionally creates a 'project_paths.csv' file + for user manipulation of metadata and for future reference - *csv* - .csv file containing the molecule names, resnames, - and paths, in that order, for the MDPOW simulation - data to be iterated over must contain header of the - form: `molecule,resname,path` + *csv* + .csv file containing the molecule names, resnames, + and paths, in that order, for the MDPOW simulation + data to be iterated over must contain header of the + form: `molecule,resname,path` - *csv_save_dir* - optionally provided directory to save .csv file, otherwise, - data will be saved in current working directory + *csv_save_dir* + optionally provided directory to save .csv file, otherwise, + data will be saved in current working directory - :returns: + :returns: - *project_paths* - :class:`pandas.DataFrame` containing MDPOW project metadata + *project_paths* + :class:`pandas.DataFrame` containing MDPOW project metadata - .. rubric:: Example + .. rubric:: Example - Typical Workflow:: + Typical Workflow:: - project_paths = project_paths(parent_directory='/foo/bar/MDPOW_projects') - automated_project_analysis(project_paths) + project_paths = project_paths(parent_directory='/foo/bar/MDPOW_projects') + automated_project_analysis(project_paths) - or:: + or:: - project_paths = project_paths(csv='/foo/bar/MDPOW.csv') - automated_project_analysis(project_paths) + project_paths = project_paths(csv='/foo/bar/MDPOW.csv') + automated_project_analysis(project_paths) """ if parent_directory is not None: - locations = [] - reg_compile = re.compile('FEP') + reg_compile = re.compile("FEP") for dirpath, dirnames, filenames in os.walk(parent_directory): - result = [dirpath.strip() for dirname in dirnames if reg_compile.match(dirname)] + result = [ + dirpath.strip() for dirname in dirnames if reg_compile.match(dirname) + ] if result: locations.append(result[0]) resnames = [] for loc in locations: - res_temp = loc.strip().split('/') + res_temp = loc.strip().split("/") resnames.append(res_temp[-1]) - project_paths = pd.DataFrame( - { - 'molecule': resnames, - 'resname': resnames, - 'path': locations - }).sort_values(by=['molecule', 'resname', 'path'] - ).reset_index(drop=True) + project_paths = ( + pd.DataFrame({"molecule": resnames, "resname": resnames, "path": locations}) + .sort_values(by=["molecule", "resname", "path"]) + .reset_index(drop=True) + ) if csv_save_dir is not None: - project_paths.to_csv(f'{csv_save_dir}/project_paths.csv', index=False) - logger.info(f'project_paths saved under {csv_save_dir}') + project_paths.to_csv(f"{csv_save_dir}/project_paths.csv", index=False) + logger.info(f"project_paths saved under {csv_save_dir}") else: current_directory = os.getcwd() - project_paths.to_csv('project_paths.csv', index=False) - logger.info(f'project_paths saved under {current_directory}') + project_paths.to_csv("project_paths.csv", index=False) + logger.info(f"project_paths saved under {current_directory}") elif csv is not None: locations = pd.read_csv(csv) - project_paths = locations.sort_values(by=['molecule', 'resname', 'path']).reset_index(drop=True) + project_paths = locations.sort_values( + by=["molecule", "resname", "path"] + ).reset_index(drop=True) return project_paths + def automated_project_analysis(project_paths, ensemble_analysis, **kwargs): """Takes a :class:`pandas.DataFrame` created by :func:`~mdpow.workflows.base.project_paths` - and iteratively runs the specified :class:`~mdpow.analysis.ensemble.EnsembleAnalysis` - for each of the projects by running the associated automated workflow - in each project directory returned by :func:`~mdpow.workflows.base.project_paths`. + and iteratively runs the specified :class:`~mdpow.analysis.ensemble.EnsembleAnalysis` + for each of the projects by running the associated automated workflow + in each project directory returned by :func:`~mdpow.workflows.base.project_paths`. - Compatibility with more automated analyses in development. + Compatibility with more automated analyses in development. - :keywords: + :keywords: - *project_paths* - :class:`pandas.DataFrame` that provides paths to MDPOW projects + *project_paths* + :class:`pandas.DataFrame` that provides paths to MDPOW projects - *ensemble_analysis* - name of the :class:`~mdpow.analysis.ensemble.EnsembleAnalysis` - that corresponds to the desired automated workflow module + *ensemble_analysis* + name of the :class:`~mdpow.analysis.ensemble.EnsembleAnalysis` + that corresponds to the desired automated workflow module - *kwargs* - keyword arguments for the supported automated workflows, - see the :mod:`~mdpow.workflows.registry` for all available - workflows and their call signatures + *kwargs* + keyword arguments for the supported automated workflows, + see the :mod:`~mdpow.workflows.registry` for all available + workflows and their call signatures - .. rubric:: Example + .. rubric:: Example - A typical workflow is the automated dihedral analysis from - :mod:`mdpow.workflows.dihedrals`, which applies the *ensemble analysis* - :class:`~mdpow.analysis.dihedral.DihedralAnalysis` to each project. - The :data:`~mdpow.workflows.registry.registry` contains this automated - workflow under the key *"DihedralAnalysis"* and so the automated execution - for all `project_paths` (obtained via :func:`project_paths`) is performed by - passing the specific key to :func:`automated_project_analysis`:: + A typical workflow is the automated dihedral analysis from + :mod:`mdpow.workflows.dihedrals`, which applies the *ensemble analysis* + :class:`~mdpow.analysis.dihedral.DihedralAnalysis` to each project. + The :data:`~mdpow.workflows.registry.registry` contains this automated + workflow under the key *"DihedralAnalysis"* and so the automated execution + for all `project_paths` (obtained via :func:`project_paths`) is performed by + passing the specific key to :func:`automated_project_analysis`:: - project_paths = project_paths(parent_directory='/foo/bar/MDPOW_projects') - automated_project_analysis(project_paths, ensemble_analysis='DihedralAnalysis', **kwargs) + project_paths = project_paths(parent_directory='/foo/bar/MDPOW_projects') + automated_project_analysis(project_paths, ensemble_analysis='DihedralAnalysis', **kwargs) """ # import inside function to avoid circular imports @@ -156,27 +159,34 @@ def automated_project_analysis(project_paths, ensemble_analysis, **kwargs): resname = row.resname dirname = row.path - logger.info(f'starting {molname}') + logger.info(f"starting {molname}") try: - registry[ensemble_analysis](dirname=dirname, resname=resname, molname=molname, **kwargs) - logger.info(f'{molname} completed') + registry[ensemble_analysis]( + dirname=dirname, resname=resname, molname=molname, **kwargs + ) + logger.info(f"{molname} completed") except KeyError as err: - msg = (f"Invalid ensemble_analysis {err}. An EnsembleAnalysis type that corresponds " - "to an existing automated workflow module must be input as a kwarg. " - "ex: ensemble_analysis='DihedralAnalysis'") - logger.error(f'{err} is an invalid selection') + msg = ( + f"Invalid ensemble_analysis {err}. An EnsembleAnalysis type that corresponds " + "to an existing automated workflow module must be input as a kwarg. " + "ex: ensemble_analysis='DihedralAnalysis'" + ) + logger.error(f"{err} is an invalid selection") raise KeyError(msg) except TypeError as err: - msg = (f"Invalid ensemble_analysis {ensemble_analysis}. An EnsembleAnalysis type that " - "corresponds to an existing automated workflow module must be input as a kwarg. " - "ex: ensemble_analysis='DihedralAnalysis'") - logger.error(f'workflow module for {ensemble_analysis} does not exist yet') + msg = ( + f"Invalid ensemble_analysis {ensemble_analysis}. An EnsembleAnalysis type that " + "corresponds to an existing automated workflow module must be input as a kwarg. " + "ex: ensemble_analysis='DihedralAnalysis'" + ) + logger.error(f"workflow module for {ensemble_analysis} does not exist yet") raise TypeError(msg) - logger.info('all analyses completed') + logger.info("all analyses completed") return + def guess_elements(atoms, rtol=1e-3): """guess elements for atoms from masses @@ -230,13 +240,15 @@ def guess_elements(atoms, rtol=1e-3): problems = np.logical_not(np.isclose(masses, guessed_masses, atol=ATOL, rtol=rtol)) # match only problematic masses against the MDA reference masses - iproblem, ielem = np.nonzero(np.isclose(masses[problems, np.newaxis], mda_masses, - atol=ATOL, rtol=rtol)) + iproblem, ielem = np.nonzero( + np.isclose(masses[problems, np.newaxis], mda_masses, atol=ATOL, rtol=rtol) + ) # We should normally find a match for each problem but just in case, assert and # give some useful information for debugging. - assert len(ielem) == sum(problems),\ - ("Not all masses could be assigned an element, " - f"missing names {set(names[problems]) - set(names[problems][iproblem])}") + assert len(ielem) == sum(problems), ( + "Not all masses could be assigned an element, " + f"missing names {set(names[problems]) - set(names[problems][iproblem])}" + ) guessed_elements[problems] = mda_elements[ielem] diff --git a/mdpow/workflows/dihedrals.py b/mdpow/workflows/dihedrals.py index 2efe2530..05e678a9 100644 --- a/mdpow/workflows/dihedrals.py +++ b/mdpow/workflows/dihedrals.py @@ -63,9 +63,9 @@ from .base import guess_elements from ..analysis import ensemble, dihedral -logger = logging.getLogger('mdpow.workflows.dihedrals') +logger = logging.getLogger("mdpow.workflows.dihedrals") -SOLVENTS_DEFAULT = ('water', 'octanol') +SOLVENTS_DEFAULT = ("water", "octanol") """Default solvents are water and octanol: * must match solvents used in project directory @@ -76,7 +76,7 @@ """ -INTERACTIONS_DEFAULT = ('Coulomb', 'VDW') +INTERACTIONS_DEFAULT = ("Coulomb", "VDW") """Default interactions set to Coulomb and VDW: * default values should not be changed @@ -84,7 +84,7 @@ """ -SMARTS_DEFAULT = '[!#1]~[!$(*#*)&!D1]-!@[!$(*#*)&!D1]~[!#1]' +SMARTS_DEFAULT = "[!#1]~[!$(*#*)&!D1]-!@[!$(*#*)&!D1]~[!#1]" """Default SMARTS string to identify relevant dihedral atom groups: * ``[!#1]`` : any atom, not Hydrogen @@ -108,89 +108,90 @@ default value: 190 mm = 718.110236229 pixels """ + def build_universe(dirname, solvents=SOLVENTS_DEFAULT): """Builds :class:`~MDAnalysis.core.universe.Universe` from the - ``./Coulomb/0000`` topology and trajectory of the project for - the first solvent specified. - - Output used by :func:`~mdpow.workflows.dihedrals.rdkit_conversion` - and :func:`~mdpow.workflows.dihedrals.get_atom_indices` to obtain atom indices - for each dihedral atom group. - - :keywords: - - *dirname* - Molecule Simulation directory. Loads simulation files present in - lambda directories into the new instance. With this method for - generating an :class:`~mdpow.analysis.ensemble.Ensemble` the - lambda directories are explored and - :meth:`~mdpow.analysis.ensemble.Ensemble._load_universe_from_dir` - searches for .gro, .gro.bz2, .gro.gz, and .tpr files for topology, - and .xtc files for trajectory. It will default to using the tpr file - available. - - *solvents* - The default solvents are documented under :data:`SOLVENTS_DEFAULT`. - Normally takes a two-tuple, but analysis is compatible with single solvent selections. - Single solvent analyses will result in a figure with fully filled violins for the single solvent. - - :returns: - - *u* - :class:`~MDAnalysis.core.universe.Universe` object + ``./Coulomb/0000`` topology and trajectory of the project for + the first solvent specified. + + Output used by :func:`~mdpow.workflows.dihedrals.rdkit_conversion` + and :func:`~mdpow.workflows.dihedrals.get_atom_indices` to obtain atom indices + for each dihedral atom group. + + :keywords: + + *dirname* + Molecule Simulation directory. Loads simulation files present in + lambda directories into the new instance. With this method for + generating an :class:`~mdpow.analysis.ensemble.Ensemble` the + lambda directories are explored and + :meth:`~mdpow.analysis.ensemble.Ensemble._load_universe_from_dir` + searches for .gro, .gro.bz2, .gro.gz, and .tpr files for topology, + and .xtc files for trajectory. It will default to using the tpr file + available. + + *solvents* + The default solvents are documented under :data:`SOLVENTS_DEFAULT`. + Normally takes a two-tuple, but analysis is compatible with single solvent selections. + Single solvent analyses will result in a figure with fully filled violins for the single solvent. + + :returns: + + *u* + :class:`~MDAnalysis.core.universe.Universe` object """ path = pathlib.Path(dirname) - topology = path / f'FEP/{solvents[0]}/Coulomb/0000' / 'md.tpr' - trajectory = path / f'FEP/{solvents[0]}/Coulomb/0000' / 'md.xtc' + topology = path / f"FEP/{solvents[0]}/Coulomb/0000" / "md.tpr" + trajectory = path / f"FEP/{solvents[0]}/Coulomb/0000" / "md.xtc" u = mda.Universe(str(topology), str(trajectory)) return u + def rdkit_conversion(u, resname): """Converts the solute, `resname`, of the - :class:`~MDAnalysis.core.universe.Universe` to :class:`rdkit.Chem.rdchem.Mol` object - for use with a SMARTS selection string to identify dihedral atom groups. + :class:`~MDAnalysis.core.universe.Universe` to :class:`rdkit.Chem.rdchem.Mol` object + for use with a SMARTS selection string to identify dihedral atom groups. - Accepts :class:`~MDAnalysis.core.universe.Universe` object made with - :func:`~mdpow.workflows.dihedrals.build_universe` and a `resname` as input. - Uses `resname` to select the solute for conversion by - :class:`~MDAnalysis.converters.RDKit.RDKitConverter` to :class:`rdkit.Chem.rdchem.Mol`, - and will add element attributes for Hydrogen if not listed in the topology, - using :func:`MDAnalysis.topology.guessers.guess_atom_element`. + Accepts :class:`~MDAnalysis.core.universe.Universe` object made with + :func:`~mdpow.workflows.dihedrals.build_universe` and a `resname` as input. + Uses `resname` to select the solute for conversion by + :class:`~MDAnalysis.converters.RDKit.RDKitConverter` to :class:`rdkit.Chem.rdchem.Mol`, + and will add element attributes for Hydrogen if not listed in the topology, + using :func:`MDAnalysis.topology.guessers.guess_atom_element`. - :keywords: + :keywords: - *u* - :class:`~MDAnalysis.core.universe.Universe` object + *u* + :class:`~MDAnalysis.core.universe.Universe` object - *resname* - `resname` for the molecule as defined in - the topology and trajectory + *resname* + `resname` for the molecule as defined in + the topology and trajectory - :returns: + :returns: - *tuple(mol, solute)* - function call returns tuple, see below + *tuple(mol, solute)* + function call returns tuple, see below - *mol* - :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` + *mol* + :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` - *solute* - the :any:`MDAnalysis` `AtomGroup` for the solute + *solute* + the :any:`MDAnalysis` `AtomGroup` for the solute """ - try: - solute = u.select_atoms(f'resname {resname}') - mol = solute.convert_to('RDKIT') + solute = u.select_atoms(f"resname {resname}") + mol = solute.convert_to("RDKIT") except AttributeError: guessed_elements = guess_elements(u.atoms) u.add_TopologyAttr("elements", guessed_elements) - solute = u.select_atoms(f'resname {resname}') - mol = solute.convert_to('RDKIT') + solute = u.select_atoms(f"resname {resname}") + mol = solute.convert_to("RDKIT") rdCoordGen.AddCoords(mol) @@ -199,58 +200,59 @@ def rdkit_conversion(u, resname): return mol, solute + def get_atom_indices(mol, SMARTS=SMARTS_DEFAULT): - '''Uses a SMARTS selection string to identify atom indices - for relevant dihedral atom groups. + """Uses a SMARTS selection string to identify atom indices + for relevant dihedral atom groups. - Requires a :class:`rdkit.Chem.rdchem.Mol` object as input - for the :data:`SMARTS_DEFAULT` kwarg to match patterns to and - identify relevant dihedral atom groups. + Requires a :class:`rdkit.Chem.rdchem.Mol` object as input + for the :data:`SMARTS_DEFAULT` kwarg to match patterns to and + identify relevant dihedral atom groups. - :keywords: + :keywords: - *mol* - :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` + *mol* + :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` - *SMARTS* - The default SMARTS string is described in detail under :data:`SMARTS_DEFAULT`. + *SMARTS* + The default SMARTS string is described in detail under :data:`SMARTS_DEFAULT`. - :returns: + :returns: - *atom_indices* - tuple of tuples of indices for each dihedral atom group + *atom_indices* + tuple of tuples of indices for each dihedral atom group - ''' + """ pattern = Chem.MolFromSmarts(SMARTS) atom_indices = mol.GetSubstructMatches(pattern) - + return atom_indices + def get_bond_indices(mol, atom_indices): - '''From the :class:`rdkit.Chem.rdchem.Mol` object, uses - `atom_indices` to determine the indices of the bonds - between those atoms for each dihedral atom group. + """From the :class:`rdkit.Chem.rdchem.Mol` object, uses + `atom_indices` to determine the indices of the bonds + between those atoms for each dihedral atom group. - :keywords: + :keywords: - *mol* - :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` + *mol* + :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` - *atom_indices* - tuple of tuples of indices for each dihedral atom group + *atom_indices* + tuple of tuples of indices for each dihedral atom group - :returns: + :returns: - *bond_indices* - tuple of tuples of indices for the bonds in each dihedral atom group + *bond_indices* + tuple of tuples of indices for the bonds in each dihedral atom group + + """ - ''' - bonds = [] for atom_index in atom_indices: - x = mol.GetBondBetweenAtoms(atom_index[0], atom_index[1]).GetIdx() y = mol.GetBondBetweenAtoms(atom_index[1], atom_index[2]).GetIdx() z = mol.GetBondBetweenAtoms(atom_index[2], atom_index[3]).GetIdx() @@ -262,137 +264,150 @@ def get_bond_indices(mol, atom_indices): return bond_indices + def get_dihedral_groups(solute, atom_indices): - '''Uses the 0-based `atom_indices` of the relevant dihedral atom groups - determined by :func:`~mdpow.workflows.dihedrals.get_atom_indices` - and returns the 1-based index names for each atom in each group. + """Uses the 0-based `atom_indices` of the relevant dihedral atom groups + determined by :func:`~mdpow.workflows.dihedrals.get_atom_indices` + and returns the 1-based index names for each atom in each group. - Requires the `atom_indices` from :func:`~mdpow.workflows.dihedrals.get_atom_indices` - to index the `solute` specified by :func:`~MDAnalysis.core.groups.select_atoms` - and return an array of the names of each atom within its respective - dihedral atom group as identified by the SMARTS selection string. + Requires the `atom_indices` from :func:`~mdpow.workflows.dihedrals.get_atom_indices` + to index the `solute` specified by :func:`~MDAnalysis.core.groups.select_atoms` + and return an array of the names of each atom within its respective + dihedral atom group as identified by the SMARTS selection string. - :keywords: + :keywords: - *solute* - the :any:`MDAnalysis` `AtomGroup` for the solute + *solute* + the :any:`MDAnalysis` `AtomGroup` for the solute - *atom_indices* - tuple of tuples of indices for each dihedral atom group + *atom_indices* + tuple of tuples of indices for each dihedral atom group - :returns: + :returns: - *dihedral_groups* - list of :func:`numpy.array` for atom names in each dihedral atom group + *dihedral_groups* + list of :func:`numpy.array` for atom names in each dihedral atom group - ''' + """ # currently uses RDKit Mol object atom indices to retrieve # atom names from the MDAnalysis solute object # RDKit-MDAnalysis index consistency is currently tested - dihedral_groups = [solute.atoms[list(atom_index)].names for atom_index - in atom_indices] + dihedral_groups = [ + solute.atoms[list(atom_index)].names for atom_index in atom_indices + ] return dihedral_groups + def get_paired_indices(atom_indices, bond_indices, dihedral_groups): - '''Combines `atom_indices` and `bond_indices` in tuples - to be paired with their respective dihedral atom groups. + """Combines `atom_indices` and `bond_indices` in tuples + to be paired with their respective dihedral atom groups. - A dictionary is created with key-value pairs as follows: - `atom_indices` and `bond_indices` are joined in a tuple - as the value, with the key being the respective member - of `dihedral_groups` to facilitate highlighting the - relevant dihedral atom group when generating violin plots. - As an example, `'C1-N2-O3-S4': ((0, 1, 2, 3), (0, 1, 2))`, - would be one key-value pair in the dictionary. + A dictionary is created with key-value pairs as follows: + `atom_indices` and `bond_indices` are joined in a tuple + as the value, with the key being the respective member + of `dihedral_groups` to facilitate highlighting the + relevant dihedral atom group when generating violin plots. + As an example, `'C1-N2-O3-S4': ((0, 1, 2, 3), (0, 1, 2))`, + would be one key-value pair in the dictionary. - :keywords: + :keywords: - *atom_indices* - tuple of tuples of indices for each dihedral atom group + *atom_indices* + tuple of tuples of indices for each dihedral atom group - *bond_indices* - tuple of tuples of indices for the bonds in each dihedral atom group + *bond_indices* + tuple of tuples of indices for the bonds in each dihedral atom group - *dihedral_groups* - list of :func:`numpy.array` for atom names in each dihedral atom group + *dihedral_groups* + list of :func:`numpy.array` for atom names in each dihedral atom group - :returns: + :returns: - *name_index_pairs* - dictionary with key-value pair for dihedral atom group, - atom indices, and bond indices - - ''' + *name_index_pairs* + dictionary with key-value pair for dihedral atom group, + atom indices, and bond indices + + """ - all_dgs = [f'{dg[0]}-{dg[1]}-{dg[2]}-{dg[3]}' for dg in dihedral_groups] + all_dgs = [f"{dg[0]}-{dg[1]}-{dg[2]}-{dg[3]}" for dg in dihedral_groups] name_index_pairs = {} - name_index_pairs = {all_dgs[i]: (atom_indices[i], bond_indices[i]) for i in range(len(all_dgs))} + name_index_pairs = { + all_dgs[i]: (atom_indices[i], bond_indices[i]) for i in range(len(all_dgs)) + } return name_index_pairs -def dihedral_groups_ensemble(dirname, atom_indices, - solvents=SOLVENTS_DEFAULT, - interactions=INTERACTIONS_DEFAULT, - start=None, stop=None, step=None): - '''Creates one :class:`~mdpow.analysis.ensemble.Ensemble` for the MDPOW - project and runs :class:`~mdpow.analysis.dihedral.DihedralAnalysis` - for each dihedral atom group identified by the SMARTS - selection string. - .. seealso:: +def dihedral_groups_ensemble( + dirname, + atom_indices, + solvents=SOLVENTS_DEFAULT, + interactions=INTERACTIONS_DEFAULT, + start=None, + stop=None, + step=None, +): + """Creates one :class:`~mdpow.analysis.ensemble.Ensemble` for the MDPOW + project and runs :class:`~mdpow.analysis.dihedral.DihedralAnalysis` + for each dihedral atom group identified by the SMARTS + selection string. - :func:`~mdpow.workflows.dihedrals.automated_dihedral_analysis`, - :class:`~mdpow.analysis.dihedral.DihedralAnalysis` + .. seealso:: - :keywords: + :func:`~mdpow.workflows.dihedrals.automated_dihedral_analysis`, + :class:`~mdpow.analysis.dihedral.DihedralAnalysis` + + :keywords: - *dirname* - Molecule Simulation directory. Loads simulation files present in - lambda directories into the new instance. With this method for - generating an :class:`~mdpow.analysis.ensemble.Ensemble` the - lambda directories are explored and - :meth:`~mdpow.analysis.ensemble.Ensemble._load_universe_from_dir` - searches for .gro, .gro.bz2, .gro.gz, and .tpr files for topology, - and .xtc files for trajectory. It will default to using the tpr file - available. + *dirname* + Molecule Simulation directory. Loads simulation files present in + lambda directories into the new instance. With this method for + generating an :class:`~mdpow.analysis.ensemble.Ensemble` the + lambda directories are explored and + :meth:`~mdpow.analysis.ensemble.Ensemble._load_universe_from_dir` + searches for .gro, .gro.bz2, .gro.gz, and .tpr files for topology, + and .xtc files for trajectory. It will default to using the tpr file + available. - *atom_indices* - tuples of atom indices for dihedral atom groups + *atom_indices* + tuples of atom indices for dihedral atom groups - .. seealso:: :func:`~mdpow.workflows.dihedrals.get_atom_indices`, :data:`SMARTS_DEFAULT` + .. seealso:: :func:`~mdpow.workflows.dihedrals.get_atom_indices`, :data:`SMARTS_DEFAULT` - *solvents* - The default solvents are documented under :data:`SOLVENTS_DEFAULT`. - Normally takes a two-tuple, but analysis is compatible with single solvent selections. - Single solvent analyses will result in a figure with fully filled violins for the single solvent. + *solvents* + The default solvents are documented under :data:`SOLVENTS_DEFAULT`. + Normally takes a two-tuple, but analysis is compatible with single solvent selections. + Single solvent analyses will result in a figure with fully filled violins for the single solvent. - *interactions* - The default interactions are documented under :data:`INTERACTIONS_DEFAULT`. + *interactions* + The default interactions are documented under :data:`INTERACTIONS_DEFAULT`. - *start, stop, step* - arguments passed to :func:`~mdpow.analysis.ensemble.EnsembleAnalysis.run`, - as parameters for iterating through the trajectories of the current ensemble + *start, stop, step* + arguments passed to :func:`~mdpow.analysis.ensemble.EnsembleAnalysis.run`, + as parameters for iterating through the trajectories of the current ensemble - .. seealso:: :class:`~mdpow.analysis.ensemble.EnsembleAnalysis` + .. seealso:: :class:`~mdpow.analysis.ensemble.EnsembleAnalysis` - :returns: + :returns: - *df* - :class:`pandas.DataFrame` of :class:`~mdpow.analysis.dihedral.DihedralAnalysis` - results, including all dihedral atom groups for molecule of current project + *df* + :class:`pandas.DataFrame` of :class:`~mdpow.analysis.dihedral.DihedralAnalysis` + results, including all dihedral atom groups for molecule of current project - ''' + """ - dih_ens = ensemble.Ensemble(dirname=dirname, - solvents=solvents, - interactions=interactions) + dih_ens = ensemble.Ensemble( + dirname=dirname, solvents=solvents, interactions=interactions + ) indices = atom_indices - all_dihedrals = [dih_ens.select_atoms(f'index {i[0]}', - f'index {i[1]}', - f'index {i[2]}', - f'index {i[3]}' ) for i in indices] + all_dihedrals = [ + dih_ens.select_atoms( + f"index {i[0]}", f"index {i[1]}", f"index {i[2]}", f"index {i[3]}" + ) + for i in indices + ] da = dihedral.DihedralAnalysis(all_dihedrals) da.run(start=start, stop=stop, step=step) @@ -400,42 +415,42 @@ def dihedral_groups_ensemble(dirname, atom_indices, return df + def save_df(df, df_save_dir, resname, molname=None): - '''Takes a :class:`pandas.DataFrame` of results from - :class:`~mdpow.analysis.dihedral.DihedralAnalysis` - as input before padding the angles to optionaly save the raw - data. + """Takes a :class:`pandas.DataFrame` of results from + :class:`~mdpow.analysis.dihedral.DihedralAnalysis` + as input before padding the angles to optionaly save the raw + data. - Optionally saves results before padding the angles for periodicity - and plotting dihedral angle frequencies as KDE violins - with :func:`~mdpow.workflows.dihedrals.dihedral_violins`. - Given a parent directory, creates subdirectory for molecule, - saves fully sampled, unpadded results :class:`pandas.DataFrame` - as a compressed csv file, default: .csv.bz2. + Optionally saves results before padding the angles for periodicity + and plotting dihedral angle frequencies as KDE violins + with :func:`~mdpow.workflows.dihedrals.dihedral_violins`. + Given a parent directory, creates subdirectory for molecule, + saves fully sampled, unpadded results :class:`pandas.DataFrame` + as a compressed csv file, default: .csv.bz2. - :keywords: + :keywords: - *df* - :class:`pandas.DataFrame` of :class:`~mdpow.analysis.dihedral.DihedralAnalysis` - results, including all dihedral atom groups for molecule of current project + *df* + :class:`pandas.DataFrame` of :class:`~mdpow.analysis.dihedral.DihedralAnalysis` + results, including all dihedral atom groups for molecule of current project - *df_save_dir* - optional, path to the location to save results :class:`pandas.DataFrame` + *df_save_dir* + optional, path to the location to save results :class:`pandas.DataFrame` - *resname* - `resname` for the molecule as defined in - the topology and trajectory + *resname* + `resname` for the molecule as defined in + the topology and trajectory - *molname* - molecule name to be used for labelling - plots, if different from `resname` + *molname* + molecule name to be used for labelling + plots, if different from `resname` - ''' + """ - df = df.sort_values(by=["selection", - "solvent", - "interaction", - "lambda"]).reset_index(drop=True) + df = df.sort_values( + by=["selection", "solvent", "interaction", "lambda"] + ).reset_index(drop=True) if molname is None: molname = resname @@ -445,44 +460,44 @@ def save_df(df, df_save_dir, resname, molname=None): os.mkdir(newdir) # time and compression level can be adjusted as kwargs - df.to_csv(f'{newdir}/{molname}_full_df.csv.bz2', - index=False, compression='bz2') + df.to_csv(f"{newdir}/{molname}_full_df.csv.bz2", index=False, compression="bz2") + + logger.info(f"Results DataFrame saved as {newdir}/{molname}_full_df.csv.bz2") - logger.info(f'Results DataFrame saved as {newdir}/{molname}_full_df.csv.bz2') def periodic_angle_padding(df, padding=45): - '''Pads the angles from the results :class:`~pandas.DataFrame` - to maintain periodicity in the violin plots. + """Pads the angles from the results :class:`~pandas.DataFrame` + to maintain periodicity in the violin plots. - Takes a :class:`pandas.DataFrame` of results from - :class:`~mdpow.analysis.dihedral.DihedralAnalysis` - or :func:`~mdpow.workflows.dihedrals.dihedral_groups_ensemble` - as input and pads the angles to maintain periodicity - for properly plotting dihedral angle frequencies as KDE violins - with :func:`~mdpow.workflows.dihedrals.dihedral_violins` and - :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins`. - Creates two new :class:`pandas.DataFrame` based on the - `padding` value specified, pads the angle values, concatenates - all three :class:`pandas.DataFrame`, maintaining original data and - adding padded values, and returns new augmented :class:`pandas.DataFrame`. + Takes a :class:`pandas.DataFrame` of results from + :class:`~mdpow.analysis.dihedral.DihedralAnalysis` + or :func:`~mdpow.workflows.dihedrals.dihedral_groups_ensemble` + as input and pads the angles to maintain periodicity + for properly plotting dihedral angle frequencies as KDE violins + with :func:`~mdpow.workflows.dihedrals.dihedral_violins` and + :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins`. + Creates two new :class:`pandas.DataFrame` based on the + `padding` value specified, pads the angle values, concatenates + all three :class:`pandas.DataFrame`, maintaining original data and + adding padded values, and returns new augmented :class:`pandas.DataFrame`. - :keywords: + :keywords: - *df* - :class:`pandas.DataFrame` of :class:`~mdpow.analysis.dihedral.DihedralAnalysis` - results, including all dihedral atom groups for molecule of current project + *df* + :class:`pandas.DataFrame` of :class:`~mdpow.analysis.dihedral.DihedralAnalysis` + results, including all dihedral atom groups for molecule of current project - *padding* - value in degrees to specify angle augmentation threshold - default: 45 + *padding* + value in degrees to specify angle augmentation threshold + default: 45 - :returns: + :returns: - *df_aug* - augmented results :class:`pandas.DataFrame` containing - padded dihedral angles as specified by `padding` + *df_aug* + augmented results :class:`pandas.DataFrame` containing + padded dihedral angles as specified by `padding` - ''' + """ df1 = df[df.dihedral > 180 - padding].copy(deep=True) df1.dihedral -= 360 @@ -492,132 +507,159 @@ def periodic_angle_padding(df, padding=45): return df_aug + def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT, plot_title=None): - '''Plots kernel density estimates (KDE) of dihedral angle frequencies for - one dihedral atom group as violin plots, using as input the augmented - :class:`pandas.DataFrame` from :func:`~mdpow.workflows.dihedrals.periodic_angle_padding`. + """Plots kernel density estimates (KDE) of dihedral angle frequencies for + one dihedral atom group as violin plots, using as input the augmented + :class:`pandas.DataFrame` from :func:`~mdpow.workflows.dihedrals.periodic_angle_padding`. - Output is converted to SVG by :func:`~mdpow.workflows.dihedrals.build_svg` - and final output is saved as PDF by :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins` + Output is converted to SVG by :func:`~mdpow.workflows.dihedrals.build_svg` + and final output is saved as PDF by :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins` - :keywords: + :keywords: - *df* - augmented results :class:`pandas.DataFrame` from - :func:`~mdpow.workflows.dihedrals.periodic_angle_padding` + *df* + augmented results :class:`pandas.DataFrame` from + :func:`~mdpow.workflows.dihedrals.periodic_angle_padding` - *width* - width of the violin element (>1 overlaps) - default: 0.9 + *width* + width of the violin element (>1 overlaps) + default: 0.9 - *solvents* - The default solvents are documented under :data:`SOLVENTS_DEFAULT`. - Normally takes a two-tuple, but analysis is compatible with single solvent selections. - Single solvent analyses will result in a figure with fully filled violins for the single solvent. + *solvents* + The default solvents are documented under :data:`SOLVENTS_DEFAULT`. + Normally takes a two-tuple, but analysis is compatible with single solvent selections. + Single solvent analyses will result in a figure with fully filled violins for the single solvent. - *plot_title* - generated by :func:`~mdpow.workflows.dihedrals.build_svg` using - `molname`, `dihedral_groups`, `atom_indices`, and `interactions` - in this order and format: f'{molname}, {name[0]} {a} | ''{col_name}' + *plot_title* + generated by :func:`~mdpow.workflows.dihedrals.build_svg` using + `molname`, `dihedral_groups`, `atom_indices`, and `interactions` + in this order and format: f'{molname}, {name[0]} {a} | ''{col_name}' - :returns: + :returns: - *g* - returns a :class:`seaborn.FacetGrid` object containing a violin plot of the - kernel density estimates (KDE) of the dihedral angle frequencies for each - dihedral atom group identified by :data:`SMARTS_DEFAULT` + *g* + returns a :class:`seaborn.FacetGrid` object containing a violin plot of the + kernel density estimates (KDE) of the dihedral angle frequencies for each + dihedral atom group identified by :data:`SMARTS_DEFAULT` - ''' + """ - df['lambda'] = df['lambda'].astype('float') / 1000 - df = df.sort_values(by=["selection", - "solvent", - "interaction", - "lambda"]).reset_index(drop=True) + df["lambda"] = df["lambda"].astype("float") / 1000 + df = df.sort_values( + by=["selection", "solvent", "interaction", "lambda"] + ).reset_index(drop=True) - width_ratios = [len(df[df['interaction'] == "Coulomb"]["lambda"].unique()) + 1, - len(df[df['interaction'] == "VDW"]["lambda"].unique()), - len(df[df['interaction'] == "Coulomb"]["lambda"].unique()) - 1] + width_ratios = [ + len(df[df["interaction"] == "Coulomb"]["lambda"].unique()) + 1, + len(df[df["interaction"] == "VDW"]["lambda"].unique()), + len(df[df["interaction"] == "Coulomb"]["lambda"].unique()) - 1, + ] # Usage in Jupyter causes matplotlib figure object output, not the completed figure # Upcoming fix in issue #260 - assert 0 < len(solvents) < 3, "one or two solvents must be specified, otherwise SOLVENTS_DEFAULT is used" + assert ( + 0 < len(solvents) < 3 + ), "one or two solvents must be specified, otherwise SOLVENTS_DEFAULT is used" split = len(solvents) > 1 - g = sns.catplot(data=df, x="lambda", y="dihedral", hue="solvent", col="interaction", - kind="violin", split=split, width=width, inner=None, cut=0, - linewidth=0.5, - hue_order=list(solvents), col_order=["Coulomb", "VDW", "Structure"], - sharex=False, sharey=True, - height=3.0, aspect=2.0, - facet_kws={'ylim': (-180, 180), - 'gridspec_kws': {'width_ratios': width_ratios, - } - } - ) + g = sns.catplot( + data=df, + x="lambda", + y="dihedral", + hue="solvent", + col="interaction", + kind="violin", + split=split, + width=width, + inner=None, + cut=0, + linewidth=0.5, + hue_order=list(solvents), + col_order=["Coulomb", "VDW", "Structure"], + sharex=False, + sharey=True, + height=3.0, + aspect=2.0, + facet_kws={ + "ylim": (-180, 180), + "gridspec_kws": { + "width_ratios": width_ratios, + }, + }, + ) g.set_xlabels(r"$\lambda$") g.set_ylabels(r"dihedral angle $\phi$") g.despine(offset=5) - axC = g.axes_dict['Coulomb'] + axC = g.axes_dict["Coulomb"] axC.yaxis.set_major_locator(plt.matplotlib.ticker.MultipleLocator(60)) axC.yaxis.set_minor_locator(plt.matplotlib.ticker.MultipleLocator(30)) - axC.yaxis.set_major_formatter(plt.matplotlib.ticker.FormatStrFormatter(r"$%g^\circ$")) + axC.yaxis.set_major_formatter( + plt.matplotlib.ticker.FormatStrFormatter(r"$%g^\circ$") + ) - axV = g.axes_dict['VDW'] + axV = g.axes_dict["VDW"] axV.yaxis.set_visible(False) axV.spines["left"].set_visible(False) - axIM = g.axes_dict['Structure'] - axIM.axis('off') + axIM = g.axes_dict["Structure"] + axIM.axis("off") g.set_titles(plot_title) return g -def build_svg(mol, molname, name_index_pairs, atom_group_selection, - solvents=SOLVENTS_DEFAULT, width=0.9): - '''Converts and combines figure components into an - SVG object to be converted and saved as a publication - quality PDF. - :keywords: +def build_svg( + mol, + molname, + name_index_pairs, + atom_group_selection, + solvents=SOLVENTS_DEFAULT, + width=0.9, +): + """Converts and combines figure components into an + SVG object to be converted and saved as a publication + quality PDF. - *mol* - :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` + :keywords: - *molname* - molecule name to be used for labelling - plots, if different from `resname` - (in this case, carried over from an upstream - decision between the two) + *mol* + :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` - *name_index_pairs* - dictionary with key-value pair for dihedral atom group, - atom indices, and bond indices + *molname* + molecule name to be used for labelling + plots, if different from `resname` + (in this case, carried over from an upstream + decision between the two) - .. seealso:: :func:`~mdpow.workflows.dihedrals.get_paired_indices` + *name_index_pairs* + dictionary with key-value pair for dihedral atom group, + atom indices, and bond indices - *atom_group_selection* - `name` of each section in the `groupby` series of atom group selections + .. seealso:: :func:`~mdpow.workflows.dihedrals.get_paired_indices` - .. seealso:: :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins` + *atom_group_selection* + `name` of each section in the `groupby` series of atom group selections - *solvents* - The default solvents are documented under :data:`SOLVENTS_DEFAULT`. - Normally takes a two-tuple, but analysis is compatible with single solvent selections. - Single solvent analyses will result in a figure with fully filled violins for the single solvent. + .. seealso:: :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins` - *width* - width of the violin element (>1 overlaps) - default: 0.9 + *solvents* + The default solvents are documented under :data:`SOLVENTS_DEFAULT`. + Normally takes a two-tuple, but analysis is compatible with single solvent selections. + Single solvent analyses will result in a figure with fully filled violins for the single solvent. - :returns: + *width* + width of the violin element (>1 overlaps) + default: 0.9 - *fig* - :mod:`svgutils` SVG figure object + :returns: - ''' + *fig* + :mod:`svgutils` SVG figure object + + """ atom_index = name_index_pairs[atom_group_selection[0]][0] bond_index = name_index_pairs[atom_group_selection[0]][1] @@ -625,14 +667,16 @@ def build_svg(mol, molname, name_index_pairs, atom_group_selection, drawer = rdMolDraw2D.MolDraw2DSVG(250, 250) drawer.DrawMolecule(mol=mol, highlightAtoms=atom_index, highlightBonds=bond_index) drawer.FinishDrawing() - svg = drawer.GetDrawingText().replace('svg:','') + svg = drawer.GetDrawingText().replace("svg:", "") mol_svg = svgutils.transform.fromstring(svg) m = mol_svg.getroot() m.scale(0.0125).moveto(21.8, 0.35) - plot_title = f'{molname}, {atom_group_selection[0]} {atom_index} | ''{col_name}' - plot = dihedral_violins(atom_group_selection[1], width=width, solvents=solvents, plot_title=plot_title) + plot_title = f"{molname}, {atom_group_selection[0]} {atom_index} | " "{col_name}" + plot = dihedral_violins( + atom_group_selection[1], width=width, solvents=solvents, plot_title=plot_title + ) plot_svg = svgutils.transform.from_mpl(plot) p = plot_svg.getroot() @@ -643,65 +687,77 @@ def build_svg(mol, molname, name_index_pairs, atom_group_selection, return fig -def plot_dihedral_violins(df, resname, mol, name_index_pairs, figdir=None, molname=None, - width=0.9, plot_pdf_width=PLOT_WIDTH_DEFAULT, solvents=SOLVENTS_DEFAULT): - '''Coordinates plotting and saving figures for all dihedral atom groups. - - Makes a subdirectory for the current project within the specified - `figdir` using `resname` or `molname` as title and saves production - quality PDFs for each dihedral atom group separately. - .. seealso:: +def plot_dihedral_violins( + df, + resname, + mol, + name_index_pairs, + figdir=None, + molname=None, + width=0.9, + plot_pdf_width=PLOT_WIDTH_DEFAULT, + solvents=SOLVENTS_DEFAULT, +): + """Coordinates plotting and saving figures for all dihedral atom groups. + + Makes a subdirectory for the current project within the specified + `figdir` using `resname` or `molname` as title and saves production + quality PDFs for each dihedral atom group separately. - :func:`~mdpow.workflows.dihedrals.automated_dihedral_analysis`, - :func:`~mdpow.workflows.dihedrals.dihedral_violins`, - :func:`~mdpow.workflows.dihedrals.build_svg` + .. seealso:: - :keywords: + :func:`~mdpow.workflows.dihedrals.automated_dihedral_analysis`, + :func:`~mdpow.workflows.dihedrals.dihedral_violins`, + :func:`~mdpow.workflows.dihedrals.build_svg` - *df* - augmented results :class:`pandas.DataFrame` from - :func:`~mdpow.workflows.dihedrals.periodic_angle_padding` + :keywords: - *resname* - `resname` for the molecule as defined in - the topology and trajectory + *df* + augmented results :class:`pandas.DataFrame` from + :func:`~mdpow.workflows.dihedrals.periodic_angle_padding` - *mol* - :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` + *resname* + `resname` for the molecule as defined in + the topology and trajectory - *name_index_pairs* - dictionary with key-value pair for dihedral atom group, - atom indices, and bond indices + *mol* + :class:`rdkit.Chem.rdchem.Mol` object converted from `solute` - .. seealso:: :func:`~mdpow.workflows.dihedrals.get_paired_indices` + *name_index_pairs* + dictionary with key-value pair for dihedral atom group, + atom indices, and bond indices - *figdir* - path to the location to save figures (REQUIRED but marked - as a kwarg for technical reasons; will be changed in #244) + .. seealso:: :func:`~mdpow.workflows.dihedrals.get_paired_indices` - *molname* - molecule name to be used for labelling - plots, if different from `resname` + *figdir* + path to the location to save figures (REQUIRED but marked + as a kwarg for technical reasons; will be changed in #244) - *width* - width of the violin element (>1 overlaps) - default: 0.9 + *molname* + molecule name to be used for labelling + plots, if different from `resname` - .. seealso:: :func:`~mdpow.workflows.dihedrals.dihedral_violins` + *width* + width of the violin element (>1 overlaps) + default: 0.9 - *plot_pdf_width* - The default value for width of plot output is described in detail under - :data:`PLOT_WIDTH_DEFAULT`. + .. seealso:: :func:`~mdpow.workflows.dihedrals.dihedral_violins` - *solvents* - The default solvents are documented under :data:`SOLVENTS_DEFAULT`. - Normally takes a two-tuple, but analysis is compatible with single solvent selections. - Single solvent analyses will result in a figure with fully filled violins for the single solvent. + *plot_pdf_width* + The default value for width of plot output is described in detail under + :data:`PLOT_WIDTH_DEFAULT`. - ''' + *solvents* + The default solvents are documented under :data:`SOLVENTS_DEFAULT`. + Normally takes a two-tuple, but analysis is compatible with single solvent selections. + Single solvent analyses will result in a figure with fully filled violins for the single solvent. + + """ - assert figdir is not None, "figdir MUST be set, even though it is a kwarg. Will be changed with #244" + assert ( + figdir is not None + ), "figdir MUST be set, even though it is a kwarg. Will be changed with #244" if molname is None: molname = resname @@ -717,17 +773,25 @@ def plot_dihedral_violins(df, resname, mol, name_index_pairs, figdir=None, molna pdf_list = [] for name in section: - - fig = build_svg(mol=mol, molname=molname, atom_group_selection=name, name_index_pairs=name_index_pairs, - solvents=solvents, width=width) + fig = build_svg( + mol=mol, + molname=molname, + atom_group_selection=name, + name_index_pairs=name_index_pairs, + solvents=solvents, + width=width, + ) figfile = pathlib.Path(newdir) / f"{molname}_{name[0]}_violins.pdf" if figdir is not None: - plot_pdf = cairosvg.svg2pdf(bytestring=fig.tostr(), write_to=str(figfile), - output_width=plot_pdf_width_px) - + plot_pdf = cairosvg.svg2pdf( + bytestring=fig.tostr(), + write_to=str(figfile), + output_width=plot_pdf_width_px, + ) + # add PDF for each dihedral atom group to all_PDFs list - pdf_list.append(f'{figfile}') + pdf_list.append(f"{figfile}") logger.info(f"Figure saved as {figfile}") @@ -739,141 +803,169 @@ def plot_dihedral_violins(df, resname, mol, name_index_pairs, figdir=None, molna merger.append(pdf) merger.write(f"{figdir}/{molname}/{molname}_all_figures.pdf") merger.close() - logger.info(f"PDF of combined figures generated and saved as {figdir}/{molname}/{molname}_all_figures.pdf") + logger.info( + f"PDF of combined figures generated and saved as {figdir}/{molname}/{molname}_all_figures.pdf" + ) return None -def automated_dihedral_analysis(dirname, resname, - figdir=None, - # figdir is required and will cause issues if not specified - # figdir=None is a temporary way to satisfy - # workflows base tests until issue #244 is resolved - # because it currently uses a **kwargs convention and the - # positional argument figdir will not carry over nicely - df_save_dir=None, molname=None, - SMARTS=SMARTS_DEFAULT, plot_pdf_width=PLOT_WIDTH_DEFAULT, - dataframe=None, padding=45, width=0.9, - solvents=SOLVENTS_DEFAULT, - interactions=INTERACTIONS_DEFAULT, - start=None, stop=None, step=None): - '''Runs :class:`~mdpow.analysis.dihedral.DihedralAnalysis` for a single MDPOW - project and creates violin plots of dihedral angle frequencies for each - relevant dihedral atom group. - - For one MDPOW project, automatically determines all relevant dihedral atom groups - in the molecule, runs :class:`~mdpow.analysis.dihedral.DihedralAnalysis` for each group, - pads the dihedral angles to maintain periodicity, creates violin plots of dihedral angle - frequencies (KDEs), and saves publication quality PDF figures for each group, separately. - - Optionally saves all pre-padded :class:`~mdpow.analysis.dihedral.DihedralAnalysis` results - as a single :class:`pandas.DataFrame` in `df_save_dir` provided. - - :keywords: - - *dirname* - Molecule Simulation directory. Loads simulation files present in - lambda directories into the new instance. With this method for - generating an :class:`~mdpow.analysis.ensemble.Ensemble` the - lambda directories are explored and - :meth:`~mdpow.analysis.ensemble.Ensemble._load_universe_from_dir` - searches for .gro, .gro.bz2, .gro.gz, and .tpr files for topology, - and .xtc files for trajectory. It will default to using the tpr file - available. - - *figdir* - path to the location to save figures (REQUIRED but marked - as a kwarg for technical reasons; will be changed in #244) - - *resname* - `resname` for the molecule as defined in - the topology and trajectory - - *df_save_dir* - optional, path to the location to save results :class:`pandas.DataFrame` - - *molname* - molecule name to be used for labelling - plots, if different from `resname` - - *SMARTS* - The default SMARTS string is described in detail under :data:`SMARTS_DEFAULT`. - - *plot_pdf_width* - The default value for width of plot output is described in detail under - :data:`PLOT_WIDTH_DEFAULT`. - - *dataframe* - optional, if :class:`~mdpow.analysis.dihedral.DihedralAnalysis` - was done prior, then results :class:`pandas.DataFrame` can be - input to utilize angle padding and violin plotting functionality - - *padding* - value in degrees - default: 45 - - .. seealso:: :func:`~mdpow.workflows.dihedrals.periodic_angle_padding` - - *width* - width of the violin element (>1 overlaps) - default: 0.9 - - .. seealso:: :func:`~mdpow.workflows.dihedrals.dihedral_violins` - - *solvents* - The default solvents are documented under :data:`SOLVENTS_DEFAULT`. - Normally takes a two-tuple, but analysis is compatible with single solvent selections. - Single solvent analyses will result in a figure with fully filled violins for the single solvent. - - *interactions* - The default interactions are documented under :data:`INTERACTIONS_DEFAULT`. - - *start, stop, step* - arguments passed to :func:`~mdpow.analysis.ensemble.EnsembleAnalysis.run`, - as parameters for iterating through the trajectories of the current ensemble - - .. seealso:: :class:`~mdpow.analysis.ensemble.EnsembleAnalysis` - - .. rubric:: Example - - Typical Workflow:: - - import dihedrals - - dihedrals.automated_dihedral_analysis(dirname='/foo/bar/MDPOW_project_data', - figdir='/foo/bar/MDPOW_figure_directory', - resname='UNK', molname='benzene', - padding=45, width=0.9, - solvents=('water','octanol'), - interactions=('Coulomb','VDW'), - start=0, stop=100, step=10) - ''' + +def automated_dihedral_analysis( + dirname, + resname, + figdir=None, + # figdir is required and will cause issues if not specified + # figdir=None is a temporary way to satisfy + # workflows base tests until issue #244 is resolved + # because it currently uses a **kwargs convention and the + # positional argument figdir will not carry over nicely + df_save_dir=None, + molname=None, + SMARTS=SMARTS_DEFAULT, + plot_pdf_width=PLOT_WIDTH_DEFAULT, + dataframe=None, + padding=45, + width=0.9, + solvents=SOLVENTS_DEFAULT, + interactions=INTERACTIONS_DEFAULT, + start=None, + stop=None, + step=None, +): + """Runs :class:`~mdpow.analysis.dihedral.DihedralAnalysis` for a single MDPOW + project and creates violin plots of dihedral angle frequencies for each + relevant dihedral atom group. + + For one MDPOW project, automatically determines all relevant dihedral atom groups + in the molecule, runs :class:`~mdpow.analysis.dihedral.DihedralAnalysis` for each group, + pads the dihedral angles to maintain periodicity, creates violin plots of dihedral angle + frequencies (KDEs), and saves publication quality PDF figures for each group, separately. + + Optionally saves all pre-padded :class:`~mdpow.analysis.dihedral.DihedralAnalysis` results + as a single :class:`pandas.DataFrame` in `df_save_dir` provided. + + :keywords: + + *dirname* + Molecule Simulation directory. Loads simulation files present in + lambda directories into the new instance. With this method for + generating an :class:`~mdpow.analysis.ensemble.Ensemble` the + lambda directories are explored and + :meth:`~mdpow.analysis.ensemble.Ensemble._load_universe_from_dir` + searches for .gro, .gro.bz2, .gro.gz, and .tpr files for topology, + and .xtc files for trajectory. It will default to using the tpr file + available. + + *figdir* + path to the location to save figures (REQUIRED but marked + as a kwarg for technical reasons; will be changed in #244) + + *resname* + `resname` for the molecule as defined in + the topology and trajectory + + *df_save_dir* + optional, path to the location to save results :class:`pandas.DataFrame` + + *molname* + molecule name to be used for labelling + plots, if different from `resname` + + *SMARTS* + The default SMARTS string is described in detail under :data:`SMARTS_DEFAULT`. + + *plot_pdf_width* + The default value for width of plot output is described in detail under + :data:`PLOT_WIDTH_DEFAULT`. + + *dataframe* + optional, if :class:`~mdpow.analysis.dihedral.DihedralAnalysis` + was done prior, then results :class:`pandas.DataFrame` can be + input to utilize angle padding and violin plotting functionality + + *padding* + value in degrees + default: 45 + + .. seealso:: :func:`~mdpow.workflows.dihedrals.periodic_angle_padding` + + *width* + width of the violin element (>1 overlaps) + default: 0.9 + + .. seealso:: :func:`~mdpow.workflows.dihedrals.dihedral_violins` + + *solvents* + The default solvents are documented under :data:`SOLVENTS_DEFAULT`. + Normally takes a two-tuple, but analysis is compatible with single solvent selections. + Single solvent analyses will result in a figure with fully filled violins for the single solvent. + + *interactions* + The default interactions are documented under :data:`INTERACTIONS_DEFAULT`. + + *start, stop, step* + arguments passed to :func:`~mdpow.analysis.ensemble.EnsembleAnalysis.run`, + as parameters for iterating through the trajectories of the current ensemble + + .. seealso:: :class:`~mdpow.analysis.ensemble.EnsembleAnalysis` + + .. rubric:: Example + + Typical Workflow:: + + import dihedrals + + dihedrals.automated_dihedral_analysis(dirname='/foo/bar/MDPOW_project_data', + figdir='/foo/bar/MDPOW_figure_directory', + resname='UNK', molname='benzene', + padding=45, width=0.9, + solvents=('water','octanol'), + interactions=('Coulomb','VDW'), + start=0, stop=100, step=10) + """ u = build_universe(dirname=dirname, solvents=solvents) mol, solute = rdkit_conversion(u=u, resname=resname) atom_indices = get_atom_indices(mol=mol, SMARTS=SMARTS) bond_indices = get_bond_indices(mol=mol, atom_indices=atom_indices) dihedral_groups = get_dihedral_groups(solute=solute, atom_indices=atom_indices) - name_index_pairs = get_paired_indices(atom_indices=atom_indices, bond_indices=bond_indices, - dihedral_groups=dihedral_groups) + name_index_pairs = get_paired_indices( + atom_indices=atom_indices, + bond_indices=bond_indices, + dihedral_groups=dihedral_groups, + ) if dataframe is not None: - df = dataframe - logger.info(f'Proceeding with results DataFrame provided.') + logger.info(f"Proceeding with results DataFrame provided.") else: - - df = dihedral_groups_ensemble(dirname=dirname, atom_indices=atom_indices, - solvents=solvents, interactions=interactions, - start=start, stop=stop, step=step) + df = dihedral_groups_ensemble( + dirname=dirname, + atom_indices=atom_indices, + solvents=solvents, + interactions=interactions, + start=start, + stop=stop, + step=step, + ) if df_save_dir is not None: save_df(df=df, df_save_dir=df_save_dir, resname=resname, molname=molname) df_aug = periodic_angle_padding(df, padding=padding) - plot_dihedral_violins(df=df_aug, resname=resname, mol=mol, name_index_pairs=name_index_pairs, figdir=figdir, molname=molname, - width=width, plot_pdf_width=plot_pdf_width, solvents=solvents) + plot_dihedral_violins( + df=df_aug, + resname=resname, + mol=mol, + name_index_pairs=name_index_pairs, + figdir=figdir, + molname=molname, + width=width, + plot_pdf_width=plot_pdf_width, + solvents=solvents, + ) logger.info(f"DihedralAnalysis completed for all projects in {dirname}") diff --git a/mdpow/workflows/registry.py b/mdpow/workflows/registry.py index 33bdd543..5320b6b8 100644 --- a/mdpow/workflows/registry.py +++ b/mdpow/workflows/registry.py @@ -28,9 +28,7 @@ # NOTE: analysis modules should NOT import registry to avoid circular imports from . import dihedrals -registry = { - 'DihedralAnalysis' : dihedrals.automated_dihedral_analysis -} +registry = {"DihedralAnalysis": dihedrals.automated_dihedral_analysis} """ In the `registry`, each entry corresponds to an :class:`~mdpow.analysis.ensemble.EnsembleAnalysis` diff --git a/scripts/mdpow-cfg2yaml.py b/scripts/mdpow-cfg2yaml.py index a46f7c4c..4931750c 100755 --- a/scripts/mdpow-cfg2yaml.py +++ b/scripts/mdpow-cfg2yaml.py @@ -18,7 +18,7 @@ full_file = [] -with open(sys.argv[1],'r') as f: +with open(sys.argv[1], "r") as f: for line in f: newline = line.strip() if not newline.startswith("#") and not newline == "": @@ -32,28 +32,31 @@ sections = [] -for x in range(len(heads)-1): - sections.append(full_file[heads[x]:heads[x+1]]) +for x in range(len(heads) - 1): + sections.append(full_file[heads[x] : heads[x + 1]]) -sections.append(full_file[heads[-1]:]) +sections.append(full_file[heads[-1] :]) yaml_formatting = {} for x in sections: options = x[1:] - split = [[str(y.split("=")[0].strip()),str(y.split("=")[1].strip()).strip()] for y in options] - yaml_formatting[x[0][1:-1]]=split + split = [ + [str(y.split("=")[0].strip()), str(y.split("=")[1].strip()).strip()] + for y in options + ] + yaml_formatting[x[0][1:-1]] = split for x in yaml_formatting: - d = dict((key,value) for (key,value) in yaml_formatting[x]) + d = dict((key, value) for (key, value) in yaml_formatting[x]) yaml_formatting[x] = d -with open("result.yml",'w') as f: - f.write(yaml.dump(yaml_formatting,default_flow_style=False)) +with open("result.yml", "w") as f: + f.write(yaml.dump(yaml_formatting, default_flow_style=False)) -with open("result.yml",'r') as infile, open(sys.argv[-1],'w') as outfile: +with open("result.yml", "r") as infile, open(sys.argv[-1], "w") as outfile: data = infile.read() - data = data.replace("'","") + data = data.replace("'", "") outfile.write(data) os.remove("result.yml") diff --git a/setup.py b/setup.py index 262f113c..d6944529 100644 --- a/setup.py +++ b/setup.py @@ -6,67 +6,77 @@ from setuptools import setup, find_packages import versioneer -setup(name="MDPOW", - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), - description="A library for computing solvation/water partitioning coefficients using molecular dynamics simulations", - long_description=open("README.rst").read(), - long_description_content_type="text/x-rst", - author="Oliver Beckstein", - author_email="orbeckst@gmail.com", - license="GPLv3", - url="https://github.com/Becksteinlab/MDPOW", - keywords="science Gromacs analysis 'molecular dynamics'", - classifiers=[ - "Development Status :: 4 - Beta", - "Environment :: Console", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", - "Operating System :: POSIX", - 'Operating System :: MacOS :: MacOS X', - 'Programming Language :: Python', - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Topic :: Scientific/Engineering :: Chemistry", - "Topic :: Scientific/Engineering :: Physics", - ], - packages=find_packages(exclude=['examples']), - scripts=['scripts/mdpow-pow', - 'scripts/mdpow-pcw', - 'scripts/mdpow-ptw', - 'scripts/mdpow-check', - 'scripts/mdpow-rebuild-fep', - 'scripts/mdpow-rebuild-simulation', - 'scripts/mdpow-equilibrium', - 'scripts/mdpow-fep', - 'scripts/mdpow-cfg2yaml.py', - 'scripts/mdpow-solvationenergy', - 'scripts/mdpow-get-runinput' - ], - package_data={'mdpow': ['top/*.dat', 'top/*.gro', 'top/*.itp', - 'top/oplsaa.ff/*', - 'top/charmm36-mar2019.ff/*', - 'top/amber99sb.ff/*', - 'templates/*'], }, - install_requires=['numpy>=1.6', 'scipy', - 'pyyaml', - 'GromacsWrapper>=0.5.1', - 'numkit', - 'six', - 'mdanalysis>=2', - 'alchemlyb>=2', - 'pandas', - 'pymbar>=4', - 'matplotlib', - 'seaborn', - 'rdkit', - 'svgutils', - 'cairosvg', - 'pypdf' - ], - #setup_requires=['pytest-runner',], - tests_require=['pytest', 'pybol', 'py'], - zip_safe=True, +setup( + name="MDPOW", + version=versioneer.get_version(), + cmdclass=versioneer.get_cmdclass(), + description="A library for computing solvation/water partitioning coefficients using molecular dynamics simulations", + long_description=open("README.rst").read(), + long_description_content_type="text/x-rst", + author="Oliver Beckstein", + author_email="orbeckst@gmail.com", + license="GPLv3", + url="https://github.com/Becksteinlab/MDPOW", + keywords="science Gromacs analysis 'molecular dynamics'", + classifiers=[ + "Development Status :: 4 - Beta", + "Environment :: Console", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", + "Operating System :: POSIX", + "Operating System :: MacOS :: MacOS X", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Topic :: Scientific/Engineering :: Chemistry", + "Topic :: Scientific/Engineering :: Physics", + ], + packages=find_packages(exclude=["examples"]), + scripts=[ + "scripts/mdpow-pow", + "scripts/mdpow-pcw", + "scripts/mdpow-ptw", + "scripts/mdpow-check", + "scripts/mdpow-rebuild-fep", + "scripts/mdpow-rebuild-simulation", + "scripts/mdpow-equilibrium", + "scripts/mdpow-fep", + "scripts/mdpow-cfg2yaml.py", + "scripts/mdpow-solvationenergy", + "scripts/mdpow-get-runinput", + ], + package_data={ + "mdpow": [ + "top/*.dat", + "top/*.gro", + "top/*.itp", + "top/oplsaa.ff/*", + "top/charmm36-mar2019.ff/*", + "top/amber99sb.ff/*", + "templates/*", + ], + }, + install_requires=[ + "numpy>=1.6", + "scipy", + "pyyaml", + "GromacsWrapper>=0.5.1", + "numkit", + "six", + "mdanalysis>=2", + "alchemlyb>=2", + "pandas", + "pymbar>=4", + "matplotlib", + "seaborn", + "rdkit", + "svgutils", + "cairosvg", + "pypdf", + ], + # setup_requires=['pytest-runner',], + tests_require=["pytest", "pybol", "py"], + zip_safe=True, ) diff --git a/versioneer.py b/versioneer.py index 64fea1c8..2b545405 100644 --- a/versioneer.py +++ b/versioneer.py @@ -1,4 +1,3 @@ - # Version: 0.18 """The Versioneer - like a rocketeer, but for versions. @@ -277,6 +276,7 @@ """ from __future__ import print_function + try: import configparser except ImportError: @@ -308,11 +308,13 @@ def get_root(): setup_py = os.path.join(root, "setup.py") versioneer_py = os.path.join(root, "versioneer.py") if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ("Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND').") + err = ( + "Versioneer was unable to run the project root directory. " + "Versioneer requires setup.py to be executed from " + "its immediate directory (like 'python setup.py COMMAND'), " + "or in a way that lets it use sys.argv[0] to find the root " + "(like 'python path/to/setup.py COMMAND')." + ) raise VersioneerBadRootError(err) try: # Certain runtime workflows (setup.py install/develop in a setuptools @@ -325,8 +327,10 @@ def get_root(): me_dir = os.path.normcase(os.path.splitext(me)[0]) vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) if me_dir != vsr_dir: - print("Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(me), versioneer_py)) + print( + "Warning: build in %s is using versioneer.py from %s" + % (os.path.dirname(me), versioneer_py) + ) except NameError: pass return root @@ -348,6 +352,7 @@ def get(parser, name): if parser.has_option("versioneer", name): return parser.get("versioneer", name) return None + cfg = VersioneerConfig() cfg.VCS = VCS cfg.style = get(parser, "style") or "" @@ -372,17 +377,18 @@ class NotThisMethod(Exception): def register_vcs_handler(vcs, method): # decorator """Decorator to mark a method as the handler for a particular VCS.""" + def decorate(f): """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} HANDLERS[vcs][method] = f return f + return decorate -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): +def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): """Call the given command(s).""" assert isinstance(commands, list) p = None @@ -390,10 +396,13 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, try: dispcmd = str([c] + args) # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) + p = subprocess.Popen( + [c] + args, + cwd=cwd, + env=env, + stdout=subprocess.PIPE, + stderr=(subprocess.PIPE if hide_stderr else None), + ) break except EnvironmentError: e = sys.exc_info()[1] @@ -418,7 +427,9 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, return stdout, p.returncode -LONG_VERSION_PY['git'] = ''' +LONG_VERSION_PY[ + "git" +] = ''' # This file helps to compute a version number in source trees obtained from # git-archive tarball (such as those provided by githubs download-from-tag # feature). Distribution tarballs (built by setup.py sdist) and build @@ -993,7 +1004,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) + tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d @@ -1002,7 +1013,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) + tags = set([r for r in refs if re.search(r"\d", r)]) if verbose: print("discarding '%s', no digits" % ",".join(refs - tags)) if verbose: @@ -1010,19 +1021,26 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): for ref in sorted(tags): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] + r = ref[len(tag_prefix) :] if verbose: print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} + return { + "version": r, + "full-revisionid": keywords["full"].strip(), + "dirty": False, + "error": None, + "date": date, + } # no suitable tags, so version is "0+unknown", but full hex is still there if verbose: print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} + return { + "version": "0+unknown", + "full-revisionid": keywords["full"].strip(), + "dirty": False, + "error": "no suitable tags", + "date": None, + } @register_vcs_handler("git", "pieces_from_vcs") @@ -1037,8 +1055,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) + out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) if rc != 0: if verbose: print("Directory %s not under git control" % root) @@ -1046,10 +1063,19 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%s*" % tag_prefix], - cwd=root) + describe_out, rc = run_command( + GITS, + [ + "describe", + "--tags", + "--dirty", + "--always", + "--long", + "--match", + "%s*" % tag_prefix, + ], + cwd=root, + ) # --long was added in git-1.5.5 if describe_out is None: raise NotThisMethod("'git describe' failed") @@ -1072,17 +1098,16 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): dirty = git_describe.endswith("-dirty") pieces["dirty"] = dirty if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] + git_describe = git_describe[: git_describe.rindex("-dirty")] # now we have TAG-NUM-gHEX or HEX if "-" in git_describe: # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) + mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) if not mo: # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) + pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out return pieces # tag @@ -1091,10 +1116,12 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if verbose: fmt = "tag '%s' doesn't start with prefix '%s'" print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) + pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( + full_tag, + tag_prefix, + ) return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] + pieces["closest-tag"] = full_tag[len(tag_prefix) :] # distance: number of commits since tag pieces["distance"] = int(mo.group(2)) @@ -1105,13 +1132,13 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): else: # HEX: no tags pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) + count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) pieces["distance"] = int(count_out) # total number of commits # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], - cwd=root)[0].strip() + date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[ + 0 + ].strip() pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces @@ -1167,16 +1194,22 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): for i in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} + return { + "version": dirname[len(parentdir_prefix) :], + "full-revisionid": None, + "dirty": False, + "error": None, + "date": None, + } else: rootdirs.append(root) root = os.path.dirname(root) # up a level if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) + print( + "Tried directories %s but none started with prefix %s" + % (str(rootdirs), parentdir_prefix) + ) raise NotThisMethod("rootdir doesn't start with parentdir_prefix") @@ -1205,11 +1238,13 @@ def versions_from_file(filename): contents = f.read() except EnvironmentError: raise NotThisMethod("unable to read _version.py") - mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) + mo = re.search( + r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S + ) if not mo: - mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) + mo = re.search( + r"version_json = '''\r\n(.*)''' # END VERSION_JSON", contents, re.M | re.S + ) if not mo: raise NotThisMethod("no version_json in _version.py") return json.loads(mo.group(1)) @@ -1218,8 +1253,7 @@ def versions_from_file(filename): def write_to_version_file(filename, versions): """Write the given version number to the given _version.py file.""" os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, - indent=1, separators=(",", ": ")) + contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": ")) with open(filename, "w") as f: f.write(SHORT_VERSION_PY % contents) @@ -1251,8 +1285,7 @@ def render_pep440(pieces): rendered += ".dirty" else: # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) + rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) if pieces["dirty"]: rendered += ".dirty" return rendered @@ -1366,11 +1399,13 @@ def render_git_describe_long(pieces): def render(pieces, style): """Render the given version pieces into the requested style.""" if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} + return { + "version": "unknown", + "full-revisionid": pieces.get("long"), + "dirty": None, + "error": pieces["error"], + "date": None, + } if not style or style == "default": style = "pep440" # the default @@ -1390,9 +1425,13 @@ def render(pieces, style): else: raise ValueError("unknown style '%s'" % style) - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} + return { + "version": rendered, + "full-revisionid": pieces["long"], + "dirty": pieces["dirty"], + "error": None, + "date": pieces.get("date"), + } class VersioneerBadRootError(Exception): @@ -1415,8 +1454,9 @@ def get_versions(verbose=False): handlers = HANDLERS.get(cfg.VCS) assert handlers, "unrecognized VCS '%s'" % cfg.VCS verbose = verbose or cfg.verbose - assert cfg.versionfile_source is not None, \ - "please set versioneer.versionfile_source" + assert ( + cfg.versionfile_source is not None + ), "please set versioneer.versionfile_source" assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" versionfile_abs = os.path.join(root, cfg.versionfile_source) @@ -1470,9 +1510,13 @@ def get_versions(verbose=False): if verbose: print("unable to compute version") - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, "error": "unable to compute version", - "date": None} + return { + "version": "0+unknown", + "full-revisionid": None, + "dirty": None, + "error": "unable to compute version", + "date": None, + } def get_version(): @@ -1521,6 +1565,7 @@ def run(self): print(" date: %s" % vers.get("date")) if vers["error"]: print(" error: %s" % vers["error"]) + cmds["version"] = cmd_version # we override "build_py" in both distutils and setuptools @@ -1553,14 +1598,15 @@ def run(self): # now locate _version.py in the new build/ directory and replace # it with an updated value if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) + target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) print("UPDATING %s" % target_versionfile) write_to_version_file(target_versionfile, versions) + cmds["build_py"] = cmd_build_py if "cx_Freeze" in sys.modules: # cx_freeze enabled? from cx_Freeze.dist import build_exe as _build_exe + # nczeczulin reports that py2exe won't like the pep440-style string # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. # setup(console=[{ @@ -1581,17 +1627,21 @@ def run(self): os.unlink(target_versionfile) with open(cfg.versionfile_source, "w") as f: LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) + f.write( + LONG + % { + "DOLLAR": "$", + "STYLE": cfg.style, + "TAG_PREFIX": cfg.tag_prefix, + "PARENTDIR_PREFIX": cfg.parentdir_prefix, + "VERSIONFILE_SOURCE": cfg.versionfile_source, + } + ) + cmds["build_exe"] = cmd_build_exe del cmds["build_py"] - if 'py2exe' in sys.modules: # py2exe enabled? + if "py2exe" in sys.modules: # py2exe enabled? try: from py2exe.distutils_buildexe import py2exe as _py2exe # py3 except ImportError: @@ -1610,13 +1660,17 @@ def run(self): os.unlink(target_versionfile) with open(cfg.versionfile_source, "w") as f: LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) + f.write( + LONG + % { + "DOLLAR": "$", + "STYLE": cfg.style, + "TAG_PREFIX": cfg.tag_prefix, + "PARENTDIR_PREFIX": cfg.parentdir_prefix, + "VERSIONFILE_SOURCE": cfg.versionfile_source, + } + ) + cmds["py2exe"] = cmd_py2exe # we override different "sdist" commands for both environments @@ -1643,8 +1697,10 @@ def make_release_tree(self, base_dir, files): # updated value target_versionfile = os.path.join(base_dir, cfg.versionfile_source) print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, - self._versioneer_generated_versions) + write_to_version_file( + target_versionfile, self._versioneer_generated_versions + ) + cmds["sdist"] = cmd_sdist return cmds @@ -1699,11 +1755,13 @@ def do_setup(): root = get_root() try: cfg = get_config_from_root(root) - except (EnvironmentError, configparser.NoSectionError, - configparser.NoOptionError) as e: + except ( + EnvironmentError, + configparser.NoSectionError, + configparser.NoOptionError, + ) as e: if isinstance(e, (EnvironmentError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", - file=sys.stderr) + print("Adding sample versioneer config to setup.cfg", file=sys.stderr) with open(os.path.join(root, "setup.cfg"), "a") as f: f.write(SAMPLE_CONFIG) print(CONFIG_ERROR, file=sys.stderr) @@ -1712,15 +1770,18 @@ def do_setup(): print(" creating %s" % cfg.versionfile_source) with open(cfg.versionfile_source, "w") as f: LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), - "__init__.py") + f.write( + LONG + % { + "DOLLAR": "$", + "STYLE": cfg.style, + "TAG_PREFIX": cfg.tag_prefix, + "PARENTDIR_PREFIX": cfg.parentdir_prefix, + "VERSIONFILE_SOURCE": cfg.versionfile_source, + } + ) + + ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") if os.path.exists(ipy): try: with open(ipy, "r") as f: @@ -1762,8 +1823,10 @@ def do_setup(): else: print(" 'versioneer.py' already in MANIFEST.in") if cfg.versionfile_source not in simple_includes: - print(" appending versionfile_source ('%s') to MANIFEST.in" % - cfg.versionfile_source) + print( + " appending versionfile_source ('%s') to MANIFEST.in" + % cfg.versionfile_source + ) with open(manifest_in, "a") as f: f.write("include %s\n" % cfg.versionfile_source) else: From 050935811375adc45419c876df248344dae633e5 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Tue, 22 Aug 2023 16:08:08 +0100 Subject: [PATCH 06/38] Add VSCode recommended settings for use with black --- .vscode/extensions.json | 6 ++++++ .vscode/settings.json | 5 +++++ 2 files changed, 11 insertions(+) create mode 100644 .vscode/extensions.json create mode 100644 .vscode/settings.json diff --git a/.vscode/extensions.json b/.vscode/extensions.json new file mode 100644 index 00000000..876fcd74 --- /dev/null +++ b/.vscode/extensions.json @@ -0,0 +1,6 @@ +{ + "recommendations": [ + "ms-python.black-formatter", + "ms-python.python" + ] +} \ No newline at end of file diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..ea9d4d09 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,5 @@ +{ + "[python]": { + "editor.formatOnSave": true + } +} \ No newline at end of file From 6cb7b4f0a728a9563bb2a9f117578dc33642de34 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Tue, 22 Aug 2023 16:29:48 +0100 Subject: [PATCH 07/38] Add black GitHub action --- .github/workflows/black.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 .github/workflows/black.yaml diff --git a/.github/workflows/black.yaml b/.github/workflows/black.yaml new file mode 100644 index 00000000..0a8b8e92 --- /dev/null +++ b/.github/workflows/black.yaml @@ -0,0 +1,10 @@ +name: Lint + +on: [push, pull_request] + +jobs: + lint: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: psf/black@stable \ No newline at end of file From 576bddb43bfc68ea6f668e2ad3c64784b8f115f3 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Tue, 22 Aug 2023 16:14:01 +0100 Subject: [PATCH 08/38] meta data updates for black formatting - Add Alex to authors - Add `black` to changes --- AUTHORS | 4 ++++ CHANGES | 3 ++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/AUTHORS b/AUTHORS index 0acf2990..19708124 100644 --- a/AUTHORS +++ b/AUTHORS @@ -39,3 +39,7 @@ their first commit. GitHub handle is optional. - Cade Duckworth (cadeduckworth) +2023 +---- + +- Alexander Moriarty (@a-ws-m) diff --git a/CHANGES b/CHANGES index c89fa9da..d9cc73f0 100644 --- a/CHANGES +++ b/CHANGES @@ -6,7 +6,7 @@ Add summary of changes for each release. Use ISO 8061 dates. Reference GitHub issues numbers and PR numbers. 2023-??-?? 0.9.0 -cadeduckworth, orbeckst, VOD555 +cadeduckworth, orbeckst, VOD555, a-ws-m Changes @@ -24,6 +24,7 @@ Changes * _prepare_universe and _conclude_universe removed from EnsembleAnalysis.run() method, no longer needed (per comments, #199) * internal log_banner() now uses logger as argument (PR #247) +* use `black` formatter for codebase (#271) Enhancements From 063b93aa7c2162f8dd5aab6739de211a733bef57 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Tue, 22 Aug 2023 16:12:22 +0100 Subject: [PATCH 09/38] At git blame ignore revisions for black formatting --- .git-blame-ignore-revs | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 .git-blame-ignore-revs diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs new file mode 100644 index 00000000..f49cfb3a --- /dev/null +++ b/.git-blame-ignore-revs @@ -0,0 +1,2 @@ +# Autoformat all files using `black` +8f061e7da99eb78353e9392d6929673da5b352a3 From 2ddf4cd1a932af84c34b03f35948bb4393090450 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Fri, 25 Aug 2023 17:25:27 -0400 Subject: [PATCH 10/38] added black badge to README --- README.rst | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index de85b25b..7c4e37c1 100644 --- a/README.rst +++ b/README.rst @@ -2,7 +2,7 @@ README for MDPOW =================== -|build| |cov| |docs| |zenodo| +|build| |cov| |docs| |black| |zenodo| .. |P_ow| replace:: *P*\ :sub:`OW` .. |P_cw| replace:: *P*\ :sub:`CW` @@ -74,9 +74,14 @@ Source code *MDPOW* is open source and published under the `GNU General Public License v3`_. Source code is available at https://github.com/Becksteinlab/MDPOW . +We use `black`_ for uniform code formatting. + .. _`GNU General Public License v3`: http://www.gnu.org/licenses/gpl-3.0.html +.. _`black`: https://github.com/psf/black + + Footnotes --------- @@ -99,6 +104,8 @@ Footnotes :target: https://zenodo.org/badge/latestdoi/44999898 :alt: Zenodo - +.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg + :target: https://github.com/psf/black + :alt: black .. _INSTALL: INSTALL.rst From 1ccaba6d73f386eabab8202e12dac184db7de683 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Fri, 18 Aug 2023 19:07:23 +0100 Subject: [PATCH 11/38] Use OOP forcefields --- mdpow/equil.py | 70 +++---- mdpow/forcefields.py | 306 +++++++++++++++++++++--------- mdpow/templates/system.top | 14 +- mdpow/templates/system_octwet.top | 16 +- mdpow/tests/test_forcefields.py | 2 +- 5 files changed, 263 insertions(+), 145 deletions(-) diff --git a/mdpow/equil.py b/mdpow/equil.py index d1ac36ff..6a18de9c 100644 --- a/mdpow/equil.py +++ b/mdpow/equil.py @@ -29,9 +29,12 @@ .. autodata:: DIST """ import pickle +import re import os, errno import shutil +from string import Template +from typing import Optional import MDAnalysis as mda @@ -139,7 +142,9 @@ class Simulation(Journalled): "energy_minimize": "em_opls.mdp", } - def __init__(self, molecule=None, **kwargs): + def __init__( + self, molecule=None, ff_class: Optional[forcefields.Forcefield] = None, **kwargs + ): """Set up Simulation instance. The *molecule* of the compound molecule should be supplied. Existing files @@ -155,8 +160,11 @@ def __init__(self, molecule=None, **kwargs): :meth:`~mdpow.equil.Simulation.save`. *dirname* base directory; all other directories are created under it + *ff_class* + A :class:`mdpow.forcefields.Forcefield` instance. *forcefield* - 'OPLS-AA' or 'CHARMM' or 'AMBER' + A string representation of the forcefield, when using one of the defaults: + 'OPLS-AA' or 'CHARMM' or 'AMBER'. Not needed when :arg:`ff_class` is specified. *solvent* 'water' or 'octanol' or 'cyclohexane' or 'wetoctanol' or 'toluene' *solventmodel* @@ -180,7 +188,17 @@ def __init__(self, molecule=None, **kwargs): filename = kwargs.pop("filename", None) dirname = kwargs.pop("dirname", self.dirname_default) - forcefield = kwargs.pop("forcefield", "OPLS-AA") + if ff_class is not None: + assert isinstance(ff_class, forcefields.Forcefield) + forcefield: forcefields.Forcefield = ff_class + else: + forcefield_name = kwargs.pop("forcefield", "OPLS-AA") + try: + forcefield = forcefields.ALL_FORCEFIELDS[forcefield_name] + except KeyError: + raise ValueError( + f"No forcefield called `{forcefield_name}` is implemented. Please amend the `mdpow.forcefields.ALL_FORCEFIELDS` dictionary if you think it should be." + ) solvent = kwargs.pop("solvent", self.solvent_default) # mdp files --- should get values from default runinput.cfg # None values in the kwarg mdp dict are ignored @@ -350,7 +368,6 @@ def topology(self, itp="drug.itp", prm=None, **kwargs): dirname = kwargs.pop("dirname", self.BASEDIR("top")) self.dirs.topology = realpath(dirname) - setting = forcefields.get_ff_paths(self.forcefield) template = forcefields.get_top_template(self.solvent_type) top_template = config.get_template(kwargs.pop("top_template", template)) @@ -367,40 +384,23 @@ def topology(self, itp="drug.itp", prm=None, **kwargs): prm_kw = '#include "{}"'.format(_prm) with in_dir(dirname): + with open(top_template, "r") as f: + top_string_template = Template(f.read()) + top_string_formatted = top_string_template.substitute( + forcefield_itp=self.forcefield.forcefield_dir / "forcefield.itp", + prm_line=f'#include "{prm_kw}"' if prm_kw else "", + compound_itp=_itp, + solvent_itp=self.forcefield.forcefield_dir / self.solvent.itp, + ions_itp=self.forcefield.ions_itp, + water_itp=self.forcefield.default_water_itp, + compound_name=self.molecule, + solvent=self.solvent_type, + ) + with open(topol, "w") as f: + f.write(top_string_formatted) shutil.copy(itp, _itp) if prm is not None: shutil.copy(prm, _prm) - gromacs.cbook.edit_txt( - top_template, - [ - ( - r'#include +"oplsaa\.ff/forcefield\.itp"', - r"oplsaa\.ff/", - setting[0], - ), - (r'#include +"compound\.itp"', r"compound\.itp", _itp), - ( - r'#include +"oplsaa\.ff/tip4p\.itp"', - r"oplsaa\.ff/tip4p\.itp", - setting[0] + self.solvent.itp, - ), - ( - r'#include +"oplsaa\.ff/ions_opls\.itp"', - r"oplsaa\.ff/ions_opls\.itp", - setting[1], - ), - ( - r'#include +"compound\.prm"', - r'#include +"compound\.prm"', - prm_kw, - ), - (r'#include +"water\.itp"', r"water\.itp", setting[2]), - (r"Compound", "solvent", self.solvent_type), - (r"Compound", "DRUG", self.molecule), - (r"DRUG\s*1", "DRUG", self.molecule), - ], - newname=topol, - ) logger.info( "[%(dirname)s] Created topology %(topol)r that includes %(_itp)r", vars() ) diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index 348944da..4d098ebe 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -55,12 +55,18 @@ """ import os +from dataclasses import dataclass from collections import defaultdict +from pathlib import Path +from typing import Dict, List, Union import logging logger = logging.getLogger("mdpow.forecefields") +HERE = Path(__file__).parent +TOP_DIR = HERE / "top" + #: Default force field. At the moment, OPLS-AA, CHARMM/CGENFF, and AMBER/GAFF #: are directly supported. However, it is not recommended to change the #: default here as this behavior is not tested. @@ -130,9 +136,10 @@ def __repr__(self): ) -def _create_water_models(watermodelsdat): +def _create_water_models(watermodelsdat: Path) -> Dict[str, GromacsSolventModel]: models = {} - for line in GMX_WATERMODELS_DAT.split("\n"): + data = watermodelsdat.read_text() + for line in data.split("\n"): line = line.strip() if not line or line.startswith("#"): continue @@ -164,7 +171,56 @@ def _create_water_models(watermodelsdat): #: model available under the force field directory. The keys are the water model #: identifiers. #: For OPLS-AA the following ones are available. -GROMACS_WATER_MODELS = _create_water_models(GMX_WATERMODELS_DAT) +GROMACS_WATER_MODELS: Dict[str, GromacsSolventModel] = { + "tip4p": GromacsSolventModel( + "tip4p", + name="TIP4P", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip4p"], + description="TIP 4-point, recommended", + ), + "tip3p": GromacsSolventModel( + "tip3p", + name="TIP3P", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip3p"], + description="TIP 3-point", + ), + "tip5p": GromacsSolventModel( + "tip5p", + name="TIP5P", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip5p"], + description="TIP 5-point", + ), + "spc": GromacsSolventModel( + "spc", + name="SPC", + coordinates=SPECIAL_WATER_COORDINATE_FILES["spc"], + description="simple point charge", + ), + "spce": GromacsSolventModel( + "spce", + name="SPC/E", + coordinates=SPECIAL_WATER_COORDINATE_FILES["spce"], + description="extended simple point charge", + ), + "m24": GromacsSolventModel( + "m24", + name="M24", + coordinates=SPECIAL_WATER_COORDINATE_FILES["m24"], + description="TIP 3-point with modified LJ (M24)", + ), + "tip4pd": GromacsSolventModel( + "tip4pd", + name="TIP4P-D", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip4pd"], + description="TIP 4-point with modified dispersion (TIP4P-D)", + ), + "tip4pew": GromacsSolventModel( + "tip4pew", + name="TIP4PEW", + coordinates=SPECIAL_WATER_COORDINATE_FILES["tip4pew"], + description="TIP 4-point modified for use with Ewald techniques (TIP4PEW)", + ), +} def get_water_model(watermodel=DEFAULT_WATER_MODEL): @@ -180,78 +236,147 @@ def get_water_model(watermodel=DEFAULT_WATER_MODEL): raise ValueError(msg) +@dataclass +class Forcefield: + """Contains information about files corresponding to a forcefield.""" + + name: str + solvent_models: Dict[str, GromacsSolventModel] + forcefield_dir: Path + ions_itp: Path + default_water_itp: Path + + def __post_init__(self): + """Check that the provided paths exist and populate the :attr:`water_models`.""" + for path_ in self.ff_paths: + if not path_.exists(): + raise ValueError(f"Could not find required forcefield files: {path_}") + + self.water_models: Dict[str, GromacsSolventModel] = _create_water_models( + self.forcefield_dir / "watermodels.dat" + ) + + @property + def ff_paths(self) -> List[Path]: + """Get the path to the forcefield directory and the ITP files for the ions and default water model.""" + return [self.forcefield_dir, self.ions_itp, self.default_water_itp] + + def __repr__(self) -> str: + """Get the name of the force field.""" + return self.name + + #: Other solvents (not water, see :data:`GROMACS_WATER_MODELS` for those). -new_octanol = """Zangi R (2018) Refinement of the OPLSAA force-field - for liquid alcohols.; ACS Omega 3(12):18089-18099. - doi: 10.1021/acsomega.8b03132""" +NEW_OCTANOL_DESC = "Zangi R (2018) Refinement of the OPLSAA force-field for liquid alcohols.; ACS Omega 3(12):18089-18099. doi: 10.1021/acsomega.8b03132" -OPLS_SOLVENT_MODELS = { - "octanol": GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct.gro" - ), - "octanolnew": GromacsSolventModel( - identifier="octanol", - itp="1octnew.itp", - coordinates="1oct.gro", - description=new_octanol, - ), - "cyclohexane": GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo.gro" - ), - "wetoctanol": GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet.gro" - ), - "wetoctanolnew": GromacsSolventModel( - identifier="wetoctanol", - itp="1octwetnew.itp", - coordinates="1octwet.gro", - description=new_octanol, - ), - "toluene": GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_oplsaa.gro" - ), -} -CHARMM_SOLVENT_MODELS = { - "octanol": GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct_charmm.gro" - ), - "wetoctanol": GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_charmm.gro" - ), - "cyclohexane": GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_charmm.gro" - ), - "toluene": GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_charmm.gro" - ), -} +#: See the file ``top/oplsaa.ff/watermodels.dat`` for a description of +#: available water models that are bundled with MDPOW. -AMBER_SOLVENT_MODELS = { - "octanol": GromacsSolventModel( - identifier="octanol", itp="1oct.itp", coordinates="1oct_amber.gro" - ), - "wetoctanol": GromacsSolventModel( - identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_amber.gro" - ), - "cyclohexane": GromacsSolventModel( - identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_amber.gro" - ), - "toluene": GromacsSolventModel( - identifier="toluene", itp="1tol.itp", coordinates="1tol_amber.gro" - ), +OPLS_AA_FF_DIR = TOP_DIR / "oplsaa.ff" +OPLS_AA = Forcefield( + "OPLS-AA", + { + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct.gro" + ), + "octanolnew": GromacsSolventModel( + identifier="octanol", + itp="1octnew.itp", + coordinates="1oct.gro", + description=NEW_OCTANOL_DESC, + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet.gro" + ), + "wetoctanolnew": GromacsSolventModel( + identifier="wetoctanol", + itp="1octwetnew.itp", + coordinates="1octwet.gro", + description=NEW_OCTANOL_DESC, + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_oplsaa.gro" + ), + }, + OPLS_AA_FF_DIR, + OPLS_AA_FF_DIR / "ions_opls.itp", + OPLS_AA_FF_DIR / "tip4p.itp", +) + +CHARMM_FF_DIR = TOP_DIR / "charmm36-mar2019.ff" +CHARMM = Forcefield( + "CHARMM", + { + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct_charmm.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_charmm.gro" + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_charmm.gro" + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_charmm.gro" + ), + }, + CHARMM_FF_DIR, + CHARMM_FF_DIR / "ions.itp", + CHARMM_FF_DIR / "tip3p.itp", +) + +AMBER_FF_DIR = TOP_DIR / "amber99sb.ff" +AMBER = Forcefield( + "AMBER", + { + "octanol": GromacsSolventModel( + identifier="octanol", itp="1oct.itp", coordinates="1oct_amber.gro" + ), + "wetoctanol": GromacsSolventModel( + identifier="wetoctanol", itp="1octwet.itp", coordinates="1octwet_amber.gro" + ), + "cyclohexane": GromacsSolventModel( + identifier="cyclohexane", itp="1cyclo.itp", coordinates="1cyclo_amber.gro" + ), + "toluene": GromacsSolventModel( + identifier="toluene", itp="1tol.itp", coordinates="1tol_amber.gro" + ), + }, + AMBER_FF_DIR, + AMBER_FF_DIR / "ions.itp", + AMBER_FF_DIR / "tip3p.itp", +) + +ALL_FORCEFIELDS: Dict[str, Forcefield] = { + "OPLS-AA": OPLS_AA, + "CHARMM": CHARMM, + "AMBER": AMBER, } #: Solvents available in GROMACS; the keys of the dictionary #: are the forcefields. GROMACS_SOLVENT_MODELS = { - "OPLS-AA": OPLS_SOLVENT_MODELS, - "CHARMM": CHARMM_SOLVENT_MODELS, - "AMBER": AMBER_SOLVENT_MODELS, + "OPLS-AA": OPLS_AA.solvent_models, + "CHARMM": CHARMM.solvent_models, + "AMBER": AMBER.solvent_models, } -def get_solvent_identifier(solvent_type, model=None, forcefield="OPLS-AA"): +def _get_forcefield(ff_name: str) -> Forcefield: + """Get the :class:`Forcefield` instance corresponding to a given name.""" + try: + return ALL_FORCEFIELDS[ff_name] + except KeyError: + raise ValueError(f"Forcefield `{ff_name}` not found.") + + +def get_solvent_identifier( + solvent_type, model=None, forcefield: Union[Forcefield, str] = OPLS_AA +): """Get the identifier for a solvent model. The identifier is needed to access a water model (i.e., a @@ -273,61 +398,54 @@ def get_solvent_identifier(solvent_type, model=None, forcefield="OPLS-AA"): of OPLS-AA forcefield, the ``model`` is used to select a specific model. For other solvents and forcefields, "model" is not required. - :Returns: Either an identifier or ``None`` + :Raises ValueError: If there is no identifier found for the combination. + + :Returns: An identifier """ + if isinstance(forcefield, str): + forcefield = _get_forcefield(forcefield) if solvent_type == "water": identifier = model if not model in (None, "water") else DEFAULT_WATER_MODEL - return identifier if identifier in GROMACS_WATER_MODELS else None - if model not in GROMACS_SOLVENT_MODELS[forcefield]: - if solvent_type in GROMACS_SOLVENT_MODELS[forcefield]: + if identifier in forcefield.water_models: + return identifier + else: + raise ValueError( + f"Cannot find {identifier} in {forcefield.name} water models." + ) + if model not in forcefield.solvent_models: + if solvent_type in forcefield.solvent_models: model = solvent_type else: - model = None + raise ValueError( + f"Solvent type {solvent_type} not available in {forcefield.name} solvent models." + ) return model -def get_solvent_model(identifier, forcefield="OPLS-AA"): +def get_solvent_model(identifier, forcefield: Union[Forcefield, str] = OPLS_AA): """Return a :class:`GromacsSolventModel` corresponding to identifier *identifier*. If identifier is "water" then the :data:`DEFAULT_WATER_MODEL` is assumed. """ + if isinstance(forcefield, str): + forcefield = _get_forcefield(forcefield) if identifier == "water": identifier = DEFAULT_WATER_MODEL try: - return GROMACS_WATER_MODELS[identifier] + return forcefield.water_models[identifier] except KeyError: try: - return GROMACS_SOLVENT_MODELS[forcefield][identifier] + return forcefield.solvent_models[identifier] except KeyError: - msg = "No solvent model with name {0} is available.".format(identifier) + msg = "No solvent model with name {0} is available for forcefield {1}.".format( + identifier, forcefield.name + ) logger.critical(msg) raise ValueError(msg) -def get_ff_paths(forcefield="OPLS-AA"): - """Return a :list: containing the forcefield directory, paths of ions - and default watermodel itp files. - """ - - settings = { - "OPLS-AA": ["oplsaa.ff/", "oplsaa.ff/ions_opls.itp", "oplsaa.ff/tip4p.itp"], - "AMBER": ["amber99sb.ff/", "amber99sb.ff/ions.itp", "amber99sb.ff/tip3p.itp"], - "CHARMM": [ - "charmm36-mar2019.ff/", - "charmm36-mar2019.ff/ions.itp", - "charmm36-mar2019.ff/tip3p.itp", - ], - } - try: - return settings[forcefield] - except KeyError: - msg = "No forcefield with name {0} is available".format(forcefield) - logger.critical(msg) - raise ValueError(msg) - - def get_top_template(identifier): """Return the topology file template suitable for the solvent model.""" diff --git a/mdpow/templates/system.top b/mdpow/templates/system.top index 21fa8baa..fefad275 100644 --- a/mdpow/templates/system.top +++ b/mdpow/templates/system.top @@ -6,22 +6,22 @@ ; to change it as needed. See the source mdpow/equil.py for details. ; Include forcefield parameters -#include "oplsaa.ff/forcefield.itp" +#include "$forcefield_itp" ; Include compound topology -#include "compound.prm" -#include "compound.itp" +$prm_line +#include "$compound_itp" ; Include solvent topology -#include "oplsaa.ff/tip4p.itp" +#include "$solvent_itp" ; Include topology for OPLS/AA ions -#include "oplsaa.ff/ions_opls.itp" +#include "$ions_itp" [ system ] ; Name -Compound DRUG in solvent +Compound $compound_name in $solvent [ molecules ] ; Compound #mols -DRUG 1 +$compound_name 1 diff --git a/mdpow/templates/system_octwet.top b/mdpow/templates/system_octwet.top index 4c8c6054..be32d0db 100644 --- a/mdpow/templates/system_octwet.top +++ b/mdpow/templates/system_octwet.top @@ -6,24 +6,24 @@ ; to change it as needed. See the source mdpow/equil.py for details. ; Include forcefield parameters -#include "oplsaa.ff/forcefield.itp" +#include "$forcefield_itp" ; Include compound topology -#include "compound.prm" -#include "compound.itp" +$prm_line +#include "$compound_itp" ; Include solvent topology -#include "oplsaa.ff/tip4p.itp" -#include "water.itp" +#include "$solvent_itp" ; Include topology for OPLS/AA ions -#include "oplsaa.ff/ions_opls.itp" +#include "$ions_itp" +#include "$water_itp" [ system ] ; Name -Compound DRUG in solvent +Compound $compound_name in $solvent [ molecules ] ; Compound #mols -DRUG 1 +$compound_name 1 ;OcOH 1 diff --git a/mdpow/tests/test_forcefields.py b/mdpow/tests/test_forcefields.py index bc5c3112..25d06488 100644 --- a/mdpow/tests/test_forcefields.py +++ b/mdpow/tests/test_forcefields.py @@ -112,7 +112,7 @@ def test_get_solvent_default_water(): defaultmodel = mdpow.forcefields.DEFAULT_WATER_MODEL assert ( mdpow.forcefields.get_solvent_model(model) - is mdpow.forcefields.GROMACS_WATER_MODELS[defaultmodel] + == mdpow.forcefields.GROMACS_WATER_MODELS[defaultmodel] ) @staticmethod From 4331ebe8fcb20acb999bf6ff655e2f7a24b465f5 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Fri, 18 Aug 2023 19:10:40 +0100 Subject: [PATCH 12/38] Add Sphinx docstring --- mdpow/forcefields.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index 4d098ebe..6d176e90 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -47,6 +47,9 @@ .. autoclass:: GromacsSolventModel :members: +.. autoclass:: Forcefield + :members: + .. autofunction:: get_water_model .. autofunction:: get_solvent_identifier From 8053d7353af727de0ebdd62a0e721b769551b2eb Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 21 Aug 2023 14:10:26 +0100 Subject: [PATCH 13/38] Change template file extensions --- mdpow/templates/{system.top => system.top.template} | 0 mdpow/templates/{system_octwet.top => system_octwet.top.template} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename mdpow/templates/{system.top => system.top.template} (100%) rename mdpow/templates/{system_octwet.top => system_octwet.top.template} (100%) diff --git a/mdpow/templates/system.top b/mdpow/templates/system.top.template similarity index 100% rename from mdpow/templates/system.top rename to mdpow/templates/system.top.template diff --git a/mdpow/templates/system_octwet.top b/mdpow/templates/system_octwet.top.template similarity index 100% rename from mdpow/templates/system_octwet.top rename to mdpow/templates/system_octwet.top.template From 68bef441e67680a1938adc8fa7f898d1ca4e3ed4 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Tue, 29 Aug 2023 16:23:59 +0100 Subject: [PATCH 14/38] Fix references to system.top --- doc/sphinx/source/init.txt | 2 +- mdpow/forcefields.py | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/sphinx/source/init.txt b/doc/sphinx/source/init.txt index f07aa47f..23e071fb 100644 --- a/doc/sphinx/source/init.txt +++ b/doc/sphinx/source/init.txt @@ -312,7 +312,7 @@ Hydration free energy Reopen the python session and set up a :class:`~mdpow.fep.Ghyd` object:: import mdpow.fep - gwat = mdpow.fep.Ghyd(molecule="OcOH", top="Equilibrium/water/top/system.top", struct="Equilibrium/water/MD_NPT/md.pdb", ndx="Equilibrium/water/solvation/main.ndx", runtime=100) + gwat = mdpow.fep.Ghyd(molecule="OcOH", top="Equilibrium/water/top/system.top.template", struct="Equilibrium/water/MD_NPT/md.pdb", ndx="Equilibrium/water/solvation/main.ndx", runtime=100) Alternatively, one can save some typing if we continue the last session and use the :class:`mdpow.equil.Simulation` object (which we can re-load from its saved diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index 92d8d28b..61152f9d 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -447,11 +447,11 @@ def get_top_template(identifier): """Return the topology file template suitable for the solvent model.""" templates = { - "water": "system.top", - "octanol": "system.top", - "cyclohexane": "system.top", - "wetoctanol": "system_octwet.top", - "toluene": "system.top", + "water": "system.top.template", + "octanol": "system.top.template", + "cyclohexane": "system.top.template", + "wetoctanol": "system_octwet.top.template", + "toluene": "system.top.template", } try: return templates[identifier] From 703442800702c654ccc609daab7247d2a65b8a02 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 21 Aug 2023 17:51:32 +0100 Subject: [PATCH 15/38] [WIP] Boilerplate for Martini benzene Pow --- .gitignore | 6 + doc/examples/martini/em.mdp | 16 + doc/examples/martini/eq.mdp | 23 + doc/examples/martini/martini-benzene.ipynb | 122 + doc/examples/martini/run.mdp | 101 + doc/examples/martini/water.gro | 2707 ++++++++++++++++++++ 6 files changed, 2975 insertions(+) create mode 100644 doc/examples/martini/em.mdp create mode 100644 doc/examples/martini/eq.mdp create mode 100644 doc/examples/martini/martini-benzene.ipynb create mode 100644 doc/examples/martini/run.mdp create mode 100644 doc/examples/martini/water.gro diff --git a/.gitignore b/.gitignore index ed42a5df..53a68245 100644 --- a/.gitignore +++ b/.gitignore @@ -15,3 +15,9 @@ coverage.xml *.lock *.npz dir.csv + +# Files for the Martini example that can be downloaded at runtime +doc/examples/martini/* +!doc/examples/martini/*.mdp +!doc/examples/martini/*.ipynb +!doc/examples/martini/water.gro diff --git a/doc/examples/martini/em.mdp b/doc/examples/martini/em.mdp new file mode 100644 index 00000000..5035d5e6 --- /dev/null +++ b/doc/examples/martini/em.mdp @@ -0,0 +1,16 @@ +integrator = steep +dt = 0.02 +nsteps = 1000 +nstxout = 0 +nstvout = 0 +nstlog = 100 +nstxtcout = 100 +xtc-precision = 1000 +rlist = 1.4 +coulombtype = Reaction-Field +rcoulomb = 1.1 +epsilon_r = 15 +vdw-type = cutoff +vdw-modifier = Potential-shift-verlet +rvdw = 1.1 +constraints = none diff --git a/doc/examples/martini/eq.mdp b/doc/examples/martini/eq.mdp new file mode 100644 index 00000000..2a15bc2a --- /dev/null +++ b/doc/examples/martini/eq.mdp @@ -0,0 +1,23 @@ +dt = 0.005 +nsteps = 25000 +nstxout = 0 +nstvout = 0 +nstlog = 1000 +nstxout-compressed = 1000 +cutoff-scheme = Verlet +coulombtype = Reaction-Field +rcoulomb = 1.1 +epsilon_r = 15 +vdw-type = cutoff +vdw-modifier = Potential-shift-verlet +rvdw = 1.1 +tcoupl = v-rescale +tc-grps = System +tau-t = 1.0 +ref-t = 300 +Pcoupl = c-rescale +Pcoupltype = isotropic +tau-p = 3.0 +compressibility = 3e-4 +ref-p = 1.0 +refcoord_scaling = all diff --git a/doc/examples/martini/martini-benzene.ipynb b/doc/examples/martini/martini-benzene.ipynb new file mode 100644 index 00000000..0e0d1b28 --- /dev/null +++ b/doc/examples/martini/martini-benzene.ipynb @@ -0,0 +1,122 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Example: using a different force field\n", + "\n", + "Here we show how to use MDPOW to calculate partition coefficients using an force field that isn't included in the package. To follow along, install `jupyter` in your `mdpow` environment.\n", + "\n", + "To implement a new force field, you will need:\n", + "\n", + "* `ITP` files for the molecule, the solvents, ions and also the general atom type definitions file (usually just named after the force field itself).\n", + "* `MDP` files for the energy minimisation, initial relaxation, NPT ensemble run and free energy calculation.\n", + "* Structure files (`.gro` or `.pdb`) for the solute and non-aqueous solvent. If you are using a type of water that does not come bundled with GROMACS, like in this example, you will also need to create an equilibrated box of pure water.\n", + "\n", + "The first thing we'll do is to download the files we need for Martini 3.0." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "from typing import Optional\n", + "\n", + "import requests as req\n", + "from zipfile import ZipFile\n", + "\n", + "HERE = Path(\".\")\n", + "\n", + "MARTINI_ITP = HERE / \"martini_v3.0.0.itp\"\n", + "MARTINI_IONS = HERE / \"martini_v3.0.0_ions_v1.itp\"\n", + "MARTINI_SMALL_MOLS = HERE / \"martini_v3.0.0_small_molecules_v1.itp\"\n", + "MARTINI_SOLVENTS = HERE / \"martini_v3.0.0_solvents_v1.itp\"\n", + "MARTINI_WATER = HERE / \"water.gro\"\n", + "MARTINI_OCTANOL = HERE / \"octanol.gro\"\n", + "\n", + "EM_FILE = HERE / \"em.mdp\"\n", + "EQ_FILE = HERE / \"eq.mdp\"\n", + "RUN_FILE = HERE / \"run.mdp\"\n", + "\n", + "def download_file(\n", + " url: str, out: Optional[Path] = None, chunk_size: int = 128, overwrite: bool = False\n", + "):\n", + " \"\"\"Utility function to download files.\"\"\"\n", + " if out is None:\n", + " out = HERE / Path(url).name\n", + "\n", + " if out.exists() and not overwrite:\n", + " return\n", + "\n", + " r = req.get(url, stream=True)\n", + " r.raise_for_status()\n", + "\n", + " with out.open(\"wb\") as f:\n", + " for chunk in r.iter_content(chunk_size=chunk_size):\n", + " f.write(chunk)\n", + "\n", + "\n", + "ZIP_DOWNLOAD = {\n", + " HERE / \"BENZ.itp\": \"https://mad.ibcp.fr/api/molecule/download?id=731653322400583591&filename=BENZ.zip\"\n", + "}\n", + "DOWNLOADS = {\n", + " MARTINI_ITP: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0.itp\",\n", + " MARTINI_IONS: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_ions_v1.itp\",\n", + " MARTINI_SMALL_MOLS: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_small_molecules_v1.itp\",\n", + " MARTINI_SOLVENTS: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_solvents_v1.itp\",\n", + "}\n", + "DOWNLOADS.update(ZIP_DOWNLOAD)\n", + "\n", + "for fname, url in DOWNLOADS.items():\n", + " download_file(url, fname)\n", + "\n", + "for zip_file in ZIP_DOWNLOAD.keys():\n", + " with ZipFile(zip_file, \"r\") as zip_ref:\n", + " zip_ref.extractall(HERE)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This should have downloaded several files to your workspace." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import gromacs\n", + "from mdpow import equil, forcefields, fep" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "mdpow", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.4" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/doc/examples/martini/run.mdp b/doc/examples/martini/run.mdp new file mode 100644 index 00000000..aed06872 --- /dev/null +++ b/doc/examples/martini/run.mdp @@ -0,0 +1,101 @@ +integrator = sd +; start time and timestep in ps = +tinit = 0 +dt = 0.020 + +nsteps = 200000 + +; We remove center of mass motion. In periodic boundary conditions, the center of mass motion is spurious; the periodic system is the same in all translational directions. +comm-mode = Linear +; number of steps for center of mass motion removal = +nstcomm = 10 + +; Output frequency for energies to log file and energy file = +nstxout = 0 +nstvout = 0 +nstfout = 0 +nstlog = 10000 +nstenergy = 10000 +nstcalcenergy = 10 +nstxtcout = 10000 + +cutoff-scheme = Verlet +nstlist = 20 +;rlist = 1.2 + +coulombtype = cutoff +coulomb-modifier = Potential-shift-verlet +rcoulomb = 1.1 +epsilon_r = 15 ; 2.5 (with polarizable water) +vdw_type = cutoff +vdw-modifier = Potential-shift-verlet +rvdw = 1.1 + +;coulombtype = Shift +;rcoulomb_switch = 0.0 +;rcoulomb = 1.2 +;epsilon_r = 15 +;vdw_type = Shift +;rvdw_switch = 0.9 +;rvdw = 1.2 + + +gen-vel = no +gen_seed = 175547 +tc-grps = System +tcoupl = v-rescale +tau_t = 1.0 +ref_t = 300 +; Pressure coupling = +Pcoupl = Parrinello-Rahman +tau_p = 4.0 +compressibility = 4.5e-5 +ref_p = 1.0 + +;lincs-iter = 2 +;lincs-order = 8 + +;-------------------- +; Free energy parameters +free-energy = yes +sc-power = 1 +sc-alpha = 0.5 +sc-r-power = 6 + +; Which intermediate state do we start with? Doesn't really matter, it leaves soon +------- +init-lambda-state = 0 + +; What are the values of lambda at the intermediate states? +;------- +vdw-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 + +; This makes sure we print out the differences in Hamiltonians between all states, and not just the neighboring states +;-------- +calc-lambda-neighbors = -1 + +; the frequency the free energy information is calculated. This +; frequency (every 0.2 ps) is pretty good for small molecule solvation. +;------- +nstdhdl = 10 + +; not required, but useful if you are doing any temperature reweighting. Without +; temperature reweighting, you don't need the total energy -- differences are enough +dhdl-print-energy = yes + +; We are doing free energies with the solute molecule alone +couple-moltype = SOLUTE + +; decharging free energy +; couple-lambda0 = vdw-q +; couple-lambda1 = vdw +; LJ decoupling free energy +; couple-lambda0 = vdw +; couple-lambda1 = none +; +; fully coupled (change for BAR!) +couple-lambda0 = vdw-q +couple-lambda1 = vdw-q + +; we are keeping the intramolecular interactions ON in all the interactions from state 0 to state 8 +couple-intramol = no diff --git a/doc/examples/martini/water.gro b/doc/examples/martini/water.gro new file mode 100644 index 00000000..81cc49ef --- /dev/null +++ b/doc/examples/martini/water.gro @@ -0,0 +1,2707 @@ +Bulk water + 2704 + 2W W 9 0.623 6.453 2.746 -0.0737 -0.1789 -0.1413 + 3W W 10 1.495 0.821 3.127 -0.1418 -0.1647 0.0677 + 4W W 11 2.276 4.379 0.851 0.2728 0.0220 0.2236 + 5W W 12 5.055 4.688 2.860 0.0937 -0.3331 -0.0833 + 6W W 13 4.012 4.510 5.068 -0.1118 -0.1475 -0.0498 + 7W W 14 3.595 3.790 5.262 -0.0778 0.2281 -0.1970 + 8W W 15 5.358 3.850 0.162 -0.4069 0.0149 -0.2239 + 9W W 16 3.026 2.679 3.002 -0.0954 -0.1023 -0.1055 + 10W W 17 1.767 5.981 3.865 -0.0407 -0.2463 0.1740 + 11W W 18 1.607 5.505 2.571 0.1889 -0.0966 -0.1597 + 12W W 19 1.525 3.724 1.065 -0.0622 -0.2190 0.1383 + 13W W 20 5.038 4.095 6.235 0.2992 0.2551 -0.0924 + 14W W 21 3.372 0.445 2.683 -0.0263 -0.1986 -0.1561 + 15W W 22 2.891 2.358 2.013 0.2005 -0.3125 -0.3680 + 16W W 23 3.484 6.747 3.727 0.0395 0.0813 -0.2420 + 17W W 24 0.394 3.593 2.307 0.0876 0.4153 -0.1754 + 18W W 25 5.421 0.071 0.703 -0.1936 0.0101 -0.0361 + 19W W 26 0.121 0.230 1.920 -0.1463 -0.1812 0.0213 + 20W W 27 5.873 3.814 1.767 0.2144 -0.2329 -0.3887 + 21W W 28 3.247 1.444 4.917 -0.2452 0.0449 -0.1365 + 22W W 29 6.536 3.378 1.289 0.0752 -0.0211 -0.4815 + 23W W 30 6.560 2.604 2.963 -0.0422 0.0859 -0.0071 + 24W W 31 3.212 5.952 2.122 0.2179 -0.0334 -0.1594 + 25W W 32 5.320 2.953 1.452 -0.0715 0.4087 0.0248 + 26W W 33 6.377 0.752 0.250 -0.1550 -0.0127 0.0174 + 27W W 34 0.698 1.568 6.237 0.0740 -0.1080 -0.0125 + 28W W 35 2.688 3.049 5.235 0.0295 0.1629 0.2172 + 29W W 36 3.273 4.052 1.223 0.1699 -0.0973 0.0092 + 30W W 37 2.431 4.545 1.793 0.1082 0.2825 -0.1479 + 31W W 38 1.455 5.386 5.294 -0.0707 0.0382 -0.1311 + 32W W 39 4.616 0.921 5.212 -0.0638 -0.1584 0.0205 + 33W W 40 3.269 5.536 4.719 0.3254 0.1263 0.1213 + 34W W 41 0.823 0.105 0.652 -0.1772 0.0511 0.0192 + 35W W 42 3.481 1.089 6.369 -0.1815 0.0325 0.0530 + 36W W 43 2.618 5.168 6.458 0.0969 0.1620 -0.2941 + 37W W 44 6.385 5.082 2.096 -0.0818 0.0769 0.2357 + 38W W 45 5.815 1.072 1.921 0.0622 0.2031 0.0505 + 39W W 46 4.785 5.907 4.110 0.1423 -0.1447 -0.4017 + 40W W 47 6.796 6.585 6.387 -0.0173 -0.0163 0.2549 + 41W W 48 1.259 3.336 3.304 0.2275 0.0985 0.0315 + 42W W 49 3.139 1.761 0.834 -0.0537 0.0305 -0.1154 + 43W W 50 5.968 3.805 6.331 0.2139 0.3587 0.0376 + 44W W 51 3.415 1.193 3.145 0.1488 -0.1317 -0.2214 + 45W W 52 4.952 5.998 1.738 -0.3219 -0.0336 -0.0133 + 46W W 53 3.505 3.173 5.824 -0.1645 -0.1756 -0.0430 + 47W W 54 5.780 6.314 3.547 -0.0756 -0.0882 -0.0656 + 48W W 55 0.097 2.465 0.167 -0.1592 -0.1234 -0.0037 + 49W W 56 4.675 2.727 1.936 0.0914 -0.2342 0.1907 + 50W W 57 6.254 1.994 0.052 -0.1546 -0.0236 0.1653 + 51W W 58 5.138 3.730 5.338 -0.3757 0.0532 -0.0515 + 52W W 59 4.158 0.392 3.947 0.1395 -0.1566 0.1498 + 53W W 60 3.600 0.648 5.838 0.1288 0.2750 0.1085 + 54W W 61 1.555 5.294 6.289 -0.0164 0.0364 -0.0824 + 55W W 62 2.276 2.197 3.599 -0.1442 0.0631 0.1655 + 56W W 63 5.420 6.654 3.909 0.0633 -0.2813 0.2127 + 57W W 64 0.722 2.399 1.416 0.2827 -0.2743 -0.0243 + 58W W 65 6.709 5.673 6.099 -0.1199 -0.3740 0.2590 + 59W W 66 0.086 5.758 0.199 0.0145 -0.2705 0.0590 + 60W W 67 1.664 0.521 5.479 -0.0370 -0.3252 0.2405 + 61W W 68 0.877 2.100 5.898 -0.1912 0.2092 -0.0338 + 62W W 69 1.461 4.768 6.323 0.1194 0.3317 -0.0010 + 63W W 70 4.388 5.306 4.807 0.4870 0.0131 0.0575 + 64W W 71 4.724 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2.818 3.653 1.065 -0.1807 0.2447 -0.2448 + 2691W W 2698 5.707 3.343 1.433 -0.1670 -0.0935 0.0519 + 2692W W 2699 6.606 0.655 4.026 -0.0801 0.1854 0.0575 + 2693W W 2700 6.573 1.203 4.149 0.1100 0.0042 -0.0778 + 2694W W 2701 6.420 0.823 6.145 -0.1045 -0.0272 -0.0958 + 2695W W 2702 1.048 5.973 1.363 -0.0304 -0.2457 0.0535 + 2696W W 2703 1.528 4.309 1.440 0.3895 -0.3613 -0.1011 + 2697W W 2704 2.350 4.015 1.670 -0.1132 0.2028 0.1334 + 2698W W 2705 4.812 1.911 4.112 -0.2072 -0.2805 0.0912 + 2699W W 2706 0.972 0.124 1.147 -0.2538 0.0397 0.0581 + 2700W W 2707 1.525 3.455 0.600 -0.1575 -0.2820 0.1895 + 2701W W 2708 1.975 6.201 6.625 0.0036 0.1664 -0.1642 + 2702W W 2709 4.301 3.342 1.379 -0.1293 -0.1352 -0.2467 + 2703W W 2710 3.671 2.397 6.009 0.0508 0.0352 0.0895 + 2704W W 2711 5.800 2.764 5.035 -0.1177 -0.1528 0.0000 + 2705W W 2712 6.639 3.898 1.301 0.0357 0.3257 -0.2098 + 6.85823 6.85823 6.85823 From 0f32aa03a7bd9c5b675c670c55dc19e2cefe8b4e Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 30 Aug 2023 17:25:21 +0100 Subject: [PATCH 16/38] Correct solvation identifier test --- mdpow/forcefields.py | 12 ++++++++++-- mdpow/tests/test_forcefields.py | 6 ++++-- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index 61152f9d..44a9221a 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -408,8 +408,15 @@ def get_solvent_identifier( forcefield = _get_forcefield(forcefield) if solvent_type == "water": - identifier = model if not model in (None, "water") else DEFAULT_WATER_MODEL - return identifier if identifier in forcefield.water_models else None + identifier = DEFAULT_WATER_MODEL if model in [None, "water"] else model + + if identifier in forcefield.water_models: + return identifier + else: + raise ValueError( + f"{identifier} is not a valid water model for {forcefield.name}." + ) + if model not in forcefield.solvent_models: if solvent_type in forcefield.solvent_models: model = solvent_type @@ -417,6 +424,7 @@ def get_solvent_identifier( raise ValueError( f"Solvent type {solvent_type} not available in {forcefield.name} solvent models." ) + return model diff --git a/mdpow/tests/test_forcefields.py b/mdpow/tests/test_forcefields.py index 25d06488..9efd509f 100644 --- a/mdpow/tests/test_forcefields.py +++ b/mdpow/tests/test_forcefields.py @@ -174,5 +174,7 @@ def test_get_solvent_identifier_solvents(self, solvent, model): @staticmethod def test_get_solvent_identifier_None(): - assert mdpow.forcefields.get_solvent_identifier("water", model="foobar") is None - assert mdpow.forcefields.get_solvent_identifier("benzene") is None + with pytest.raises(ValueError): + mdpow.forcefields.get_solvent_identifier("water", model="foobar") + with pytest.raises(ValueError): + mdpow.forcefields.get_solvent_identifier("benzene") From a2f5cbf4b08b885e6bf9dd535b74f727153cc70f Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 30 Aug 2023 17:25:30 +0100 Subject: [PATCH 17/38] Add pytest settings for VSCode --- .vscode/settings.json | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index ea9d4d09..5124b543 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,5 +1,10 @@ { "[python]": { "editor.formatOnSave": true - } + }, + "python.testing.pytestArgs": [ + "mdpow" + ], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true } \ No newline at end of file From e26d8e5fdabd412aedb719c3ed51610db9ce149b Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 30 Aug 2023 18:04:43 +0100 Subject: [PATCH 18/38] Add typehinting --- mdpow/tests/test_solvation.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/mdpow/tests/test_solvation.py b/mdpow/tests/test_solvation.py index d2d75404..56b99b73 100644 --- a/mdpow/tests/test_solvation.py +++ b/mdpow/tests/test_solvation.py @@ -1,5 +1,7 @@ import os import shutil +from pathlib import Path +from typing import Dict, Type from gromacs.utilities import in_dir import gromacs @@ -10,7 +12,7 @@ from . import RESOURCES -sims = { +sims: Dict[str, Type[equil.Simulation]] = { "water": equil.WaterSimulation, "octanol": equil.OctanolSimulation, "cyclohexane": equil.CyclohexaneSimulation, @@ -35,7 +37,7 @@ def setup(tmpdir): return newdir.dirname -def solvation(setup, solvent, ff="OPLS-AA"): +def solvation(setup: Path, solvent: str, ff="OPLS-AA"): itp = test_file[ff] with in_dir(setup, create=False): try: From 5140b74b0c4492a1299935fd062ecd07aa957303 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 30 Aug 2023 18:05:25 +0100 Subject: [PATCH 19/38] Fix top file suffix after changing from template --- mdpow/equil.py | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/mdpow/equil.py b/mdpow/equil.py index 6a18de9c..92d4de5b 100644 --- a/mdpow/equil.py +++ b/mdpow/equil.py @@ -33,6 +33,7 @@ import os, errno import shutil +from pathlib import Path from string import Template from typing import Optional @@ -371,7 +372,18 @@ def topology(self, itp="drug.itp", prm=None, **kwargs): template = forcefields.get_top_template(self.solvent_type) top_template = config.get_template(kwargs.pop("top_template", template)) - topol = kwargs.pop("topol", os.path.basename(top_template)) + + default_top_path = Path(top_template) + if ".top" in default_top_path.suffixes: + # Include all suffixes up to that one + default_top_name = default_top_path.name + default_top_name = ( + default_top_name[: default_top_name.index(".top")] + ".top" + ) + else: + default_top_name = default_top_path.with_suffix(".top").name + + topol = kwargs.pop("topol", default_top_name) self.top_template = top_template itp = os.path.realpath(itp) _itp = os.path.basename(itp) From 2f578f5cf9bd791c5ac7708bd6826f030b63d971 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 30 Aug 2023 18:12:44 +0100 Subject: [PATCH 20/38] Remove `system_packages` key --- .readthedocs.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 479fbf75..decf5fb8 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -17,5 +17,4 @@ formats: python: version: 3.8 install: - - requirements: doc/requirements.txt - system_packages: true \ No newline at end of file + - requirements: doc/requirements.txt \ No newline at end of file From dca3dd266bbd4d655f56fdd036d3c2596623263a Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 30 Aug 2023 20:12:59 +0100 Subject: [PATCH 21/38] Add Octanol box --- .gitignore | 1 + doc/examples/martini/octanol.gro | 2253 ++++++++++++++++++++++++++++++ 2 files changed, 2254 insertions(+) create mode 100644 doc/examples/martini/octanol.gro diff --git a/.gitignore b/.gitignore index 53a68245..bb822933 100644 --- a/.gitignore +++ b/.gitignore @@ -21,3 +21,4 @@ doc/examples/martini/* !doc/examples/martini/*.mdp !doc/examples/martini/*.ipynb !doc/examples/martini/water.gro 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0.601 4.114 0.888 -0.2497 -0.1670 0.0617 + 592OCO C2 1775 0.366 3.931 0.595 -0.0467 -0.2049 0.1198 + 592OCO PC 1776 0.383 3.943 0.265 0.0797 0.2418 0.3254 + 593OCO C1 1777 5.907 2.194 4.371 -0.0374 0.3065 0.3456 + 593OCO C2 1778 5.812 2.303 4.730 0.0924 -0.2215 -0.0023 + 593OCO PC 1779 5.976 2.359 5.046 0.0292 -0.1892 0.5755 + 594OCO C1 1780 1.875 5.985 1.648 0.3051 -0.3264 0.0418 + 594OCO C2 1781 1.519 5.883 1.566 0.2555 -0.1032 0.2267 + 594OCO PC 1782 1.256 5.764 1.317 0.0826 -0.0690 -0.0842 + 595OCO C1 1783 2.202 2.107 3.020 0.1721 0.2155 -0.2998 + 595OCO C2 1784 1.998 2.357 3.239 -0.1534 -0.1967 -0.1733 + 595OCO PC 1785 1.773 2.539 3.221 0.3215 0.0053 0.0074 + 596OCO C1 1786 5.574 5.718 4.759 -0.0465 -0.1869 -0.1237 + 596OCO C2 1787 5.740 5.752 5.117 -0.0621 -0.2528 -0.5423 + 596OCO PC 1788 5.746 5.729 5.512 -0.0373 -0.0412 0.1100 + 597OCO C1 1789 5.205 1.453 3.945 -0.4411 0.2522 0.0607 + 597OCO C2 1790 5.396 1.737 4.151 0.3029 0.0746 -0.1861 + 597OCO PC 1791 5.592 1.696 4.449 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C2 1826 2.553 2.299 4.529 0.2635 0.1259 -0.0989 + 609OCO PC 1827 2.903 2.365 4.576 0.0601 -0.0828 0.0798 + 610OCO C1 1828 1.383 0.749 2.122 0.0970 0.0665 0.1671 + 610OCO C2 1829 1.685 0.483 2.236 -0.1230 0.0865 0.0328 + 610OCO PC 1830 2.023 0.478 2.328 0.3113 -0.1125 0.0651 + 611OCO C1 1831 0.658 4.036 2.155 -0.0351 -0.3929 -0.0445 + 611OCO C2 1832 0.536 3.732 1.954 0.0317 0.2725 -0.1103 + 611OCO PC 1833 0.606 3.546 1.675 -0.0251 0.0886 0.1123 + 612OCO C1 1834 0.183 6.053 2.420 0.0967 -0.0122 0.0925 + 612OCO C2 1835 0.527 6.080 2.526 0.1820 0.0547 -0.0041 + 612OCO PC 1836 0.825 5.890 2.563 -0.0337 0.2922 0.0795 + 613OCO C1 1837 1.887 1.293 0.096 0.0426 0.4001 -0.0125 + 613OCO C2 1838 1.637 1.553 0.073 0.1044 -0.1037 -0.0044 + 613OCO PC 1839 1.369 1.816 0.061 -0.3580 0.2259 0.1325 + 614OCO C1 1840 4.674 1.675 1.579 -0.3017 -0.0020 0.3863 + 614OCO C2 1841 4.412 1.896 1.761 0.2080 -0.4611 -0.0934 + 614OCO PC 1842 4.076 1.930 1.859 -0.6157 -0.2202 0.1326 + 615OCO C1 1843 0.147 5.988 0.202 -0.0768 -0.3833 -0.2296 + 615OCO C2 1844 0.055 5.909 -0.169 -0.0777 -0.0035 0.1428 + 615OCO PC 1845 0.220 5.968 -0.478 0.2196 0.2705 -0.3132 + 616OCO C1 1846 1.181 5.659 2.268 -0.0351 0.2710 -0.2370 + 616OCO C2 1847 0.843 5.546 2.252 0.0735 -0.0215 -0.1603 + 616OCO PC 1848 0.563 5.636 2.190 0.1840 -0.1924 -0.3569 + 617OCO C1 1849 2.689 0.567 3.929 -0.0080 -0.0570 0.0702 + 617OCO C2 1850 2.445 0.416 3.676 -0.2916 -0.1887 -0.3718 + 617OCO PC 1851 2.147 0.220 3.706 0.0649 0.1965 -0.1249 + 618OCO C1 1852 3.732 2.715 1.413 -0.1693 0.0137 -0.0392 + 618OCO C2 1853 3.807 2.988 1.661 -0.2187 -0.2369 -0.0455 + 618OCO PC 1854 4.002 3.208 1.788 0.2405 0.0784 -0.3015 + 619OCO C1 1855 4.598 5.360 2.637 0.4670 -0.0696 -0.5133 + 619OCO C2 1856 4.510 5.707 2.646 0.4601 -0.3816 -0.0436 + 619OCO PC 1857 4.469 6.024 2.794 0.2115 0.1712 -0.1311 + 620OCO C1 1858 5.850 0.711 4.083 -0.0698 0.2036 -0.1769 + 620OCO C2 1859 5.736 0.390 3.844 -0.2377 -0.0532 -0.2271 + 620OCO PC 1860 5.515 0.222 3.806 -0.0721 -0.0614 0.0884 + 621OCO C1 1861 4.639 4.068 1.997 -0.1039 0.2344 -0.0110 + 621OCO C2 1862 5.039 3.984 1.985 0.3374 0.1979 -0.2423 + 621OCO PC 1863 5.377 3.918 1.909 0.2487 0.0360 -0.1521 + 622OCO C1 1864 5.542 1.217 1.906 0.0144 -0.0087 0.0847 + 622OCO C2 1865 5.155 1.124 1.950 0.1062 0.2356 0.1402 + 622OCO PC 1866 4.835 1.136 2.121 0.0344 -0.1879 0.0613 + 623OCO C1 1867 3.716 5.983 1.715 0.0557 0.1420 0.2181 + 623OCO C2 1868 3.637 6.142 1.431 -0.1261 0.0505 0.5023 + 623OCO PC 1869 3.702 6.211 1.119 0.2156 -0.0347 0.0907 + 624OCO C1 1870 1.544 2.898 3.006 0.1302 0.3894 -0.1513 + 624OCO C2 1871 1.329 2.640 3.108 -0.0829 -0.0665 0.2077 + 624OCO PC 1872 1.161 2.395 2.930 -0.2042 0.2367 -0.2301 + 625OCO C1 1873 2.678 2.449 2.238 0.0378 0.2144 -0.1258 + 625OCO C2 1874 2.765 2.319 1.857 -0.0389 -0.4392 0.3967 + 625OCO PC 1875 2.698 2.248 1.508 -0.1480 0.3622 -0.0546 + 626OCO C1 1876 3.824 1.714 1.471 -0.2385 -0.1652 0.2844 + 626OCO C2 1877 4.018 1.483 1.717 -0.0281 0.7202 0.3535 + 626OCO PC 1878 4.247 1.404 1.924 -0.4596 -0.4789 -0.0866 + 627OCO C1 1879 2.535 1.733 0.460 0.2360 -0.2532 0.0740 + 627OCO C2 1880 2.713 1.833 0.159 -0.0106 0.2323 -0.2354 + 627OCO PC 1881 2.698 2.004 -0.193 -0.0400 -0.1336 0.0113 + 628OCO C1 1882 0.084 3.728 2.898 0.0872 0.1124 -0.3398 + 628OCO C2 1883 0.300 3.442 2.829 -0.1465 0.0030 -0.0264 + 628OCO PC 1884 0.553 3.248 2.861 -0.2957 -0.0848 0.2929 + 629OCO C1 1885 4.254 2.079 3.604 -0.0618 0.2798 -0.0081 + 629OCO C2 1886 4.222 1.887 3.237 -0.3191 0.1116 -0.0031 + 629OCO PC 1887 4.344 1.792 2.958 -0.2241 -0.3798 0.0062 + 630OCO C1 1888 1.883 0.706 4.551 -0.0012 -0.2955 0.0406 + 630OCO C2 1889 2.107 1.003 4.692 0.1170 -0.1788 0.0406 + 630OCO PC 1890 2.333 1.269 4.618 -0.1707 -0.3077 -0.4035 + 631OCO C1 1891 0.448 2.888 2.882 -0.1560 0.2137 0.0174 + 631OCO C2 1892 0.597 2.887 2.508 0.1408 0.0843 -0.1083 + 631OCO PC 1893 0.596 2.946 2.157 0.0927 0.1820 0.2524 + 632OCO C1 1894 5.297 3.376 0.342 0.1670 0.1772 -0.3525 + 632OCO C2 1895 5.259 3.706 0.196 0.0385 0.1480 -0.1334 + 632OCO PC 1896 5.116 3.892 -0.015 -0.1375 -0.4096 -0.3597 + 633OCO C1 1897 5.468 5.290 4.202 0.1304 0.1839 0.4192 + 633OCO C2 1898 5.462 5.144 4.525 -0.2474 0.0660 0.2611 + 633OCO PC 1899 5.696 5.130 4.762 -0.3157 0.0766 0.0778 + 634OCO C1 1900 1.752 0.004 1.178 -0.0338 0.1290 0.3246 + 634OCO C2 1901 2.032 -0.173 1.058 0.0344 0.1682 -0.0327 + 634OCO PC 1902 2.228 -0.409 0.933 0.3585 -0.1960 -0.3771 + 635OCO C1 1903 3.740 2.579 0.958 0.0025 0.0921 0.2329 + 635OCO C2 1904 4.032 2.716 0.681 0.0528 -0.0538 0.1401 + 635OCO PC 1905 4.319 2.880 0.613 -0.0156 -0.1328 0.1682 + 636OCO C1 1906 1.899 3.042 2.663 -0.1354 -0.3106 0.2204 + 636OCO C2 1907 2.271 3.040 2.662 -0.2131 0.3004 -0.3580 + 636OCO PC 1908 2.593 2.908 2.788 0.1823 0.6048 0.2145 + 637OCO C1 1909 0.576 3.482 3.909 0.2366 0.0291 -0.2532 + 637OCO C2 1910 0.681 3.143 3.844 -0.1084 0.3140 -0.1667 + 637OCO PC 1911 0.500 2.829 3.984 -0.0032 -0.4873 -0.1600 + 638OCO C1 1912 2.825 0.998 3.907 0.1330 -0.0463 -0.0263 + 638OCO C2 1913 2.444 0.950 3.869 0.1198 0.4128 0.1152 + 638OCO PC 1914 2.135 1.010 3.690 -0.1391 -0.0051 0.0375 + 639OCO C1 1915 2.673 0.010 2.043 0.2981 0.1649 0.0312 + 639OCO C2 1916 2.408 -0.084 1.845 -0.0135 0.2087 -0.1413 + 639OCO PC 1917 2.368 -0.177 1.548 -0.4519 0.0097 -0.1693 + 640OCO C1 1918 0.977 5.922 4.975 0.0898 0.1339 -0.0780 + 640OCO C2 1919 1.243 5.718 4.892 0.0569 0.2476 0.0038 + 640OCO PC 1920 1.441 5.526 4.776 0.2652 0.0680 -0.1601 + 641OCO C1 1921 1.254 1.322 3.736 0.0375 0.4445 -0.1111 + 641OCO C2 1922 1.166 1.029 3.889 0.1845 0.0339 0.0486 + 641OCO PC 1923 0.995 0.749 3.895 -0.2744 0.0718 0.2911 + 642OCO C1 1924 2.831 1.228 1.501 0.0795 -0.0773 -0.1757 + 642OCO C2 1925 2.689 1.488 1.304 0.2491 0.0419 -0.1158 + 642OCO PC 1926 2.752 1.794 1.272 0.0738 0.1094 -0.1406 + 643OCO C1 1927 3.213 3.604 1.225 -0.2191 0.1647 -0.0471 + 643OCO C2 1928 3.483 3.755 1.504 0.1369 -0.1827 0.3542 + 643OCO PC 1929 3.771 3.626 1.600 0.1332 -0.1510 0.0840 + 644OCO C1 1930 3.484 0.906 3.491 -0.0986 0.1880 -0.0798 + 644OCO C2 1931 3.209 1.129 3.452 -0.1032 0.0490 -0.0929 + 644OCO PC 1932 3.030 1.396 3.315 0.0958 -0.2697 -0.1445 + 645OCO C1 1933 3.460 0.392 1.894 -0.0556 -0.1050 0.0933 + 645OCO C2 1934 3.556 0.369 2.248 0.0781 -0.0614 -0.0191 + 645OCO PC 1935 3.597 0.170 2.531 0.2794 0.1199 0.2251 + 646OCO C1 1936 4.225 2.005 1.299 0.2231 0.0492 -0.0504 + 646OCO C2 1937 3.982 1.849 1.051 0.4549 0.1461 -0.1413 + 646OCO PC 1938 3.827 1.592 0.896 0.2101 -0.1475 0.2834 + 647OCO C1 1939 5.899 2.771 5.018 0.3420 -0.0765 0.4185 + 647OCO C2 1940 5.653 2.888 5.326 -0.1684 -0.3364 -0.3619 + 647OCO PC 1941 5.389 3.006 5.562 0.2258 0.2373 0.0829 + 648OCO C1 1942 3.344 4.606 0.269 -0.2041 0.1403 0.0759 + 648OCO C2 1943 3.399 5.017 0.167 0.2521 0.2252 -0.0311 + 648OCO PC 1944 3.360 5.318 0.010 0.2042 0.1221 -0.1595 + 649OCO C1 1945 0.438 6.015 0.798 -0.0239 -0.0254 -0.0709 + 649OCO C2 1946 0.353 6.267 0.495 -0.0407 0.0497 0.1002 + 649OCO PC 1947 0.318 6.519 0.285 0.5196 -0.0961 -0.0675 + 650OCO C1 1948 5.858 3.593 2.176 -0.3602 0.1016 0.0034 + 650OCO C2 1949 5.708 3.516 2.452 0.2294 -0.0004 0.2267 + 650OCO PC 1950 5.389 3.479 2.614 0.1082 0.1376 0.2008 + 651OCO C1 1951 0.689 2.544 1.222 0.1856 -0.2790 -0.2932 + 651OCO C2 1952 0.679 2.187 1.032 -0.1026 0.2856 -0.0714 + 651OCO PC 1953 0.883 1.979 0.922 -0.0468 -0.1382 0.0797 + 652OCO C1 1954 4.847 2.080 1.541 -0.3233 0.0151 0.0187 + 652OCO C2 1955 5.166 2.199 1.357 0.0279 0.2449 0.4768 + 652OCO PC 1956 5.370 2.247 1.038 -0.2353 -0.2137 0.2345 + 653OCO C1 1957 2.275 1.545 3.505 0.1616 0.2493 0.2801 + 653OCO C2 1958 2.026 1.782 3.428 0.2481 0.1632 0.0769 + 653OCO PC 1959 1.859 2.069 3.525 -0.1051 -0.0300 -0.3468 + 654OCO C1 1960 3.872 1.863 4.865 0.0976 0.1243 0.2883 + 654OCO C2 1961 3.504 1.821 4.678 -0.1145 -0.3719 0.1199 + 654OCO PC 1962 3.382 1.850 4.323 0.0551 -0.0879 0.1094 + 655OCO C1 1963 3.187 4.679 0.724 0.0370 0.4245 0.0371 + 655OCO C2 1964 3.484 4.698 0.946 0.2777 -0.1937 0.0241 + 655OCO PC 1965 3.821 4.712 0.990 0.1684 -0.1383 0.1539 + 656OCO C1 1966 4.453 3.860 0.481 -0.0679 0.5613 0.2950 + 656OCO C2 1967 4.374 3.986 0.114 0.1025 -0.3696 0.3156 + 656OCO PC 1968 4.515 4.085 -0.190 0.1563 -0.5886 -0.1334 + 657OCO C1 1969 0.588 6.042 2.074 -0.2063 0.0093 -0.1117 + 657OCO C2 1970 0.962 5.855 1.933 0.3292 0.3589 -0.0229 + 657OCO PC 1971 1.221 5.703 1.802 0.0985 0.5722 0.0781 + 658OCO C1 1972 5.427 0.076 4.547 0.1815 -0.1926 0.1449 + 658OCO C2 1973 5.604 0.274 4.887 -0.1583 0.2846 0.3528 + 658OCO PC 1974 5.528 0.544 5.096 0.0313 -0.0583 0.1574 + 659OCO C1 1975 3.289 1.005 4.083 -0.3437 -0.3948 -0.0491 + 659OCO C2 1976 3.168 0.672 4.193 -0.1873 -0.1593 -0.2062 + 659OCO PC 1977 3.259 0.342 4.187 -0.0548 0.2154 -0.1969 + 660OCO C1 1978 4.552 1.244 3.216 -0.0622 0.1826 0.0283 + 660OCO C2 1979 4.194 1.156 3.090 0.3649 0.2386 0.2855 + 660OCO PC 1980 4.119 1.083 2.713 0.3361 0.2103 0.0656 + 661OCO C1 1981 0.628 4.796 0.674 -0.1014 0.0231 0.0176 + 661OCO C2 1982 1.003 4.935 0.729 0.1040 0.2552 0.4082 + 661OCO PC 1983 1.328 4.779 0.739 -0.1573 -0.1291 -0.2617 + 662OCO C1 1984 5.057 0.132 3.996 -0.2582 0.1184 -0.0481 + 662OCO C2 1985 4.761 0.317 4.095 -0.1759 -0.3661 -0.0703 + 662OCO PC 1986 4.426 0.358 4.064 0.0862 -0.1464 0.1312 + 663OCO C1 1987 0.443 4.275 4.858 0.2431 -0.0967 -0.2740 + 663OCO C2 1988 0.699 4.012 4.802 0.1656 0.1555 -0.1501 + 663OCO PC 1989 1.014 3.941 4.627 0.0375 -0.3171 0.0182 + 664OCO C1 1990 2.136 2.994 1.716 0.2555 -0.0834 0.0408 + 664OCO C2 1991 2.190 2.609 1.843 0.0802 -0.3618 -0.0874 + 664OCO PC 1992 2.232 2.450 2.174 -0.0936 -0.3080 -0.0535 + 665OCO C1 1993 3.290 4.091 4.672 -0.3253 -0.1153 -0.3519 + 665OCO C2 1994 3.016 3.871 4.554 -0.1596 0.0433 0.1014 + 665OCO PC 1995 2.742 3.827 4.728 0.4540 0.3118 0.2468 + 666OCO C1 1996 0.971 5.613 4.310 0.3198 -0.0890 0.0490 + 666OCO C2 1997 0.802 5.612 4.654 0.4047 -0.0168 -0.0967 + 666OCO PC 1998 0.675 5.438 4.972 0.0476 -0.0605 0.0040 + 667OCO C1 1999 1.365 3.245 4.278 -0.1285 -0.0658 0.1704 + 667OCO C2 2000 1.430 2.896 4.179 0.0677 -0.0349 -0.7275 + 667OCO PC 2001 1.352 2.631 3.991 0.0975 0.1052 -0.2146 + 668OCO C1 2002 1.740 3.973 1.120 -0.2775 -0.0938 -0.0536 + 668OCO C2 2003 2.068 3.824 1.049 0.0269 0.1024 -0.0705 + 668OCO PC 2004 2.391 3.740 1.137 0.1898 0.0744 0.0988 + 669OCO C1 2005 1.389 1.150 0.963 -0.2419 0.1632 0.0643 + 669OCO C2 2006 1.254 1.417 1.184 0.0520 -0.0784 0.0051 + 669OCO PC 2007 1.185 1.461 1.502 -0.0623 -0.0425 0.6436 + 670OCO C1 2008 2.075 3.107 3.432 0.1242 -0.5803 -0.0983 + 670OCO C2 2009 2.005 3.276 3.109 -0.3165 0.3369 0.1761 + 670OCO PC 2010 2.046 3.424 2.778 0.0429 0.0629 -0.1372 + 671OCO C1 2011 1.251 3.965 3.351 -0.1072 -0.0201 0.1911 + 671OCO C2 2012 1.278 3.673 3.672 0.2313 0.2310 0.4657 + 671OCO PC 2013 1.256 3.575 3.998 -0.4343 -0.0349 -0.1039 + 672OCO C1 2014 5.831 0.190 1.132 0.1663 0.1726 0.0169 + 672OCO C2 2015 5.815 0.607 1.041 0.0496 0.0788 0.0327 + 672OCO PC 2016 5.808 0.807 0.741 -0.1322 0.1031 -0.0130 + 673OCO C1 2017 0.061 2.600 3.184 -0.1392 0.4494 0.3516 + 673OCO C2 2018 -0.142 2.380 2.922 -0.3927 -0.0728 -0.0742 + 673OCO PC 2019 -0.408 2.300 2.811 0.0403 -0.2082 0.2249 + 674OCO C1 2020 5.887 0.984 2.659 -0.1387 -0.1261 0.1576 + 674OCO C2 2021 6.006 0.863 2.995 -0.2194 0.1187 -0.0553 + 674OCO PC 2022 6.275 0.790 3.182 0.1191 0.2799 -0.2254 + 675OCO C1 2023 2.345 2.908 4.566 0.3727 -0.0657 -0.1279 + 675OCO C2 2024 2.387 3.019 4.949 0.0566 -0.1178 -0.0112 + 675OCO PC 2025 2.581 3.233 5.171 0.0065 0.0749 0.0785 + 676OCO C1 2026 1.651 1.392 3.954 -0.1992 0.1421 -0.2790 + 676OCO C2 2027 1.654 1.042 4.067 -0.0899 -0.0035 0.0725 + 676OCO PC 2028 1.526 0.717 4.022 -0.1399 -0.0117 -0.3147 + 677OCO C1 2029 2.007 1.623 4.817 -0.3966 -0.3517 -0.1486 + 677OCO C2 2030 1.654 1.582 4.663 0.0125 -0.1662 0.4800 + 677OCO PC 2031 1.315 1.657 4.669 -0.1138 0.0031 -0.1092 + 678OCO C1 2032 1.142 4.330 4.596 -0.0452 -0.3121 -0.0120 + 678OCO C2 2033 1.138 4.149 4.941 -0.2928 -0.1166 0.0464 + 678OCO PC 2034 1.380 3.930 5.085 0.4308 -0.1004 -0.2579 + 679OCO C1 2035 0.527 5.872 1.309 -0.0417 0.3252 0.2692 + 679OCO C2 2036 0.330 5.614 1.084 -0.0420 0.3386 -0.3429 + 679OCO PC 2037 0.349 5.368 0.837 -0.0865 0.0163 0.0245 + 680OCO C1 2038 0.862 2.069 1.853 -0.0477 -0.1775 -0.1401 + 680OCO C2 2039 1.020 1.869 1.585 -0.0162 -0.0694 -0.0205 + 680OCO PC 2040 1.016 1.770 1.249 -0.5106 -0.1804 0.1478 + 681OCO C1 2041 3.194 0.688 3.124 0.0824 0.0705 -0.1170 + 681OCO C2 2042 3.325 0.359 3.373 0.3420 0.0397 -0.2580 + 681OCO PC 2043 3.327 0.113 3.577 -0.2648 -0.0887 -0.0063 + 682OCO C1 2044 2.571 3.222 3.066 0.3806 0.0286 0.1132 + 682OCO C2 2045 2.383 3.557 3.086 -0.0389 0.2520 -0.0506 + 682OCO PC 2046 2.230 3.868 3.162 -0.1177 -0.1710 -0.2360 + 683OCO C1 2047 4.324 4.485 0.001 -0.3261 -0.0635 0.1780 + 683OCO C2 2048 4.281 4.829 0.195 -0.2110 0.0692 0.2827 + 683OCO PC 2049 4.401 5.174 0.230 -0.2177 -0.2034 0.0604 + 684OCO C1 2050 1.280 2.363 0.469 -0.0706 0.2975 -0.3061 + 684OCO C2 2051 1.482 2.534 0.739 -0.2754 0.0160 -0.5683 + 684OCO PC 2052 1.487 2.700 1.061 0.0692 0.3279 -0.1101 + 685OCO C1 2053 5.326 0.597 0.807 -0.0943 0.0545 -0.0076 + 685OCO C2 2054 4.917 0.511 0.909 -0.1389 0.0244 -0.0691 + 685OCO PC 2055 4.600 0.421 0.972 0.0569 0.2001 0.0166 + 686OCO C1 2056 3.247 1.442 1.034 -0.1235 0.0172 0.1618 + 686OCO C2 2057 3.438 1.535 0.722 0.2262 0.3668 -0.2004 + 686OCO PC 2058 3.629 1.641 0.515 0.2400 -0.1899 0.1828 + 687OCO C1 2059 1.000 0.268 0.260 -0.1195 -0.1559 0.0360 + 687OCO C2 2060 1.309 0.110 0.036 0.0991 0.1629 -0.1019 + 687OCO PC 2061 1.576 -0.122 -0.090 -0.2555 0.3071 -0.0004 + 688OCO C1 2062 0.395 1.304 3.455 0.0471 0.1993 -0.1274 + 688OCO C2 2063 0.478 1.641 3.593 0.0738 -0.2018 0.0579 + 688OCO PC 2064 0.695 1.913 3.657 0.2891 -0.0267 0.1422 + 689OCO C1 2065 1.597 4.681 2.708 -0.1210 0.1705 0.0940 + 689OCO C2 2066 1.439 4.859 3.047 -0.2003 -0.2345 0.0575 + 689OCO PC 2067 1.332 4.972 3.332 -0.0668 0.3261 -0.0103 + 690OCO C1 2068 5.528 2.894 0.971 -0.2299 0.1824 0.2204 + 690OCO C2 2069 5.763 2.713 1.169 0.0616 0.1678 -0.0721 + 690OCO PC 2070 5.946 2.689 1.486 -0.0527 -0.0885 -0.3474 + 691OCO C1 2071 3.932 3.830 1.225 0.1051 0.3252 0.0403 + 691OCO C2 2072 4.076 4.171 1.257 -0.2598 0.1424 -0.1389 + 691OCO PC 2073 4.065 4.548 1.308 -0.0331 0.0485 -0.3678 + 692OCO C1 2074 2.005 1.441 2.694 -0.0460 -0.2180 0.2662 + 692OCO C2 2075 2.145 1.107 2.509 0.1375 -0.3745 -0.1784 + 692OCO PC 2076 2.283 0.813 2.497 -0.0538 0.3291 -0.1533 + 693OCO C1 2077 3.870 4.490 3.454 -0.1644 -0.1639 0.2630 + 693OCO C2 2078 3.763 4.391 3.110 0.1250 0.2493 0.1325 + 693OCO PC 2079 3.572 4.528 2.918 -0.2313 0.3598 0.3553 + 694OCO C1 2080 5.038 2.576 1.797 -0.1790 -0.3132 0.0888 + 694OCO C2 2081 5.229 2.209 1.801 0.1020 -0.6238 -0.1100 + 694OCO PC 2082 5.517 2.034 1.884 0.0037 0.4258 -0.0593 + 695OCO C1 2083 3.329 0.851 1.672 0.4779 -0.0048 -0.0495 + 695OCO C2 2084 3.130 0.648 1.442 -0.0643 -0.0413 0.3434 + 695OCO PC 2085 2.797 0.507 1.459 0.0268 0.0794 0.1513 + 696OCO C1 2086 5.958 2.408 2.487 0.1637 -0.0726 -0.4591 + 696OCO C2 2087 6.211 2.256 2.231 0.1436 0.0449 -0.1531 + 696OCO PC 2088 6.394 2.115 1.971 -0.0210 0.0449 0.0505 + 697OCO C1 2089 4.065 2.979 2.291 0.0784 0.4078 -0.2165 + 697OCO C2 2090 4.190 3.323 2.322 0.3035 -0.0583 0.0332 + 697OCO PC 2091 4.452 3.538 2.168 0.0760 -0.0126 -0.1672 + 698OCO C1 2092 4.343 4.914 4.170 -0.1523 -0.0247 -0.0523 + 698OCO C2 2093 4.350 4.728 4.463 -0.1464 0.0646 -0.1513 + 698OCO PC 2094 4.262 4.406 4.473 -0.1659 0.1753 0.0905 + 699OCO C1 2095 0.508 0.511 0.735 0.3380 -0.0233 -0.3576 + 699OCO C2 2096 0.800 0.661 0.643 -0.1145 0.3526 0.1034 + 699OCO PC 2097 0.917 0.901 0.495 -0.2404 -0.3276 -0.1432 + 700OCO C1 2098 3.601 5.062 2.719 0.2919 -0.0161 0.0400 + 700OCO C2 2099 3.219 5.126 2.885 -0.0483 0.0324 0.1750 + 700OCO PC 2100 2.949 5.078 3.075 0.0840 0.2768 -0.1746 + 701OCO C1 2101 3.586 3.322 1.380 -0.0325 -0.1342 -0.0620 + 701OCO C2 2102 3.537 3.276 1.007 -0.0929 -0.2476 -0.0618 + 701OCO PC 2103 3.331 3.424 0.789 -0.3737 0.3055 -0.0561 + 702OCO C1 2104 5.078 2.113 2.754 0.2990 -0.7366 0.2770 + 702OCO C2 2105 5.036 2.206 3.099 -0.2535 -0.1100 0.1268 + 702OCO PC 2106 4.957 2.471 3.333 -0.0945 -0.0773 -0.1624 + 703OCO C1 2107 2.906 4.535 2.064 -0.2603 -0.1647 0.0813 + 703OCO C2 2108 2.740 4.219 2.223 0.1178 0.0019 -0.0289 + 703OCO PC 2109 2.876 3.985 2.403 -0.2469 -0.1447 0.1650 + 704OCO C1 2110 0.353 0.039 1.636 0.0311 0.1167 0.1335 + 704OCO C2 2111 -0.012 0.049 1.590 0.0873 -0.4857 -0.0015 + 704OCO PC 2112 -0.325 0.022 1.628 0.3480 0.2747 0.1741 + 705OCO C1 2113 1.500 0.880 2.587 0.2324 -0.4618 0.1863 + 705OCO C2 2114 1.790 0.904 2.391 -0.0655 0.1927 0.0469 + 705OCO PC 2115 2.011 0.912 2.136 -0.1331 0.2476 0.1838 + 706OCO C1 2116 3.637 3.707 2.933 -0.1889 -0.2160 0.4267 + 706OCO C2 2117 3.955 3.864 2.792 -0.3707 0.0135 0.0034 + 706OCO PC 2118 4.187 4.049 2.939 0.1552 -0.3154 0.0045 + 707OCO C1 2119 2.752 3.049 2.392 0.0633 -0.2162 0.1718 + 707OCO C2 2120 3.126 2.906 2.407 0.0729 0.1725 -0.1160 + 707OCO PC 2121 3.425 2.838 2.554 0.3391 0.0349 -0.1953 + 708OCO C1 2122 0.140 2.003 3.019 0.1393 0.0192 0.0903 + 708OCO C2 2123 0.239 1.654 3.002 -0.1431 -0.0444 -0.0334 + 708OCO PC 2124 0.545 1.498 2.850 -0.2075 0.0695 0.0640 + 709OCO C1 2125 1.855 5.026 3.118 0.1312 0.0452 -0.1374 + 709OCO C2 2126 2.193 5.213 3.176 0.4087 -0.2310 -0.4034 + 709OCO PC 2127 2.431 5.398 3.043 0.3734 -0.2689 0.0659 + 710OCO C1 2128 0.986 4.299 0.732 0.0515 0.1281 0.0296 + 710OCO C2 2129 1.335 4.345 0.821 -0.0503 0.1072 -0.5185 + 710OCO PC 2130 1.607 4.420 0.728 0.1130 0.2315 0.4815 + 711OCO C1 2131 3.803 3.718 0.119 -0.2745 -0.0127 0.2363 + 711OCO C2 2132 3.733 3.731 -0.284 -0.0051 0.2791 0.0299 + 711OCO PC 2133 3.571 3.857 -0.539 -0.4012 0.0714 0.2427 + 712OCO C1 2134 4.924 0.798 0.537 -0.2035 0.2126 0.1235 + 712OCO C2 2135 4.907 0.684 0.172 -0.0318 -0.0805 -0.1369 + 712OCO PC 2136 4.775 0.743 -0.130 0.1711 0.1977 -0.0931 + 713OCO C1 2137 0.340 2.275 3.273 -0.1512 0.6275 -0.1982 + 713OCO C2 2138 0.047 2.271 3.437 0.2143 0.1049 -0.2282 + 713OCO PC 2139 -0.309 2.234 3.398 0.0084 -0.3583 -0.0224 + 714OCO C1 2140 4.824 3.349 0.938 -0.0511 -0.1055 -0.0695 + 714OCO C2 2141 4.715 3.121 1.240 -0.0212 -0.1854 0.0109 + 714OCO PC 2142 4.811 2.980 1.542 -0.2774 0.0526 0.1127 + 715OCO C1 2143 1.794 5.413 0.663 -0.1989 -0.0231 0.1592 + 715OCO C2 2144 1.968 5.335 1.021 0.1487 -0.3130 -0.0577 + 715OCO PC 2145 2.050 5.483 1.350 -0.3285 -0.3516 -0.2291 + 716OCO C1 2146 2.105 1.433 1.278 0.3707 0.0761 -0.0083 + 716OCO C2 2147 2.325 1.737 1.433 -0.4232 -0.4229 0.0131 + 716OCO PC 2148 2.552 1.861 1.705 0.0406 0.0568 0.1210 + 717OCO C1 2149 0.616 0.388 2.399 0.0914 0.0226 0.4032 + 717OCO C2 2150 0.991 0.272 2.326 -0.2159 -0.2695 0.0977 + 717OCO PC 2151 1.341 0.166 2.269 0.4139 0.1536 -0.3698 + 718OCO C1 2152 3.551 0.716 2.600 -0.0369 0.0720 0.0242 + 718OCO C2 2153 3.171 0.670 2.674 0.0467 0.2682 0.1292 + 718OCO PC 2154 2.978 0.396 2.766 -0.3388 0.1702 0.1055 + 719OCO C1 2155 5.538 5.352 3.756 -0.0001 0.2871 0.2376 + 719OCO C2 2156 5.920 5.311 3.740 0.1790 -0.1238 0.2734 + 719OCO PC 2157 6.211 5.179 3.877 -0.2611 0.5927 -0.0694 + 720OCO C1 2158 3.791 2.188 0.128 -0.1193 0.3966 0.0244 + 720OCO C2 2159 3.976 1.969 0.400 0.2012 0.1652 0.2413 + 720OCO PC 2160 4.119 1.752 0.639 -0.4702 -0.2873 0.1808 + 721OCO C1 2161 6.001 4.568 1.159 0.2551 -0.0361 -0.2775 + 721OCO C2 2162 5.750 4.585 1.458 -0.2066 -0.0983 0.3974 + 721OCO PC 2163 5.440 4.620 1.575 0.2084 -0.0827 -0.3394 + 722OCO C1 2164 2.848 1.582 2.965 -0.0337 0.3519 0.2617 + 722OCO C2 2165 2.613 1.354 3.174 0.0666 0.6764 -0.0787 + 722OCO PC 2166 2.486 1.150 3.392 -0.0292 0.0646 -0.0595 + 723OCO C1 2167 3.112 4.201 0.475 -0.1394 -0.2141 -0.1373 + 723OCO C2 2168 3.407 4.353 0.659 0.3281 0.1712 0.3006 + 723OCO PC 2169 3.704 4.475 0.619 0.0924 0.0065 -0.2186 + 724OCO C1 2170 4.249 5.559 3.162 0.1245 0.2650 0.2993 + 724OCO C2 2171 4.024 5.901 3.057 -0.1231 0.4420 0.1332 + 724OCO PC 2172 3.848 6.174 2.860 -0.3592 0.1527 0.1516 + 725OCO C1 2173 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-0.0572 0.2451 -0.1906 + 748OCO C2 2243 0.966 0.001 1.275 -0.2778 0.4871 -0.2025 + 748OCO PC 2244 1.020 0.025 1.569 -0.1029 -0.2183 0.0655 + 749OCO C1 2245 3.252 1.099 2.466 -0.0524 -0.0329 -0.2207 + 749OCO C2 2246 3.484 1.194 2.754 -0.0305 0.0727 0.3049 + 749OCO PC 2247 3.723 1.012 2.861 0.1847 -0.1283 -0.3124 + 750OCO C1 2248 1.049 3.302 4.764 0.1780 0.2375 0.1459 + 750OCO C2 2249 0.998 3.498 4.433 -0.3796 -0.1152 -0.0004 + 750OCO PC 2250 0.837 3.667 4.228 0.0132 -0.0938 -0.3093 + 6.06429 6.06429 5.05357 From 780a2fbc72ff1c42d8e716259d48dd4d7e2ded89 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 30 Aug 2023 20:13:05 +0100 Subject: [PATCH 22/38] [WIP] solvation --- doc/examples/martini/martini-benzene.ipynb | 182 +++++++++++++++++++-- 1 file changed, 165 insertions(+), 17 deletions(-) diff --git a/doc/examples/martini/martini-benzene.ipynb b/doc/examples/martini/martini-benzene.ipynb index 0e0d1b28..d04cc75f 100644 --- a/doc/examples/martini/martini-benzene.ipynb +++ b/doc/examples/martini/martini-benzene.ipynb @@ -19,7 +19,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -29,18 +29,24 @@ "import requests as req\n", "from zipfile import ZipFile\n", "\n", + "\n", "HERE = Path(\".\")\n", + "MARTINI_FF = HERE / \"martini.ff\"\n", + "\n", + "MARTINI_ITP = MARTINI_FF / \"forcefield.itp\"\n", + "MARTINI_IONS = MARTINI_FF / \"martini_v3.0.0_ions_v1.itp\"\n", + "MARTINI_SMALL_MOLS = MARTINI_FF / \"martini_v3.0.0_small_molecules_v1.itp\"\n", + "MARTINI_SOLVENTS = MARTINI_FF / \"martini_v3.0.0_solvents_v1.itp\"\n", + "BENZENE_ITP = MARTINI_FF / \"BENZ.itp\"\n", "\n", - "MARTINI_ITP = HERE / \"martini_v3.0.0.itp\"\n", - "MARTINI_IONS = HERE / \"martini_v3.0.0_ions_v1.itp\"\n", - "MARTINI_SMALL_MOLS = HERE / \"martini_v3.0.0_small_molecules_v1.itp\"\n", - "MARTINI_SOLVENTS = HERE / \"martini_v3.0.0_solvents_v1.itp\"\n", "MARTINI_WATER = HERE / \"water.gro\"\n", "MARTINI_OCTANOL = HERE / \"octanol.gro\"\n", + "MARTINI_BENZENE = MARTINI_FF / \"output-conect.pdb\"\n", + "\n", + "EM_FILE = MARTINI_FF / \"em.mdp\"\n", + "EQ_FILE = MARTINI_FF / \"eq.mdp\"\n", + "RUN_FILE = MARTINI_FF / \"run.mdp\"\n", "\n", - "EM_FILE = HERE / \"em.mdp\"\n", - "EQ_FILE = HERE / \"eq.mdp\"\n", - "RUN_FILE = HERE / \"run.mdp\"\n", "\n", "def download_file(\n", " url: str, out: Optional[Path] = None, chunk_size: int = 128, overwrite: bool = False\n", @@ -61,13 +67,14 @@ "\n", "\n", "ZIP_DOWNLOAD = {\n", - " HERE / \"BENZ.itp\": \"https://mad.ibcp.fr/api/molecule/download?id=731653322400583591&filename=BENZ.zip\"\n", + " HERE\n", + " / \"BENZ.itp\": \"https://mad.ibcp.fr/api/molecule/download?id=731653322400583591&filename=BENZ.zip\"\n", "}\n", "DOWNLOADS = {\n", - " MARTINI_ITP: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0.itp\",\n", - " MARTINI_IONS: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_ions_v1.itp\",\n", - " MARTINI_SMALL_MOLS: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_small_molecules_v1.itp\",\n", - " MARTINI_SOLVENTS: \"https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_solvents_v1.itp\",\n", + " MARTINI_ITP: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0.itp\",\n", + " MARTINI_IONS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_ions_v1.itp\",\n", + " MARTINI_SMALL_MOLS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_small_molecules_v1.itp\",\n", + " MARTINI_SOLVENTS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_solvents_v1.itp\",\n", "}\n", "DOWNLOADS.update(ZIP_DOWNLOAD)\n", "\n", @@ -76,14 +83,118 @@ "\n", "for zip_file in ZIP_DOWNLOAD.keys():\n", " with ZipFile(zip_file, \"r\") as zip_ref:\n", - " zip_ref.extractall(HERE)" + " zip_ref.extractall(MARTINI_FF)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This should have downloaded several files to your workspace.\n", + "\n", + "We also need to make a `watermodels.dat` file in the `martini.ff` subdirectory.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "56" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "WATERMODEL_DAT = MARTINI_FF / \"watermodels.dat\"\n", + "\n", + "WATERMODEL_DAT.write_text(\"martini-water\\tMARTINI-WATER\\tMartini default water model.\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "This should have downloaded several files to your workspace." + "Next, we set up the files for the Martini 3.0 forcefield." + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [], + "source": [ + "from mdpow.forcefields import Forcefield, GromacsSolventModel\n", + "\n", + "MARTINI = Forcefield(\n", + " \"Martini\",\n", + " solvent_models={\n", + " \"water\": GromacsSolventModel(\n", + " identifier=\"martini-water\", itp=MARTINI_SOLVENTS.absolute(), coordinates=MARTINI_WATER.absolute()\n", + " ),\n", + " \"octanol\": GromacsSolventModel(\n", + " identifier=\"octanol\", itp=MARTINI_SOLVENTS.absolute(), coordinates=MARTINI_OCTANOL.absolute()\n", + " ),\n", + " },\n", + " forcefield_dir=MARTINI_FF.absolute(),\n", + " ions_itp=MARTINI_IONS.absolute(),\n", + " default_water_itp=MARTINI_SOLVENTS.absolute(),\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{'name': 'Martini', 'solvent_models': {'water': {'identifier': 'martini-water', 'name': 'MARTINI-WATER', 'itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_solvents_v1.itp'), 'coordinates': PosixPath('/home/awsm/MDPOW/doc/examples/martini/water.gro'), 'description': None, 'forcefield': 'OPLS-AA'}, 'octanol': {'identifier': 'octanol', 'name': 'OCTANOL', 'itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_solvents_v1.itp'), 'coordinates': PosixPath('/home/awsm/MDPOW/doc/examples/martini/octanol.gro'), 'description': None, 'forcefield': 'OPLS-AA'}}, 'forcefield_dir': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff'), 'ions_itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_ions_v1.itp'), 'default_water_itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_solvents_v1.itp')}\n" + ] + } + ], + "source": [ + "from dataclasses import asdict\n", + "\n", + "martini_dict = asdict(MARTINI)\n", + "print(martini_dict)" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "ename": "ValueError", + "evalue": "tip4p is not a valid water model for Martini.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[12], line 3\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mmdpow\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mequil\u001b[39;00m \u001b[39mimport\u001b[39;00m WaterSimulation\n\u001b[0;32m----> 3\u001b[0m sim \u001b[39m=\u001b[39m WaterSimulation(molecule\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mBENZ\u001b[39;49m\u001b[39m\"\u001b[39;49m, ff_class\u001b[39m=\u001b[39;49mMARTINI)\n\u001b[1;32m 4\u001b[0m sim\u001b[39m.\u001b[39mtopology(\u001b[39mstr\u001b[39m(BENZENE_ITP))\n\u001b[1;32m 5\u001b[0m sim\u001b[39m.\u001b[39msolvate(struct\u001b[39m=\u001b[39mMARTINI_BENZENE)\n", + "File \u001b[0;32m~/MDPOW/mdpow/equil.py:251\u001b[0m, in \u001b[0;36mSimulation.__init__\u001b[0;34m(self, molecule, ff_class, **kwargs)\u001b[0m\n\u001b[1;32m 249\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mforcefield \u001b[39m=\u001b[39m forcefield\n\u001b[1;32m 250\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39msolvent_type \u001b[39m=\u001b[39m solvent\n\u001b[0;32m--> 251\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39msolventmodel_identifier \u001b[39m=\u001b[39m forcefields\u001b[39m.\u001b[39;49mget_solvent_identifier(\n\u001b[1;32m 252\u001b[0m solvent,\n\u001b[1;32m 253\u001b[0m model\u001b[39m=\u001b[39;49msolventmodel,\n\u001b[1;32m 254\u001b[0m forcefield\u001b[39m=\u001b[39;49mforcefield,\n\u001b[1;32m 255\u001b[0m )\n\u001b[1;32m 256\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39msolventmodel_identifier \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m 257\u001b[0m msg \u001b[39m=\u001b[39m \u001b[39m\"\u001b[39m\u001b[39mNo parameters for solvent \u001b[39m\u001b[39m{0}\u001b[39;00m\u001b[39m and solventmodel \u001b[39m\u001b[39m{1}\u001b[39;00m\u001b[39m available.\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m.\u001b[39mformat(\n\u001b[1;32m 258\u001b[0m solvent, solventmodel\n\u001b[1;32m 259\u001b[0m )\n", + "File \u001b[0;32m~/MDPOW/mdpow/forcefields.py:417\u001b[0m, in \u001b[0;36mget_solvent_identifier\u001b[0;34m(solvent_type, model, forcefield)\u001b[0m\n\u001b[1;32m 415\u001b[0m \u001b[39mreturn\u001b[39;00m identifier\n\u001b[1;32m 416\u001b[0m \u001b[39melse\u001b[39;00m:\n\u001b[0;32m--> 417\u001b[0m \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(\n\u001b[1;32m 418\u001b[0m \u001b[39mf\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m{\u001b[39;00midentifier\u001b[39m}\u001b[39;00m\u001b[39m is not a valid water model for \u001b[39m\u001b[39m{\u001b[39;00mforcefield\u001b[39m.\u001b[39mname\u001b[39m}\u001b[39;00m\u001b[39m.\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 419\u001b[0m )\n\u001b[1;32m 421\u001b[0m \u001b[39mif\u001b[39;00m model \u001b[39mnot\u001b[39;00m \u001b[39min\u001b[39;00m forcefield\u001b[39m.\u001b[39msolvent_models:\n\u001b[1;32m 422\u001b[0m \u001b[39mif\u001b[39;00m solvent_type \u001b[39min\u001b[39;00m forcefield\u001b[39m.\u001b[39msolvent_models:\n", + "\u001b[0;31mValueError\u001b[0m: tip4p is not a valid water model for Martini." + ] + } + ], + "source": [ + "from mdpow.equil import WaterSimulation\n", + "\n", + "sim = WaterSimulation(molecule=\"BENZ\", ff_class=MARTINI)\n", + "sim.topology(str(BENZENE_ITP))\n", + "sim.solvate(struct=MARTINI_BENZENE)\n", + "sim.energy_minimize()\n", + "sim.MD_relaxed(runtime=5) # should be at least 1e3 ps for production not just 5 ps" ] }, { @@ -92,8 +203,45 @@ "metadata": {}, "outputs": [], "source": [ + "\n", + "# run simulation externally or use MDrunner\n", + "# (see docs for using mpi etc)\n", "import gromacs\n", - "from mdpow import equil, forcefields, fep" + "\n", + "r = gromacs.run.MDrunner(\n", + " dirname=sim.dirs[\"MD_relaxed\"],\n", + " deffnm=\"md\",\n", + " c=\"md.pdb\",\n", + " cpi=True,\n", + " append=True,\n", + " v=True,\n", + ")\n", + "r.run() # runs mdrun in the python shell\n", + "\n", + "\n", + "sim.MD(\n", + " runtime=10, qscript=[\"local.sh\"]\n", + ") # should be at least 10e3 ps for production, not just 10 ps\n", + "# run simulation\n", + "r = gromacs.run.MDrunner(\n", + " dirname=sim.dirs[\"MD_NPT\"], deffnm=\"md\", c=\"md.pdb\", cpi=True, append=True, v=True\n", + ")\n", + "r.run() # runs mdrun in the python shell\n", + "\n", + "\n", + "import mdpow.fep\n", + "\n", + "gwat = mdpow.fep.Ghyd(simulation=sim, runtime=10)\n", + "gwat.setup()\n", + "\n", + "# run multiple simulations on cluster\n", + "\n", + "\n", + "O = mdpow.equil.OctanolSimulation(molecule=\"BNZ\")\n", + "O.topology(\"benzene.itp\")\n", + "O.solvate(struct=\"benzene.pdb\")\n", + "O.energy_minimize()\n", + "O.MD_relaxed(runtime=0.5)" ] } ], @@ -113,7 +261,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.4" + "version": "3.11.5" }, "orig_nbformat": 4 }, From 636677645de9006e7034f00de144aaad3da30bca Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 30 Aug 2023 20:20:06 +0100 Subject: [PATCH 23/38] Make default water model forcefield-specific --- mdpow/equil.py | 10 ++++--- mdpow/forcefields.py | 53 ++++++++++++++------------------- mdpow/tests/test_forcefields.py | 8 ++--- 3 files changed, 32 insertions(+), 39 deletions(-) diff --git a/mdpow/equil.py b/mdpow/equil.py index 92d4de5b..3bdc4a92 100644 --- a/mdpow/equil.py +++ b/mdpow/equil.py @@ -169,10 +169,12 @@ def __init__( *solvent* 'water' or 'octanol' or 'cyclohexane' or 'wetoctanol' or 'toluene' *solventmodel* - ``None`` chooses the default (e.g, :data:`mdpow.forcefields.DEFAULT_WATER_MODEL` - for ``solvent == "water"``. Other options are the models defined in - :data:`mdpow.forcefields.GROMACS_WATER_MODELS`. At the moment, there are no - alternative parameterizations included for other solvents. + ``None`` chooses the default (e.g, the + :class:`mdpow.forcefields.Forcefield` default water model for + ``solvent == "water"``. Other options are the models defined in + :data:`mdpow.forcefields.GROMACS_WATER_MODELS`. At the moment, + there are no alternative parameterizations included for other + solvents. *mdp* dict with keys corresponding to the stages ``energy_minimize``, ``MD_restrained``, ``MD_relaxed``, diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index 44a9221a..d922ef37 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -17,7 +17,6 @@ files. .. autodata:: DEFAULT_FORCEFIELD -.. autodata:: DEFAULT_WATER_MODEL Solvent models @@ -216,20 +215,8 @@ def _create_water_models(watermodelsdat: Path) -> Dict[str, GromacsSolventModel] ), } -#: Use the default water model unless another water model is chosen in the -#: :ref:`run input file ` file by setting the -#: ``setup.watermodel`` parameter. -#: -#: .. warning:: -#: Select the native water model **manually** and do not rely on the default -#: set here. For CHARMM/GAFF the CHARMM TIP3P model is recommended. -#: For AMBER/GAFF the TIP3P mdeol is often used. Choosing the correct water model -#: is a *scientific* decision that *you* have to make conscientiously. -#: -DEFAULT_WATER_MODEL = "tip4p" - -def get_water_model(watermodel=DEFAULT_WATER_MODEL): +def get_water_model(watermodel="tip4p"): """Return a :class:`GromacsSolventModel` corresponding to identifier *watermodel*""" try: @@ -251,6 +238,7 @@ class Forcefield: forcefield_dir: Path ions_itp: Path default_water_itp: Path + default_water_model: str = "tip4p" def __post_init__(self): """Check that the provided paths exist and populate the :attr:`water_models`.""" @@ -329,6 +317,7 @@ def __repr__(self) -> str: CHARMM_FF_DIR, CHARMM_FF_DIR / "ions.itp", CHARMM_FF_DIR / "tip3p.itp", + default_water_model="tip3p", ) AMBER_FF_DIR = TOP_DIR / "amber99sb.ff" @@ -351,6 +340,7 @@ def __repr__(self) -> str: AMBER_FF_DIR, AMBER_FF_DIR / "ions.itp", AMBER_FF_DIR / "tip3p.itp", + default_water_model="tip3p", ) ALL_FORCEFIELDS: Dict[str, Forcefield] = { @@ -382,23 +372,21 @@ def get_solvent_identifier( """Get the identifier for a solvent model. The identifier is needed to access a water model (i.e., a - :class:`GromacsSolventModel`) through - :func:`get_solvent_model`. Because we have multiple water models - but only limited other solvents, the organization of these models - is a bit convoluted and it is best to obtain the desired water - model in these two steps:: + :class:`GromacsSolventModel`) through :func:`get_solvent_model`. Because we + have multiple water models but only limited other solvents, the organization + of these models is a bit convoluted and it is best to obtain the desired + water model in these two steps:: - identifier = get_solvent_identifier("water", model="tip3p") - model = get_solvent_model(identifier) + identifier = get_solvent_identifier("water", model="tip3p") model = + get_solvent_model(identifier) - For ``solvent_type`` *water*: either provide ``None`` or "water" - for the specific ``model`` (and the default - :data:`DEFAULT_WATER_MODEL` will be selected, or a specific water - model such as "tip3p" or "spce" (see - :data:`GROMACS_WATER_MODELS`). For other "octanol" or "wetoctanol" - of OPLS-AA forcefield, the ``model`` is used to select a specific - model. For other solvents and forcefields, "model" is not required. + For ``solvent_type`` *water*: either provide ``None`` or "water" for the + specific ``model`` (and the default water model for the :class:`Forcefield` + will be selected, or a specific water model such as "tip3p" or "spce" (see + :data:`GROMACS_WATER_MODELS`). For other "octanol" or "wetoctanol" of + OPLS-AA forcefield, the ``model`` is used to select a specific model. For + other solvents and forcefields, "model" is not required. :Raises ValueError: If there is no identifier found for the combination. @@ -408,7 +396,9 @@ def get_solvent_identifier( forcefield = _get_forcefield(forcefield) if solvent_type == "water": - identifier = DEFAULT_WATER_MODEL if model in [None, "water"] else model + identifier = ( + forcefield.default_water_model if model in [None, "water"] else model + ) if identifier in forcefield.water_models: return identifier @@ -431,13 +421,14 @@ def get_solvent_identifier( def get_solvent_model(identifier, forcefield: Union[Forcefield, str] = OPLS_AA): """Return a :class:`GromacsSolventModel` corresponding to identifier *identifier*. - If identifier is "water" then the :data:`DEFAULT_WATER_MODEL` is assumed. + If identifier is "water" then the default water model for the :class:`Forcefield` is assumed. + """ if isinstance(forcefield, str): forcefield = _get_forcefield(forcefield) if identifier == "water": - identifier = DEFAULT_WATER_MODEL + identifier = forcefield.default_water_model try: return forcefield.water_models[identifier] except KeyError: diff --git a/mdpow/tests/test_forcefields.py b/mdpow/tests/test_forcefields.py index 9efd509f..6d361a94 100644 --- a/mdpow/tests/test_forcefields.py +++ b/mdpow/tests/test_forcefields.py @@ -63,7 +63,7 @@ def test_solvent(self, solvent_name): class TestWatermodels(object): @staticmethod def test_default_water_model(): - assert mdpow.forcefields.DEFAULT_WATER_MODEL == "tip4p" + assert mdpow.forcefields.OPLS_AA.default_water_model == "tip4p" def test_watermodelsdat(self): included_watermodels = open(mdpow.config.topfiles["watermodels.dat"]).read() @@ -93,7 +93,7 @@ def _simple_line_parser(string): @staticmethod def test_get_water_model(): - model = mdpow.forcefields.DEFAULT_WATER_MODEL + model = mdpow.forcefields.OPLS_AA.default_water_model assert ( mdpow.forcefields.get_water_model(model) is mdpow.forcefields.GROMACS_WATER_MODELS[model] @@ -109,7 +109,7 @@ class TestSolventModels(object): @staticmethod def test_get_solvent_default_water(): model = "water" - defaultmodel = mdpow.forcefields.DEFAULT_WATER_MODEL + defaultmodel = mdpow.forcefields.OPLS_AA.default_water_model assert ( mdpow.forcefields.get_solvent_model(model) == mdpow.forcefields.GROMACS_WATER_MODELS[defaultmodel] @@ -157,7 +157,7 @@ def test_get_solvent_toluene(self, forcefield): def test_get_solvent_identifier_default_is_water(): assert ( mdpow.forcefields.get_solvent_identifier("water") - is mdpow.forcefields.DEFAULT_WATER_MODEL + is mdpow.forcefields.OPLS_AA.default_water_model ) @pytest.mark.parametrize("model", WATERMODELS) From 301111e2afe98788e9432656c4a6f37695804772 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 30 Aug 2023 20:34:06 +0100 Subject: [PATCH 24/38] [WIP] use new default water models --- doc/examples/martini/martini-benzene.ipynb | 55 +++++++++++++--------- 1 file changed, 34 insertions(+), 21 deletions(-) diff --git a/doc/examples/martini/martini-benzene.ipynb b/doc/examples/martini/martini-benzene.ipynb index d04cc75f..f309c44c 100644 --- a/doc/examples/martini/martini-benzene.ipynb +++ b/doc/examples/martini/martini-benzene.ipynb @@ -126,7 +126,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 11, "metadata": {}, "outputs": [], "source": [ @@ -136,54 +136,66 @@ " \"Martini\",\n", " solvent_models={\n", " \"water\": GromacsSolventModel(\n", - " identifier=\"martini-water\", itp=MARTINI_SOLVENTS.absolute(), coordinates=MARTINI_WATER.absolute()\n", + " identifier=\"martini-water\",\n", + " itp=MARTINI_SOLVENTS.absolute(),\n", + " coordinates=MARTINI_WATER.absolute(),\n", + " forcefield=\"Martini\",\n", " ),\n", " \"octanol\": GromacsSolventModel(\n", - " identifier=\"octanol\", itp=MARTINI_SOLVENTS.absolute(), coordinates=MARTINI_OCTANOL.absolute()\n", + " identifier=\"octanol\",\n", + " itp=MARTINI_SOLVENTS.absolute(),\n", + " coordinates=MARTINI_OCTANOL.absolute(),\n", + " forcefield=\"Martini\",\n", " ),\n", " },\n", " forcefield_dir=MARTINI_FF.absolute(),\n", " ions_itp=MARTINI_IONS.absolute(),\n", " default_water_itp=MARTINI_SOLVENTS.absolute(),\n", + " default_water_model=\"martini-water\",\n", ")" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "{'name': 'Martini', 'solvent_models': {'water': {'identifier': 'martini-water', 'name': 'MARTINI-WATER', 'itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_solvents_v1.itp'), 'coordinates': PosixPath('/home/awsm/MDPOW/doc/examples/martini/water.gro'), 'description': None, 'forcefield': 'OPLS-AA'}, 'octanol': {'identifier': 'octanol', 'name': 'OCTANOL', 'itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_solvents_v1.itp'), 'coordinates': PosixPath('/home/awsm/MDPOW/doc/examples/martini/octanol.gro'), 'description': None, 'forcefield': 'OPLS-AA'}}, 'forcefield_dir': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff'), 'ions_itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_ions_v1.itp'), 'default_water_itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_solvents_v1.itp')}\n" + "water\n", + "\n", + "octanol\n", + "\n" ] } ], "source": [ "from dataclasses import asdict\n", "\n", - "martini_dict = asdict(MARTINI)\n", - "print(martini_dict)" + "for solvent_name, solvent_model in MARTINI.solvent_models.items():\n", + " print(solvent_name)\n", + " print(solvent_model)" ] }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 6, "metadata": {}, "outputs": [ { - "ename": "ValueError", - "evalue": "tip4p is not a valid water model for Martini.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[12], line 3\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mmdpow\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mequil\u001b[39;00m \u001b[39mimport\u001b[39;00m WaterSimulation\n\u001b[0;32m----> 3\u001b[0m sim \u001b[39m=\u001b[39m WaterSimulation(molecule\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mBENZ\u001b[39;49m\u001b[39m\"\u001b[39;49m, ff_class\u001b[39m=\u001b[39;49mMARTINI)\n\u001b[1;32m 4\u001b[0m sim\u001b[39m.\u001b[39mtopology(\u001b[39mstr\u001b[39m(BENZENE_ITP))\n\u001b[1;32m 5\u001b[0m sim\u001b[39m.\u001b[39msolvate(struct\u001b[39m=\u001b[39mMARTINI_BENZENE)\n", - "File \u001b[0;32m~/MDPOW/mdpow/equil.py:251\u001b[0m, in \u001b[0;36mSimulation.__init__\u001b[0;34m(self, molecule, ff_class, **kwargs)\u001b[0m\n\u001b[1;32m 249\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mforcefield \u001b[39m=\u001b[39m forcefield\n\u001b[1;32m 250\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39msolvent_type \u001b[39m=\u001b[39m solvent\n\u001b[0;32m--> 251\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39msolventmodel_identifier \u001b[39m=\u001b[39m forcefields\u001b[39m.\u001b[39;49mget_solvent_identifier(\n\u001b[1;32m 252\u001b[0m solvent,\n\u001b[1;32m 253\u001b[0m model\u001b[39m=\u001b[39;49msolventmodel,\n\u001b[1;32m 254\u001b[0m forcefield\u001b[39m=\u001b[39;49mforcefield,\n\u001b[1;32m 255\u001b[0m )\n\u001b[1;32m 256\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39msolventmodel_identifier \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m 257\u001b[0m msg \u001b[39m=\u001b[39m \u001b[39m\"\u001b[39m\u001b[39mNo parameters for solvent \u001b[39m\u001b[39m{0}\u001b[39;00m\u001b[39m and solventmodel \u001b[39m\u001b[39m{1}\u001b[39;00m\u001b[39m available.\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m.\u001b[39mformat(\n\u001b[1;32m 258\u001b[0m solvent, solventmodel\n\u001b[1;32m 259\u001b[0m )\n", - "File \u001b[0;32m~/MDPOW/mdpow/forcefields.py:417\u001b[0m, in \u001b[0;36mget_solvent_identifier\u001b[0;34m(solvent_type, model, forcefield)\u001b[0m\n\u001b[1;32m 415\u001b[0m \u001b[39mreturn\u001b[39;00m identifier\n\u001b[1;32m 416\u001b[0m \u001b[39melse\u001b[39;00m:\n\u001b[0;32m--> 417\u001b[0m \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(\n\u001b[1;32m 418\u001b[0m \u001b[39mf\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m{\u001b[39;00midentifier\u001b[39m}\u001b[39;00m\u001b[39m is not a valid water model for \u001b[39m\u001b[39m{\u001b[39;00mforcefield\u001b[39m.\u001b[39mname\u001b[39m}\u001b[39;00m\u001b[39m.\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 419\u001b[0m )\n\u001b[1;32m 421\u001b[0m \u001b[39mif\u001b[39;00m model \u001b[39mnot\u001b[39;00m \u001b[39min\u001b[39;00m forcefield\u001b[39m.\u001b[39msolvent_models:\n\u001b[1;32m 422\u001b[0m \u001b[39mif\u001b[39;00m solvent_type \u001b[39min\u001b[39;00m forcefield\u001b[39m.\u001b[39msolvent_models:\n", - "\u001b[0;31mValueError\u001b[0m: tip4p is not a valid water model for Martini." + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top] Created topology 'system.top' that includes 'BENZ.itp'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{'itp': 'martini-water.itp', 'box': 'martini-water.gro', 'distance': 1.0}\n" ] } ], @@ -192,9 +204,10 @@ "\n", "sim = WaterSimulation(molecule=\"BENZ\", ff_class=MARTINI)\n", "sim.topology(str(BENZENE_ITP))\n", - "sim.solvate(struct=MARTINI_BENZENE)\n", - "sim.energy_minimize()\n", - "sim.MD_relaxed(runtime=5) # should be at least 1e3 ps for production not just 5 ps" + "print(sim.solvent)\n", + "# sim.solvate(struct=MARTINI_BENZENE)\n", + "# sim.energy_minimize()\n", + "# sim.MD_relaxed(runtime=5) # should be at least 1e3 ps for production not just 5 ps" ] }, { From 8cbd11990592df9c866bd2d29edec90130f9ff30 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 30 Aug 2023 21:41:49 +0100 Subject: [PATCH 25/38] [WIP] Fixes some things --- .gitignore | 1 + doc/examples/martini/benzene.pdb | 13 + doc/examples/martini/em.mdp | 7 +- doc/examples/martini/eq.mdp | 1 + doc/examples/martini/martini-benzene.ipynb | 1504 +++++++++++++++++++- doc/examples/martini/run.mdp | 1 + mdpow/forcefields.py | 42 +- 7 files changed, 1508 insertions(+), 61 deletions(-) create mode 100644 doc/examples/martini/benzene.pdb diff --git a/.gitignore b/.gitignore index bb822933..0a5924b1 100644 --- a/.gitignore +++ b/.gitignore @@ -22,3 +22,4 @@ doc/examples/martini/* !doc/examples/martini/*.ipynb !doc/examples/martini/water.gro !doc/examples/martini/octanol.gro +!doc/examples/martini/benzene.pdb diff --git a/doc/examples/martini/benzene.pdb b/doc/examples/martini/benzene.pdb new file mode 100644 index 00000000..a6fdaba3 --- /dev/null +++ b/doc/examples/martini/benzene.pdb @@ -0,0 +1,13 @@ +REMARK GENERATED BY TRJCONV +TITLE This is an auto generated system +REMARK THIS IS A SIMULATION BOX +CRYST1 150.000 150.000 180.000 90.00 90.00 90.00 P 1 1 +MODEL 1 +ATOM 1 R1 BENZ 1 30.920 6.600 24.160 1.00 0.00 +ATOM 2 R2 BENZ 1 28.820 5.000 23.610 1.00 0.00 +ATOM 3 R3 BENZ 1 29.860 6.580 21.680 1.00 0.00 +TER +ENDMDL +CONECT 1 2 +CONECT 2 3 +CONECT 1 3 diff --git a/doc/examples/martini/em.mdp b/doc/examples/martini/em.mdp index 5035d5e6..d807c1a2 100644 --- a/doc/examples/martini/em.mdp +++ b/doc/examples/martini/em.mdp @@ -1,3 +1,4 @@ +include = integrator = steep dt = 0.02 nsteps = 1000 @@ -6,11 +7,11 @@ nstvout = 0 nstlog = 100 nstxtcout = 100 xtc-precision = 1000 -rlist = 1.4 +rlist = 1.0 coulombtype = Reaction-Field -rcoulomb = 1.1 +rcoulomb = 1.0 epsilon_r = 15 vdw-type = cutoff vdw-modifier = Potential-shift-verlet -rvdw = 1.1 +rvdw = 1.0 constraints = none diff --git a/doc/examples/martini/eq.mdp b/doc/examples/martini/eq.mdp index 2a15bc2a..0be94d32 100644 --- a/doc/examples/martini/eq.mdp +++ b/doc/examples/martini/eq.mdp @@ -1,3 +1,4 @@ +include = dt = 0.005 nsteps = 25000 nstxout = 0 diff --git a/doc/examples/martini/martini-benzene.ipynb b/doc/examples/martini/martini-benzene.ipynb index f309c44c..132fbc64 100644 --- a/doc/examples/martini/martini-benzene.ipynb +++ b/doc/examples/martini/martini-benzene.ipynb @@ -19,7 +19,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 19, "metadata": {}, "outputs": [], "source": [ @@ -32,20 +32,21 @@ "\n", "HERE = Path(\".\")\n", "MARTINI_FF = HERE / \"martini.ff\"\n", + "MARTINI_FF.mkdir(exist_ok=True)\n", "\n", "MARTINI_ITP = MARTINI_FF / \"forcefield.itp\"\n", "MARTINI_IONS = MARTINI_FF / \"martini_v3.0.0_ions_v1.itp\"\n", "MARTINI_SMALL_MOLS = MARTINI_FF / \"martini_v3.0.0_small_molecules_v1.itp\"\n", "MARTINI_SOLVENTS = MARTINI_FF / \"martini_v3.0.0_solvents_v1.itp\"\n", - "BENZENE_ITP = MARTINI_FF / \"BENZ.itp\"\n", + "BENZENE_ITP = MARTINI_SMALL_MOLS\n", "\n", "MARTINI_WATER = HERE / \"water.gro\"\n", "MARTINI_OCTANOL = HERE / \"octanol.gro\"\n", - "MARTINI_BENZENE = MARTINI_FF / \"output-conect.pdb\"\n", + "MARTINI_BENZENE = HERE / \"benzene.pdb\"\n", "\n", - "EM_FILE = MARTINI_FF / \"em.mdp\"\n", - "EQ_FILE = MARTINI_FF / \"eq.mdp\"\n", - "RUN_FILE = MARTINI_FF / \"run.mdp\"\n", + "EM_FILE = HERE / \"em.mdp\"\n", + "EQ_FILE = HERE / \"eq.mdp\"\n", + "RUN_FILE = HERE / \"run.mdp\"\n", "\n", "\n", "def download_file(\n", @@ -66,24 +67,15 @@ " f.write(chunk)\n", "\n", "\n", - "ZIP_DOWNLOAD = {\n", - " HERE\n", - " / \"BENZ.itp\": \"https://mad.ibcp.fr/api/molecule/download?id=731653322400583591&filename=BENZ.zip\"\n", - "}\n", "DOWNLOADS = {\n", " MARTINI_ITP: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0.itp\",\n", " MARTINI_IONS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_ions_v1.itp\",\n", " MARTINI_SMALL_MOLS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_small_molecules_v1.itp\",\n", " MARTINI_SOLVENTS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_solvents_v1.itp\",\n", "}\n", - "DOWNLOADS.update(ZIP_DOWNLOAD)\n", "\n", "for fname, url in DOWNLOADS.items():\n", - " download_file(url, fname)\n", - "\n", - "for zip_file in ZIP_DOWNLOAD.keys():\n", - " with ZipFile(zip_file, \"r\") as zip_ref:\n", - " zip_ref.extractall(MARTINI_FF)" + " download_file(url, fname)" ] }, { @@ -97,7 +89,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 20, "metadata": {}, "outputs": [ { @@ -106,7 +98,7 @@ "56" ] }, - "execution_count": 2, + "execution_count": 20, "metadata": {}, "output_type": "execute_result" } @@ -126,7 +118,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 21, "metadata": {}, "outputs": [], "source": [ @@ -135,12 +127,6 @@ "MARTINI = Forcefield(\n", " \"Martini\",\n", " solvent_models={\n", - " \"water\": GromacsSolventModel(\n", - " identifier=\"martini-water\",\n", - " itp=MARTINI_SOLVENTS.absolute(),\n", - " coordinates=MARTINI_WATER.absolute(),\n", - " forcefield=\"Martini\",\n", - " ),\n", " \"octanol\": GromacsSolventModel(\n", " identifier=\"octanol\",\n", " itp=MARTINI_SOLVENTS.absolute(),\n", @@ -152,22 +138,28 @@ " ions_itp=MARTINI_IONS.absolute(),\n", " default_water_itp=MARTINI_SOLVENTS.absolute(),\n", " default_water_model=\"martini-water\",\n", + " water_models={\n", + " \"martini-water\": GromacsSolventModel(\n", + " identifier=\"martini-water\",\n", + " itp=MARTINI_SOLVENTS.absolute(),\n", + " coordinates=str(MARTINI_WATER.absolute()),\n", + " forcefield=\"Martini\",\n", + " ),\n", + " },\n", ")" ] }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "water\n", - "\n", "octanol\n", - "\n" + "{'identifier': 'octanol', 'name': 'OCTANOL', 'itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_solvents_v1.itp'), 'coordinates': PosixPath('/home/awsm/MDPOW/doc/examples/martini/octanol.gro'), 'description': None, 'forcefield': 'Martini'}\n" ] } ], @@ -176,38 +168,1474 @@ "\n", "for solvent_name, solvent_model in MARTINI.solvent_models.items():\n", " print(solvent_name)\n", - " print(solvent_model)" + " print(asdict(solvent_model))" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 30, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top] Created topology 'system.top' that includes 'BENZ.itp'\n" + "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/water.gro'...\n", + " :-) GROMACS - gmx editconf, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", + "Command line:\n", + " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 1.0\n", + "\n", + "\n", + "Back Off! I just backed up boxed.gro to ./#boxed.gro.13#\n", + "\n", + "GROMACS reminds you: \"That Was Really Cool\" (Butthead)\n", + "\n", + " :-) GROMACS - gmx solvate, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", + "Command line:\n", + " gmx solvate -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -cp boxed.gro -cs /home/awsm/MDPOW/doc/examples/martini/water.gro -o solvated.gro\n", + "\n", + "Reading solute configuration\n", + "Reading solvent configuration\n", + "\n", + "Initialising inter-atomic distances...\n", + "Generating solvent configuration\n", + "Will generate new solvent configuration of 1x1x1 boxes\n", + "Solvent box contains 107 atoms in 107 residues\n", + "Removed 10 solvent atoms due to solvent-solvent overlap\n", + "Removed 1 solvent atoms due to solute-solvent overlap\n", + "Sorting configuration\n", + "Found 1 molecule type:\n", + " W ( 1 atoms): 96 residues\n", + "Generated solvent containing 96 atoms in 96 residues\n", + "Writing generated configuration to solvated.gro\n", + "\n", + "Back Off! I just backed up solvated.gro to ./#solvated.gro.13#\n", + "\n", + "Output configuration contains 99 atoms in 97 residues\n", + "Volume : 8.2737 (nm^3)\n", + "Density : 3549.33 (g/l)\n", + "Number of solvent molecules: 96 \n", + "\n", + "Processing topology\n", + "\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#system.top.14#\n", + "\n", + "GROMACS reminds you: \"It Just Tastes Better\" (Burger King)\n", + "\n", + "gromacs.setup: INFO Solvated system with /home/awsm/MDPOW/doc/examples/martini/water.gro\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "{'itp': 'martini-water.itp', 'box': 'martini-water.gro', 'distance': 1.0}\n" + "Note that major changes are planned in future for editconf, to improve usability and utility.\n", + "Read 3 atoms\n", + "Volume: 4050 nm^3, corresponds to roughly 1822500 electrons\n", + "No velocities found\n", + " system size : 0.210 0.160 0.248 (nm)\n", + " diameter : 0.270 (nm)\n", + " center : 2.987 0.606 2.315 (nm)\n", + " box vectors : 15.000 15.000 18.000 (nm)\n", + " box angles : 90.00 90.00 90.00 (degrees)\n", + " box volume :4050.00 (nm^3)\n", + " shift : -1.284 1.097 -1.512 (nm)\n", + "new center : 1.703 1.703 0.803 (nm)\n", + "new box vectors : 2.270 2.270 2.270 (nm)\n", + "new box angles : 60.00 60.00 90.00 (degrees)\n", + "new box volume : 8.27 (nm^3)\n", + "\n", + "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n", + " based on residue and atom names, since they could not be\n", + " definitively assigned from the information in your input\n", + " files. These guessed numbers might deviate from the mass\n", + " and radius of the atom type. Please check the output\n", + " files if necessary. Note, that this functionality may\n", + " be removed in a future GROMACS version. Please, consider\n", + " using another file format for your input.\n", + "\n", + "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n", + "from the source below. This means the results may be different\n", + "compared to previous GROMACS versions.\n", + "\n", + "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n", + "A. Bondi\n", + "van der Waals Volumes and Radii\n", + "J. Phys. Chem. 68 (1964) pp. 441-451\n", + "-------- -------- --- Thank You --- -------- --------\n", + "\n", + "Adding line for 96 solvent molecules with resname (W) to topology file (/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.cbook: INFO system total charge qtot = 0\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation] After solvation: total charge qtot = 0 = 0\n", + "gromacs.cbook: INFO system total charge qtot = 0\n", + "gromacs.setup: INFO Building the main index file 'main.ndx'...\n", + " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", + "Command line:\n", + " gmx make_ndx -f ionized.tpr -o main.ndx\n", + "\n", + "\n", + "Reading structure file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.26#\n", + "\n", + "GROMACS reminds you: \"It Just Tastes Better\" (Burger King)\n", + "\n", + " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", + "Command line:\n", + " gmx make_ndx -f ionized.tpr -n main.ndx -o main.ndx\n", + "\n", + "\n", + "Reading structure file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.27#\n", + "\n", + "GROMACS reminds you: \"It Just Tastes Better\" (Burger King)\n", + "\n", + " :-) GROMACS - gmx trjconv, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", + "Command line:\n", + " gmx trjconv -ur compact -center -boxcenter tric -pbc mol -f ionized.gro -s ionized.tpr -o compact.pdb -n main.ndx\n", + "\n", + "Will write pdb: Protein data bank file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Group 0 ( System) has 99 elements\n", + "Group 1 ( Other) has 99 elements\n", + "Group 2 ( BENZ) has 3 elements\n", + "Group 3 ( W) has 96 elements\n", + "Group 4 ( __main__) has 3 elements\n", + "Group 5 (__environment__) has 96 elements\n", + "Select a group: Group 0 ( System) has 99 elements\n", + "Group 1 ( Other) has 99 elements\n", + "Group 2 ( BENZ) has 3 elements\n", + "Group 3 ( W) has 96 elements\n", + "Group 4 ( __main__) has 3 elements\n", + "Group 5 (__environment__) has 96 elements\n", + "Select a group: Reading frames from gro file 'This is an auto generated system', 99 atoms.\n", + "Reading frame 0 time 0.000 \n", + "Precision of ionized.gro is 0.001 (nm)\n", + "\n", + "Back Off! I just backed up compact.pdb to ./#compact.pdb.13#\n", + "Last frame 0 time 0.000 \n", + " -> frame 0 time 0.000 \n", + "Last written: frame 0 time 0.000\n", + "\n", + "\n", + "GROMACS reminds you: \"It Just Tastes Better\" (Burger King)\n", + "\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -f /tmp/tmpbri3j0j8.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -nov\n", + "\n", + "\n", + "NOTE 1 [file /tmp/tmpbri3j0j8.mdp]:\n", + " For a correct single-point energy evaluation with nsteps = 0, use\n", + " continuation = yes to avoid constraining the input coordinates.\n", + "\n", + "\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#pp_system.top.13#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Note that major changes are planned in future for trjconv, to improve usability and utility.\n", + "Select group for centering\n", + "Selected 4: '__main__'\n", + "Select group for output\n", + "Selected 0: 'System'\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "atom name 46 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 47 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 48 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 49 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 50 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 51 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 52 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 53 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 54 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 55 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 56 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 57 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 58 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 59 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 60 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 61 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 62 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 63 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 64 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 65 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "(more than 20 non-matching atom names)\n", + "\n", + "WARNING 1 [file system.top, line 28]:\n", + " 54 non-matching atom names\n", + " atom names from\n", + " /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top\n", + " will be used\n", + " atom names from\n", + " /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro\n", + " will be ignored\n", + "\n", + "\n", + "\n", + "NOTE 2 [file system.top, line 28]:\n", + " For energy conservation with LINCS, lincs_iter should be 2 or larger.\n", + "\n", + "\n", + "Number of degrees of freedom in T-Coupling group rest is 291.00\n", + "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "\n", + "NOTE 3 [file /tmp/tmpbri3j0j8.mdp]:\n", + " NVE simulation with an initial temperature of zero: will use a Verlet\n", + " buffer of 10%. Check your energy drift!\n", + "\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"This simulation is not as the former.\" (Malvolio, Act II, scene V of Shaphespeare's Twelfth Night)\n", + "\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top', mdp='em.mdp' ...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'em.mdp': ['maxwarn', 'pp']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'maxwarn': 1, 'pp': 'processed.top'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'maxwarn': 1, 'pp': 'processed.top'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em\n", + "Command line:\n", + " gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -maxwarn 1 -pp processed.top\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.7#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1526199919\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "atom name 46 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 47 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 48 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 49 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 50 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 51 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 52 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 53 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 54 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 55 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 56 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 57 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 58 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 59 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 60 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 61 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 62 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 63 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 64 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 65 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "(more than 20 non-matching atom names)\n", + "Analysing residue names:\n", + "There are: 97 Other residues\n", + "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", + "\n", + "This run will generate roughly 0 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "atom name 46 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 47 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 48 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 49 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 50 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 51 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 52 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 53 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 54 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 55 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 56 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 57 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 58 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 59 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 60 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 61 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 62 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 63 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 64 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 65 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "(more than 20 non-matching atom names)\n", + "\n", + "WARNING 1 [file system.top, line 28]:\n", + " 54 non-matching atom names\n", + " atom names from\n", + " /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top\n", + " will be used\n", + " atom names from\n", + " /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro\n", + " will be ignored\n", + "\n", + "\n", + "Number of degrees of freedom in T-Coupling group rest is 291.00\n", + "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up em.tpr to ./#em.tpr.3#\n", + "\n", + "GROMACS reminds you: \"This simulation is not as the former.\" (Malvolio, Act II, scene V of Shaphespeare's Twelfth Night)\n", + "\n", + "gromacs.run : WARNING No 'mdrun_d' binary found so trying 'mdrun' instead.\n", + "(Note that energy minimization runs better with mdrun_d.)\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/run.py:423: AutoCorrectionWarning: No 'mdrun_d' binary found so trying 'mdrun' instead.\n", + "(Note that energy minimization runs better with mdrun_d.)\n", + " warnings.warn(wmsg, category=AutoCorrectionWarning)\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em\n", + "Command line:\n", + " gmx mdrun -v -stepout 10 -deffnm em -c em.pdb\n", + "\n" ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -219464132\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "atom name 46 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 47 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 48 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 49 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 50 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 51 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 52 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 53 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 54 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 55 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 56 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 57 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 58 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 59 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 60 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 61 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 62 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 63 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 64 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "atom name 65 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "\n", + "(more than 20 non-matching atom names)\n", + "Analysing residue names:\n", + "There are: 97 Other residues\n", + "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", + "\n", + "This run will generate roughly 0 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n", + "Back Off! I just backed up em.log to ./#em.log.3#\n", + "Reading file em.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "NOTE: Parallelization is limited by the small number of atoms,\n", + " only starting 1 thread-MPI ranks.\n", + " You can use the -nt and/or -ntmpi option to optimize the number of threads.\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "\n", + "Back Off! I just backed up em.trr to ./#em.trr.3#\n", + "\n", + "Back Off! I just backed up em.edr to ./#em.edr.3#\n", + "\n", + "Steepest Descents:\n", + " Tolerance (Fmax) = 1.00000e+01\n", + " Number of steps = 1000\n", + "Step= 0, Dmax= 1.0e-02 nm, Epot= 1.23531e+06 Fmax= 1.48149e+07, atom= 4\n", + "Step= 1, Dmax= 1.0e-02 nm, Epot= 7.70813e+05 Fmax= 5.61453e+06, atom= 86\n", + "Step= 2, Dmax= 1.2e-02 nm, Epot= 4.81154e+05 Fmax= 2.27826e+06, atom= 86\n", + "Step= 3, Dmax= 1.4e-02 nm, Epot= 3.05902e+05 Fmax= 8.26141e+05, atom= 86\n", + "Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88718e+05 Fmax= 3.05413e+05, atom= 91\n", + "Step= 5, Dmax= 2.1e-02 nm, Epot= 1.14388e+05 Fmax= 1.57159e+05, atom= 27\n", + "Step= 6, Dmax= 2.5e-02 nm, Epot= 7.08726e+04 Fmax= 9.21310e+04, atom= 38\n", + "Step= 7, Dmax= 3.0e-02 nm, Epot= 4.49159e+04 Fmax= 8.27843e+04, atom= 48\n", + "Step= 8, Dmax= 3.6e-02 nm, Epot= 3.34613e+04 Fmax= 6.48167e+04, atom= 94\n", + "Step= 9, Dmax= 4.3e-02 nm, Epot= 2.52637e+04 Fmax= 8.72701e+04, atom= 48\n", + "Step= 10, Dmax= 5.2e-02 nm, Epot= 2.04773e+04 Fmax= 2.73106e+04, atom= 91\n", + "Step= 11, Dmax= 6.2e-02 nm, Epot= 1.41021e+04 Fmax= 9.10967e+04, atom= 48\n", + "Step= 12, Dmax= 7.4e-02 nm, Epot= 1.10696e+04 Fmax= 1.60415e+04, atom= 48\n", + "Step= 13, Dmax= 8.9e-02 nm, Epot= 7.72396e+03 Fmax= 4.26140e+04, atom= 48\n", + "Step= 14, Dmax= 1.1e-01 nm, Epot= 5.96311e+03 Fmax= 8.74381e+03, atom= 86\n", + "Step= 16, Dmax= 6.4e-02 nm, Epot= 4.68375e+03 Fmax= 1.05593e+04, atom= 28\n", + "Step= 17, Dmax= 7.7e-02 nm, Epot= 4.47625e+03 Fmax= 2.86871e+04, atom= 62\n", + "Step= 18, Dmax= 9.2e-02 nm, Epot= 3.49467e+03 Fmax= 1.84483e+04, atom= 34\n", + "Step= 19, Dmax= 1.1e-01 nm, Epot= 3.05704e+03 Fmax= 1.57467e+04, atom= 50\n", + "Step= 21, Dmax= 6.7e-02 nm, Epot= 2.48774e+03 Fmax= 8.35716e+03, atom= 93\n", + "Step= 22, Dmax= 8.0e-02 nm, Epot= 1.98686e+03 Fmax= 5.53022e+03, atom= 93\n", + "Step= 23, Dmax= 9.6e-02 nm, Epot= 1.72792e+03 Fmax= 7.55378e+03, atom= 50\n", + "Step= 25, Dmax= 5.8e-02 nm, Epot= 1.19236e+03 Fmax= 4.54330e+03, atom= 53\n", + "Step= 26, Dmax= 6.9e-02 nm, Epot= 1.18750e+03 Fmax= 7.87388e+03, atom= 30\n", + "Step= 27, Dmax= 8.3e-02 nm, Epot= 1.17387e+03 Fmax= 1.21579e+04, atom= 30\n", + "Step= 29, Dmax= 5.0e-02 nm, Epot= 6.19271e+02 Fmax= 3.14347e+03, atom= 99\n", + "Step= 30, Dmax= 6.0e-02 nm, Epot= 5.13212e+02 Fmax= 5.61843e+03, atom= 99\n", + "Step= 31, Dmax= 7.2e-02 nm, Epot= 3.89048e+02 Fmax= 4.97197e+03, atom= 99\n", + "Step= 33, Dmax= 4.3e-02 nm, Epot= 1.51418e+02 Fmax= 1.37543e+03, atom= 63\n", + "Step= 34, Dmax= 5.2e-02 nm, Epot= 2.70003e+01 Fmax= 5.00114e+03, atom= 63\n", + "Step= 35, Dmax= 6.2e-02 nm, Epot= -7.81142e+01 Fmax= 3.32794e+03, atom= 99\n", + "Step= 37, Dmax= 3.7e-02 nm, Epot= -2.16465e+02 Fmax= 1.01594e+03, atom= 59\n", + "Step= 39, Dmax= 2.2e-02 nm, Epot= -2.91331e+02 Fmax= 1.56361e+03, atom= 73\n", + "Step= 40, Dmax= 2.7e-02 nm, Epot= -3.18646e+02 Fmax= 2.12704e+03, atom= 73\n", + "Step= 41, Dmax= 3.2e-02 nm, Epot= -3.34565e+02 Fmax= 3.10421e+03, atom= 73\n", + "Step= 42, Dmax= 3.8e-02 nm, Epot= -3.95506e+02 Fmax= 1.98314e+03, atom= 73\n", + "Step= 44, Dmax= 2.3e-02 nm, Epot= -4.58630e+02 Fmax= 8.56395e+02, atom= 38\n", + "Step= 46, Dmax= 1.4e-02 nm, Epot= -4.94776e+02 Fmax= 6.96671e+02, atom= 45\n", + "Step= 47, Dmax= 1.7e-02 nm, Epot= -5.09859e+02 Fmax= 1.51727e+03, atom= 73\n", + "Step= 48, Dmax= 2.0e-02 nm, Epot= -5.55774e+02 Fmax= 8.37062e+02, atom= 45\n", + "Step= 50, Dmax= 1.2e-02 nm, Epot= -5.86000e+02 Fmax= 5.55214e+02, atom= 73\n", + "Step= 51, Dmax= 1.4e-02 nm, Epot= -6.08029e+02 Fmax= 9.46368e+02, atom= 38\n", + "Step= 52, Dmax= 1.7e-02 nm, Epot= -6.29567e+02 Fmax= 1.10282e+03, atom= 73\n", + "Step= 53, Dmax= 2.1e-02 nm, Epot= -6.49759e+02 Fmax= 1.07976e+03, atom= 38\n", + "Step= 55, Dmax= 1.2e-02 nm, Epot= -6.94500e+02 Fmax= 3.55241e+02, atom= 73\n", + "Step= 56, Dmax= 1.5e-02 nm, Epot= -7.16639e+02 Fmax= 1.25705e+03, atom= 63\n", + "Step= 57, Dmax= 1.8e-02 nm, Epot= -7.57033e+02 Fmax= 7.75228e+02, atom= 63\n", + "Step= 59, Dmax= 1.1e-02 nm, Epot= -7.84539e+02 Fmax= 3.70427e+02, atom= 63\n", + "Step= 60, Dmax= 1.3e-02 nm, Epot= -8.10124e+02 Fmax= 9.55604e+02, atom= 63\n", + "Step= 61, Dmax= 1.5e-02 nm, Epot= -8.39097e+02 Fmax= 6.57462e+02, atom= 63\n", + "Step= 62, Dmax= 1.9e-02 nm, Epot= -8.49229e+02 Fmax= 1.20918e+03, atom= 63\n", + "Step= 63, Dmax= 2.2e-02 nm, Epot= -8.77608e+02 Fmax= 1.01717e+03, atom= 63\n", + "Step= 65, Dmax= 1.3e-02 nm, Epot= -9.10259e+02 Fmax= 3.59827e+02, atom= 63\n", + "Step= 66, Dmax= 1.6e-02 nm, Epot= -9.34776e+02 Fmax= 1.04464e+03, atom= 15\n", + "Step= 67, Dmax= 1.9e-02 nm, Epot= -9.59352e+02 Fmax= 7.90866e+02, atom= 63\n", + "Step= 68, Dmax= 2.3e-02 nm, Epot= -9.59384e+02 Fmax= 1.36825e+03, atom= 15\n", + "Step= 69, Dmax= 2.8e-02 nm, Epot= -9.80644e+02 Fmax= 1.12403e+03, atom= 15\n", + "Step= 71, Dmax= 1.7e-02 nm, Epot= -1.02460e+03 Fmax= 4.27435e+02, atom= 88\n", + "Step= 72, Dmax= 2.0e-02 nm, Epot= -1.03181e+03 Fmax= 1.05550e+03, atom= 88\n", + "Step= 73, Dmax= 2.4e-02 nm, Epot= -1.04573e+03 Fmax= 1.21505e+03, atom= 88\n", + "Step= 74, Dmax= 2.9e-02 nm, Epot= -1.05552e+03 Fmax= 1.18349e+03, atom= 88\n", + "Step= 76, Dmax= 1.7e-02 nm, Epot= -1.10137e+03 Fmax= 3.32521e+02, atom= 44\n", + "Step= 78, Dmax= 1.0e-02 nm, Epot= -1.11650e+03 Fmax= 5.03713e+02, atom= 14\n", + "Step= 79, Dmax= 1.2e-02 nm, Epot= -1.12894e+03 Fmax= 4.89832e+02, atom= 14\n", + "Step= 80, Dmax= 1.5e-02 nm, Epot= -1.13128e+03 Fmax= 8.31786e+02, atom= 14\n", + "Step= 81, Dmax= 1.8e-02 nm, Epot= -1.14755e+03 Fmax= 6.72474e+02, atom= 46\n", + "Step= 83, Dmax= 1.1e-02 nm, Epot= -1.17210e+03 Fmax= 2.97577e+02, atom= 46\n", + "Step= 84, Dmax= 1.3e-02 nm, Epot= -1.17536e+03 Fmax= 9.14939e+02, atom= 46\n", + "Step= 85, Dmax= 1.5e-02 nm, Epot= -1.19793e+03 Fmax= 5.24850e+02, atom= 46\n", + "Step= 87, Dmax= 9.2e-03 nm, Epot= -1.20948e+03 Fmax= 3.28243e+02, atom= 46\n", + "Step= 88, Dmax= 1.1e-02 nm, Epot= -1.21731e+03 Fmax= 6.92502e+02, atom= 46\n", + "Step= 89, Dmax= 1.3e-02 nm, Epot= -1.22834e+03 Fmax= 5.56511e+02, atom= 46\n", + "Step= 90, Dmax= 1.6e-02 nm, Epot= -1.23074e+03 Fmax= 9.32022e+02, atom= 46\n", + "Step= 91, Dmax= 1.9e-02 nm, Epot= -1.24063e+03 Fmax= 8.60424e+02, atom= 46\n", + "Step= 93, Dmax= 1.1e-02 nm, Epot= -1.25583e+03 Fmax= 2.07618e+02, atom= 30\n", + "Step= 94, Dmax= 1.4e-02 nm, Epot= -1.26051e+03 Fmax= 1.26640e+03, atom= 46\n", + "Step= 95, Dmax= 1.7e-02 nm, Epot= -1.28203e+03 Fmax= 3.99836e+02, atom= 46\n", + "Step= 97, Dmax= 9.9e-03 nm, Epot= -1.28888e+03 Fmax= 5.17173e+02, atom= 46\n", + "Step= 98, Dmax= 1.2e-02 nm, Epot= -1.29499e+03 Fmax= 5.82943e+02, atom= 46\n", + "Step= 99, Dmax= 1.4e-02 nm, Epot= -1.29985e+03 Fmax= 7.82873e+02, atom= 46\n", + "Step= 100, Dmax= 1.7e-02 nm, Epot= -1.30525e+03 Fmax= 8.13948e+02, atom= 46\n", + "Step= 101, Dmax= 2.1e-02 nm, Epot= -1.30580e+03 Fmax= 1.16789e+03, atom= 46\n", + "Step= 102, Dmax= 2.5e-02 nm, Epot= -1.31098e+03 Fmax= 1.12892e+03, atom= 46\n", + "Step= 104, Dmax= 1.5e-02 nm, Epot= -1.33203e+03 Fmax= 2.01087e+02, atom= 46\n", + "Step= 106, Dmax= 8.9e-03 nm, Epot= -1.34061e+03 Fmax= 6.26878e+02, atom= 46\n", + "Step= 107, Dmax= 1.1e-02 nm, Epot= -1.34988e+03 Fmax= 4.26997e+02, atom= 46\n", + "Step= 108, Dmax= 1.3e-02 nm, Epot= -1.35419e+03 Fmax= 7.14250e+02, atom= 46\n", + "Step= 109, Dmax= 1.5e-02 nm, Epot= -1.36088e+03 Fmax= 7.60130e+02, atom= 46\n", + "Step= 110, Dmax= 1.8e-02 nm, Epot= -1.36367e+03 Fmax= 9.08721e+02, atom= 46\n", + "Step= 111, Dmax= 2.2e-02 nm, Epot= -1.36485e+03 Fmax= 1.22558e+03, atom= 46\n", + "Step= 112, Dmax= 2.7e-02 nm, Epot= -1.36898e+03 Fmax= 1.17562e+03, atom= 46\n", + "Step= 114, Dmax= 1.6e-02 nm, Epot= -1.39228e+03 Fmax= 2.36480e+02, atom= 46\n", + "Step= 116, Dmax= 9.6e-03 nm, Epot= -1.39959e+03 Fmax= 5.78072e+02, atom= 46\n", + "Step= 117, Dmax= 1.1e-02 nm, Epot= -1.40737e+03 Fmax= 5.47191e+02, atom= 46\n", + "Step= 118, Dmax= 1.4e-02 nm, Epot= -1.41186e+03 Fmax= 6.38350e+02, atom= 46\n", + "Step= 119, Dmax= 1.7e-02 nm, Epot= -1.41413e+03 Fmax= 9.57934e+02, atom= 46\n", + "Step= 120, Dmax= 2.0e-02 nm, Epot= -1.42141e+03 Fmax= 7.80371e+02, atom= 46\n", + "Step= 122, Dmax= 1.2e-02 nm, Epot= -1.43407e+03 Fmax= 2.81777e+02, atom= 46\n", + "Step= 123, Dmax= 1.4e-02 nm, Epot= -1.43572e+03 Fmax= 8.72953e+02, atom= 46\n", + "Step= 124, Dmax= 1.7e-02 nm, Epot= -1.44639e+03 Fmax= 7.29953e+02, atom= 46\n", + "Step= 126, Dmax= 1.0e-02 nm, Epot= -1.45629e+03 Fmax= 1.85111e+02, atom= 30\n", + "Step= 127, Dmax= 1.2e-02 nm, Epot= -1.46028e+03 Fmax= 1.04938e+03, atom= 46\n", + "Step= 128, Dmax= 1.5e-02 nm, Epot= -1.47469e+03 Fmax= 2.83085e+02, atom= 46\n", + "Step= 130, Dmax= 8.9e-03 nm, Epot= -1.47935e+03 Fmax= 5.61673e+02, atom= 46\n", + "Step= 131, Dmax= 1.1e-02 nm, Epot= -1.48561e+03 Fmax= 3.03875e+02, atom= 46\n", + "Step= 133, Dmax= 6.4e-03 nm, Epot= -1.49090e+03 Fmax= 2.85057e+02, atom= 46\n", + "Step= 134, Dmax= 7.7e-03 nm, Epot= -1.49596e+03 Fmax= 2.88499e+02, atom= 46\n", + "Step= 135, Dmax= 9.2e-03 nm, Epot= -1.49959e+03 Fmax= 5.89020e+02, atom= 46\n", + "Step= 136, Dmax= 1.1e-02 nm, Epot= -1.50638e+03 Fmax= 2.94146e+02, atom= 46\n", + "Step= 138, Dmax= 6.6e-03 nm, Epot= -1.51145e+03 Fmax= 3.05515e+02, atom= 46\n", + "Step= 139, Dmax= 8.0e-03 nm, Epot= -1.51616e+03 Fmax= 2.78040e+02, atom= 46\n", + "Step= 140, Dmax= 9.6e-03 nm, Epot= -1.51886e+03 Fmax= 6.15229e+02, atom= 46\n", + "Step= 141, Dmax= 1.1e-02 nm, Epot= -1.52638e+03 Fmax= 2.84333e+02, atom= 30\n", + "Step= 143, Dmax= 6.9e-03 nm, Epot= -1.53121e+03 Fmax= 3.18607e+02, atom= 46\n", + "Step= 144, Dmax= 8.3e-03 nm, Epot= -1.53569e+03 Fmax= 2.78624e+02, atom= 30\n", + "Step= 145, Dmax= 9.9e-03 nm, Epot= -1.53753e+03 Fmax= 6.07045e+02, atom= 46\n", + "Step= 146, Dmax= 1.2e-02 nm, Epot= -1.54532e+03 Fmax= 2.98561e+02, atom= 30\n", + "Step= 148, Dmax= 7.1e-03 nm, Epot= -1.55019e+03 Fmax= 3.00360e+02, atom= 46\n", + "Step= 149, Dmax= 8.6e-03 nm, Epot= -1.55414e+03 Fmax= 3.00495e+02, atom= 30\n", + "Step= 150, Dmax= 1.0e-02 nm, Epot= -1.55495e+03 Fmax= 5.71855e+02, atom= 46\n", + "Step= 151, Dmax= 1.2e-02 nm, Epot= -1.56241e+03 Fmax= 3.35835e+02, atom= 30\n", + "Step= 153, Dmax= 7.4e-03 nm, Epot= -1.56823e+03 Fmax= 2.56194e+02, atom= 46\n", + "Step= 154, Dmax= 8.9e-03 nm, Epot= -1.57018e+03 Fmax= 3.84893e+02, atom= 95\n", + "Step= 155, Dmax= 1.1e-02 nm, Epot= -1.57306e+03 Fmax= 4.55866e+02, atom= 95\n", + "Step= 156, Dmax= 1.3e-02 nm, Epot= -1.57432e+03 Fmax= 5.59437e+02, atom= 95\n", + "Step= 157, Dmax= 1.5e-02 nm, Epot= -1.57665e+03 Fmax= 6.60315e+02, atom= 95\n", + "Step= 159, Dmax= 9.2e-03 nm, Epot= -1.59074e+03 Fmax= 1.27129e+02, atom= 95\n", + "Step= 160, Dmax= 1.1e-02 nm, Epot= -1.59725e+03 Fmax= 6.63711e+02, atom= 65\n", + "Step= 161, Dmax= 1.3e-02 nm, Epot= -1.60372e+03 Fmax= 4.06029e+02, atom= 95\n", + "Step= 163, Dmax= 7.9e-03 nm, Epot= -1.60863e+03 Fmax= 1.94396e+02, atom= 65\n", + "Step= 164, Dmax= 9.5e-03 nm, Epot= -1.61065e+03 Fmax= 5.21003e+02, atom= 95\n", + "Step= 165, Dmax= 1.1e-02 nm, Epot= -1.61651e+03 Fmax= 3.72184e+02, atom= 65\n", + "Step= 167, Dmax= 6.9e-03 nm, Epot= -1.62090e+03 Fmax= 1.83671e+02, atom= 95\n", + "Step= 168, Dmax= 8.2e-03 nm, Epot= -1.62404e+03 Fmax= 4.55366e+02, atom= 65\n", + "Step= 169, Dmax= 9.9e-03 nm, Epot= -1.62830e+03 Fmax= 3.16952e+02, atom= 95\n", + "Step= 170, Dmax= 1.2e-02 nm, Epot= -1.62842e+03 Fmax= 6.45156e+02, atom= 65\n", + "Step= 171, Dmax= 1.4e-02 nm, Epot= -1.63357e+03 Fmax= 4.58465e+02, atom= 95\n", + "Step= 173, Dmax= 8.5e-03 nm, Epot= -1.63939e+03 Fmax= 1.79413e+02, atom= 65\n", + "Step= 174, Dmax= 1.0e-02 nm, Epot= -1.63977e+03 Fmax= 5.76793e+02, atom= 65\n", + "Step= 175, Dmax= 1.2e-02 nm, Epot= -1.64675e+03 Fmax= 3.92461e+02, atom= 65\n", + "Step= 177, Dmax= 7.4e-03 nm, Epot= -1.65116e+03 Fmax= 1.79598e+02, atom= 95\n", + "Step= 178, Dmax= 8.9e-03 nm, Epot= -1.65245e+03 Fmax= 5.45644e+02, atom= 65\n", + "Step= 179, Dmax= 1.1e-02 nm, Epot= -1.65816e+03 Fmax= 2.85069e+02, atom= 65\n", + "Step= 181, Dmax= 6.4e-03 nm, Epot= -1.66154e+03 Fmax= 2.02405e+02, atom= 65\n", + "Step= 182, Dmax= 7.7e-03 nm, Epot= -1.66363e+03 Fmax= 3.70369e+02, atom= 65\n", + "Step= 183, Dmax= 9.2e-03 nm, Epot= -1.66692e+03 Fmax= 3.42580e+02, atom= 65\n", + "Step= 184, Dmax= 1.1e-02 nm, Epot= -1.66748e+03 Fmax= 4.92426e+02, atom= 65\n", + "Step= 185, Dmax= 1.3e-02 nm, Epot= -1.66979e+03 Fmax= 5.35548e+02, atom= 65\n", + "Step= 187, Dmax= 7.9e-03 nm, Epot= -1.67671e+03 Fmax= 1.02893e+02, atom= 95\n", + "Step= 188, Dmax= 9.5e-03 nm, Epot= -1.67961e+03 Fmax= 6.22062e+02, atom= 65\n", + "Step= 189, Dmax= 1.1e-02 nm, Epot= -1.68615e+03 Fmax= 2.93349e+02, atom= 65\n", + "Step= 191, Dmax= 6.9e-03 nm, Epot= -1.68891e+03 Fmax= 2.20704e+02, atom= 65\n", + "Step= 192, Dmax= 8.2e-03 nm, Epot= -1.68979e+03 Fmax= 4.06780e+02, atom= 65\n", + "Step= 193, Dmax= 9.9e-03 nm, Epot= -1.69276e+03 Fmax= 3.47940e+02, atom= 65\n", + "Step= 195, Dmax= 5.9e-03 nm, Epot= -1.69632e+03 Fmax= 1.15212e+02, atom= 65\n", + "Step= 196, Dmax= 7.1e-03 nm, Epot= -1.69782e+03 Fmax= 4.42169e+02, atom= 65\n", + "Step= 197, Dmax= 8.5e-03 nm, Epot= -1.70194e+03 Fmax= 2.30295e+02, atom= 65\n", + "Step= 199, Dmax= 5.1e-03 nm, Epot= -1.70411e+03 Fmax= 1.56805e+02, atom= 65\n", + "Step= 200, Dmax= 6.1e-03 nm, Epot= -1.70533e+03 Fmax= 3.20711e+02, atom= 65\n", + "Step= 201, Dmax= 7.4e-03 nm, Epot= -1.70776e+03 Fmax= 2.43531e+02, atom= 65\n", + "Step= 203, Dmax= 4.4e-03 nm, Epot= -1.71000e+03 Fmax= 1.06450e+02, atom= 59\n", + "Step= 204, Dmax= 5.3e-03 nm, Epot= -1.71168e+03 Fmax= 2.91243e+02, atom= 65\n", + "Step= 205, Dmax= 6.4e-03 nm, Epot= -1.71386e+03 Fmax= 2.09332e+02, atom= 65\n", + "Step= 206, Dmax= 7.6e-03 nm, Epot= -1.71392e+03 Fmax= 3.82881e+02, atom= 65\n", + "Step= 207, Dmax= 9.2e-03 nm, Epot= -1.71592e+03 Fmax= 3.34820e+02, atom= 65\n", + "Step= 209, Dmax= 5.5e-03 nm, Epot= -1.71896e+03 Fmax= 1.01078e+02, atom= 59\n", + "Step= 210, Dmax= 6.6e-03 nm, Epot= -1.71976e+03 Fmax= 3.60549e+02, atom= 65\n", + "Step= 211, Dmax= 7.9e-03 nm, Epot= -1.72212e+03 Fmax= 2.54754e+02, atom= 65\n", + "Step= 213, Dmax= 4.8e-03 nm, Epot= -1.72412e+03 Fmax= 1.16027e+02, atom= 65\n", + "Step= 214, Dmax= 5.7e-03 nm, Epot= -1.72419e+03 Fmax= 3.30170e+02, atom= 65\n", + "Step= 215, Dmax= 6.8e-03 nm, Epot= -1.72647e+03 Fmax= 2.09114e+02, atom= 65\n", + "Step= 217, Dmax= 4.1e-03 nm, Epot= -1.72793e+03 Fmax= 1.09336e+02, atom= 65\n", + "Step= 218, Dmax= 4.9e-03 nm, Epot= -1.72823e+03 Fmax= 2.76009e+02, atom= 65\n", + "Step= 219, Dmax= 5.9e-03 nm, Epot= -1.72989e+03 Fmax= 1.84592e+02, atom= 65\n", + "Step= 221, Dmax= 3.5e-03 nm, Epot= -1.73112e+03 Fmax= 9.15048e+01, atom= 65\n", + "Step= 222, Dmax= 4.3e-03 nm, Epot= -1.73148e+03 Fmax= 2.43456e+02, atom= 65\n", + "Step= 223, Dmax= 5.1e-03 nm, Epot= -1.73290e+03 Fmax= 1.56505e+02, atom= 65\n", + "Step= 225, Dmax= 3.1e-03 nm, Epot= -1.73389e+03 Fmax= 8.39731e+01, atom= 65\n", + "Step= 226, Dmax= 3.7e-03 nm, Epot= -1.73434e+03 Fmax= 1.99155e+02, atom= 65\n", + "Step= 227, Dmax= 4.4e-03 nm, Epot= -1.73537e+03 Fmax= 1.47313e+02, atom= 65\n", + "Step= 229, Dmax= 2.6e-03 nm, Epot= -1.73627e+03 Fmax= 5.81890e+01, atom= 59\n", + "Step= 230, Dmax= 3.2e-03 nm, Epot= -1.73677e+03 Fmax= 1.95169e+02, atom= 65\n", + "Step= 231, Dmax= 3.8e-03 nm, Epot= -1.73789e+03 Fmax= 1.01485e+02, atom= 65\n", + "Step= 233, Dmax= 2.3e-03 nm, Epot= -1.73851e+03 Fmax= 8.04922e+01, atom= 65\n", + "Step= 234, Dmax= 2.7e-03 nm, Epot= -1.73895e+03 Fmax= 1.27947e+02, atom= 65\n", + "Step= 235, Dmax= 3.3e-03 nm, Epot= -1.73946e+03 Fmax= 1.33032e+02, atom= 65\n", + "Step= 236, Dmax= 4.0e-03 nm, Epot= -1.73967e+03 Fmax= 1.71057e+02, atom= 65\n", + "Step= 237, Dmax= 4.7e-03 nm, Epot= -1.73986e+03 Fmax= 2.03708e+02, atom= 65\n", + "Step= 238, Dmax= 5.7e-03 nm, Epot= -1.73986e+03 Fmax= 2.36179e+02, atom= 65\n", + "Step= 240, Dmax= 3.4e-03 nm, Epot= -1.74177e+03 Fmax= 4.15057e+01, atom= 59\n", + "Step= 241, Dmax= 4.1e-03 nm, Epot= -1.74187e+03 Fmax= 2.32512e+02, atom= 80\n", + "Step= 242, Dmax= 4.9e-03 nm, Epot= -1.74305e+03 Fmax= 1.67802e+02, atom= 80\n", + "Step= 244, Dmax= 3.0e-03 nm, Epot= -1.74397e+03 Fmax= 6.03771e+01, atom= 94\n", + "Step= 246, Dmax= 1.8e-03 nm, Epot= -1.74432e+03 Fmax= 8.91181e+01, atom= 80\n", + "Step= 247, Dmax= 2.1e-03 nm, Epot= -1.74471e+03 Fmax= 7.21345e+01, atom= 80\n", + "Step= 248, Dmax= 2.6e-03 nm, Epot= -1.74489e+03 Fmax= 1.40228e+02, atom= 80\n", + "Step= 249, Dmax= 3.1e-03 nm, Epot= -1.74542e+03 Fmax= 9.65080e+01, atom= 80\n", + "Step= 251, Dmax= 1.8e-03 nm, Epot= -1.74586e+03 Fmax= 5.76928e+01, atom= 80\n", + "Step= 252, Dmax= 2.2e-03 nm, Epot= -1.74618e+03 Fmax= 1.04045e+02, atom= 80\n", + "Step= 253, Dmax= 2.6e-03 nm, Epot= -1.74650e+03 Fmax= 1.14614e+02, atom= 80\n", + "Step= 254, Dmax= 3.2e-03 nm, Epot= -1.74675e+03 Fmax= 1.30348e+02, atom= 80\n", + "Step= 255, Dmax= 3.8e-03 nm, Epot= -1.74683e+03 Fmax= 1.81353e+02, atom= 80\n", + "Step= 256, Dmax= 4.6e-03 nm, Epot= -1.74716e+03 Fmax= 1.76935e+02, atom= 80\n", + "Step= 258, Dmax= 2.7e-03 nm, Epot= -1.74798e+03 Fmax= 5.10490e+01, atom= 80\n", + "Step= 259, Dmax= 3.3e-03 nm, Epot= -1.74815e+03 Fmax= 1.88293e+02, atom= 80\n", + "Step= 260, Dmax= 3.9e-03 nm, Epot= -1.74875e+03 Fmax= 1.35292e+02, atom= 80\n", + "Step= 262, Dmax= 2.4e-03 nm, Epot= -1.74924e+03 Fmax= 5.20099e+01, atom= 94\n", + "Step= 263, Dmax= 2.8e-03 nm, Epot= -1.74940e+03 Fmax= 1.76078e+02, atom= 80\n", + "Step= 264, Dmax= 3.4e-03 nm, Epot= -1.75002e+03 Fmax= 9.18823e+01, atom= 80\n", + "Step= 266, Dmax= 2.0e-03 nm, Epot= -1.75035e+03 Fmax= 7.99091e+01, atom= 80\n", + "Step= 267, Dmax= 2.5e-03 nm, Epot= -1.75060e+03 Fmax= 1.08156e+02, atom= 80\n", + "Step= 268, Dmax= 2.9e-03 nm, Epot= -1.75084e+03 Fmax= 1.36140e+02, atom= 80\n", + "Step= 269, Dmax= 3.5e-03 nm, Epot= -1.75110e+03 Fmax= 1.41605e+02, atom= 80\n", + "Step= 271, Dmax= 2.1e-03 nm, Epot= -1.75162e+03 Fmax= 3.73844e+01, atom= 80\n", + "Step= 272, Dmax= 2.5e-03 nm, Epot= -1.75213e+03 Fmax= 1.40692e+02, atom= 80\n", + "Step= 273, Dmax= 3.1e-03 nm, Epot= -1.75253e+03 Fmax= 1.12604e+02, atom= 80\n", + "Step= 274, Dmax= 3.7e-03 nm, Epot= -1.75260e+03 Fmax= 1.76181e+02, atom= 80\n", + "Step= 275, Dmax= 4.4e-03 nm, Epot= -1.75286e+03 Fmax= 1.85809e+02, atom= 80\n", + "Step= 277, Dmax= 2.6e-03 nm, Epot= -1.75358e+03 Fmax= 3.03199e+01, atom= 94\n", + "Step= 278, Dmax= 3.2e-03 nm, Epot= -1.75428e+03 Fmax= 1.86278e+02, atom= 80\n", + "Step= 279, Dmax= 3.8e-03 nm, Epot= -1.75487e+03 Fmax= 1.19407e+02, atom= 80\n", + "Step= 281, Dmax= 2.3e-03 nm, Epot= -1.75528e+03 Fmax= 7.31812e+01, atom= 80\n", + "Step= 282, Dmax= 2.7e-03 nm, Epot= -1.75551e+03 Fmax= 1.38715e+02, atom= 80\n", + "Step= 283, Dmax= 3.3e-03 nm, Epot= -1.75584e+03 Fmax= 1.35888e+02, atom= 80\n", + "Step= 284, Dmax= 3.9e-03 nm, Epot= -1.75597e+03 Fmax= 1.79115e+02, atom= 80\n", + "Step= 285, Dmax= 4.7e-03 nm, Epot= -1.75611e+03 Fmax= 2.12816e+02, atom= 80\n", + "Step= 286, Dmax= 5.7e-03 nm, Epot= -1.75621e+03 Fmax= 2.46678e+02, atom= 80\n", + "Step= 288, Dmax= 3.4e-03 nm, Epot= -1.75735e+03 Fmax= 4.35506e+01, atom= 80\n", + "Step= 289, Dmax= 4.1e-03 nm, Epot= -1.75764e+03 Fmax= 2.55520e+02, atom= 80\n", + "Step= 290, Dmax= 4.9e-03 nm, Epot= -1.75852e+03 Fmax= 1.54277e+02, atom= 80\n", + "Step= 292, Dmax= 2.9e-03 nm, Epot= -1.75904e+03 Fmax= 8.29253e+01, atom= 94\n", + "Step= 293, Dmax= 3.5e-03 nm, Epot= -1.75905e+03 Fmax= 2.08779e+02, atom= 80\n", + "Step= 294, Dmax= 4.2e-03 nm, Epot= -1.75973e+03 Fmax= 1.33541e+02, atom= 94\n", + "Step= 296, Dmax= 2.5e-03 nm, Epot= -1.76021e+03 Fmax= 8.37206e+01, atom= 80\n", + "Step= 297, Dmax= 3.1e-03 nm, Epot= -1.76043e+03 Fmax= 1.57650e+02, atom= 94\n", + "Step= 298, Dmax= 3.7e-03 nm, Epot= -1.76083e+03 Fmax= 1.50947e+02, atom= 80\n", + "Step= 299, Dmax= 4.4e-03 nm, Epot= -1.76093e+03 Fmax= 2.06243e+02, atom= 80\n", + "Step= 300, Dmax= 5.3e-03 nm, Epot= -1.76112e+03 Fmax= 2.34984e+02, atom= 80\n", + "Step= 301, Dmax= 6.3e-03 nm, Epot= -1.76112e+03 Fmax= 2.86036e+02, atom= 80\n", + "Step= 303, Dmax= 3.8e-03 nm, Epot= -1.76260e+03 Fmax= 4.27467e+01, atom= 80\n", + "Step= 304, Dmax= 4.6e-03 nm, Epot= -1.76305e+03 Fmax= 2.94402e+02, atom= 94\n", + "Step= 305, Dmax= 5.5e-03 nm, Epot= -1.76417e+03 Fmax= 1.67546e+02, atom= 80\n", + "Step= 307, Dmax= 3.3e-03 nm, Epot= -1.76475e+03 Fmax= 1.00350e+02, atom= 94\n", + "Step= 309, Dmax= 2.0e-03 nm, Epot= -1.76517e+03 Fmax= 6.91986e+01, atom= 80\n", + "Step= 310, Dmax= 2.4e-03 nm, Epot= -1.76558e+03 Fmax= 1.20130e+02, atom= 94\n", + "Step= 311, Dmax= 2.8e-03 nm, Epot= -1.76598e+03 Fmax= 1.20165e+02, atom= 80\n", + "Step= 312, Dmax= 3.4e-03 nm, Epot= -1.76628e+03 Fmax= 1.59300e+02, atom= 94\n", + "Step= 313, Dmax= 4.1e-03 nm, Epot= -1.76657e+03 Fmax= 1.85532e+02, atom= 80\n", + "Step= 314, Dmax= 4.9e-03 nm, Epot= -1.76680e+03 Fmax= 2.20684e+02, atom= 94\n", + "Step= 315, Dmax= 5.9e-03 nm, Epot= -1.76681e+03 Fmax= 2.74426e+02, atom= 80\n", + "Step= 316, Dmax= 7.0e-03 nm, Epot= -1.76691e+03 Fmax= 3.14860e+02, atom= 94\n", + "Step= 318, Dmax= 4.2e-03 nm, Epot= -1.76869e+03 Fmax= 5.57988e+01, atom= 80\n", + "Step= 319, Dmax= 5.1e-03 nm, Epot= -1.76872e+03 Fmax= 3.44266e+02, atom= 94\n", + "Step= 320, Dmax= 6.1e-03 nm, Epot= -1.77022e+03 Fmax= 1.76829e+02, atom= 80\n", + "Step= 322, Dmax= 3.7e-03 nm, Epot= -1.77083e+03 Fmax= 1.26146e+02, atom= 94\n", + "Step= 324, Dmax= 2.2e-03 nm, Epot= -1.77135e+03 Fmax= 6.51935e+01, atom= 80\n", + "Step= 325, Dmax= 2.6e-03 nm, Epot= -1.77184e+03 Fmax= 1.47039e+02, atom= 94\n", + "Step= 326, Dmax= 3.2e-03 nm, Epot= -1.77235e+03 Fmax= 1.23268e+02, atom= 80\n", + "Step= 327, Dmax= 3.8e-03 nm, Epot= -1.77259e+03 Fmax= 1.93876e+02, atom= 94\n", + "Step= 328, Dmax= 4.5e-03 nm, Epot= -1.77304e+03 Fmax= 1.94069e+02, atom= 80\n", + "Step= 329, Dmax= 5.5e-03 nm, Epot= -1.77307e+03 Fmax= 2.67682e+02, atom= 94\n", + "Step= 330, Dmax= 6.5e-03 nm, Epot= -1.77331e+03 Fmax= 2.89155e+02, atom= 80\n", + "Step= 332, Dmax= 3.9e-03 nm, Epot= -1.77491e+03 Fmax= 3.91085e+01, atom= 94\n", + "Step= 333, Dmax= 4.7e-03 nm, Epot= -1.77533e+03 Fmax= 3.31564e+02, atom= 80\n", + "Step= 334, Dmax= 5.7e-03 nm, Epot= -1.77731e+03 Fmax= 1.63203e+02, atom= 94\n", + "Step= 336, Dmax= 3.4e-03 nm, Epot= -1.77789e+03 Fmax= 1.28061e+02, atom= 80\n", + "Step= 337, Dmax= 4.1e-03 nm, Epot= -1.77807e+03 Fmax= 2.20862e+02, atom= 94\n", + "Step= 338, Dmax= 4.9e-03 nm, Epot= -1.77865e+03 Fmax= 1.99452e+02, atom= 80\n", + "Step= 340, Dmax= 2.9e-03 nm, Epot= -1.77954e+03 Fmax= 4.95994e+01, atom= 94\n", + "Step= 341, Dmax= 3.5e-03 nm, Epot= -1.78015e+03 Fmax= 2.37474e+02, atom= 80\n", + "Step= 342, Dmax= 4.2e-03 nm, Epot= -1.78122e+03 Fmax= 1.26553e+02, atom= 94\n", + "Step= 344, Dmax= 2.5e-03 nm, Epot= -1.78176e+03 Fmax= 9.38963e+01, atom= 80\n", + "Step= 345, Dmax= 3.0e-03 nm, Epot= -1.78217e+03 Fmax= 1.64874e+02, atom= 94\n", + "Step= 346, Dmax= 3.6e-03 nm, Epot= -1.78271e+03 Fmax= 1.50207e+02, atom= 80\n", + "Step= 347, Dmax= 4.4e-03 nm, Epot= -1.78290e+03 Fmax= 2.26860e+02, atom= 94\n", + "Step= 348, Dmax= 5.3e-03 nm, Epot= -1.78337e+03 Fmax= 2.26253e+02, atom= 80\n", + "Step= 350, Dmax= 3.2e-03 nm, Epot= -1.78443e+03 Fmax= 4.25156e+01, atom= 94\n", + "Step= 351, Dmax= 3.8e-03 nm, Epot= -1.78520e+03 Fmax= 2.60945e+02, atom= 80\n", + "Step= 352, Dmax= 4.5e-03 nm, Epot= -1.78645e+03 Fmax= 1.35998e+02, atom= 94\n", + "Step= 354, Dmax= 2.7e-03 nm, Epot= -1.78699e+03 Fmax= 1.02894e+02, atom= 80\n", + "Step= 355, Dmax= 3.3e-03 nm, Epot= -1.78736e+03 Fmax= 1.77904e+02, atom= 94\n", + "Step= 356, Dmax= 3.9e-03 nm, Epot= -1.78789e+03 Fmax= 1.64462e+02, atom= 80\n", + "Step= 357, Dmax= 4.7e-03 nm, Epot= -1.78803e+03 Fmax= 2.43316e+02, atom= 94\n", + "Step= 358, Dmax= 5.6e-03 nm, Epot= -1.78845e+03 Fmax= 2.48512e+02, atom= 80\n", + "Step= 360, Dmax= 3.4e-03 nm, Epot= -1.78965e+03 Fmax= 4.07283e+01, atom= 94\n", + "Step= 361, Dmax= 4.1e-03 nm, Epot= -1.79033e+03 Fmax= 2.95734e+02, atom= 80\n", + "Step= 362, Dmax= 4.9e-03 nm, Epot= -1.79187e+03 Fmax= 1.33302e+02, atom= 94\n", + "Step= 364, Dmax= 2.9e-03 nm, Epot= -1.79236e+03 Fmax= 1.23954e+02, atom= 80\n", + "Step= 365, Dmax= 3.5e-03 nm, Epot= -1.79270e+03 Fmax= 1.80543e+02, atom= 94\n", + "Step= 366, Dmax= 4.2e-03 nm, Epot= -1.79313e+03 Fmax= 1.89348e+02, atom= 80\n", + "Step= 367, Dmax= 5.1e-03 nm, Epot= -1.79330e+03 Fmax= 2.50611e+02, atom= 94\n", + "Step= 368, Dmax= 6.1e-03 nm, Epot= -1.79351e+03 Fmax= 2.80963e+02, atom= 80\n", + "Step= 370, Dmax= 3.6e-03 nm, Epot= -1.79494e+03 Fmax= 3.15234e+01, atom= 68\n", + "Step= 371, Dmax= 4.4e-03 nm, Epot= -1.79602e+03 Fmax= 3.18779e+02, atom= 80\n", + "Step= 372, Dmax= 5.2e-03 nm, Epot= -1.79775e+03 Fmax= 1.52025e+02, atom= 94\n", + "Step= 374, Dmax= 3.1e-03 nm, Epot= -1.79825e+03 Fmax= 1.25696e+02, atom= 80\n", + "Step= 375, Dmax= 3.8e-03 nm, Epot= -1.79847e+03 Fmax= 2.03004e+02, atom= 94\n", + "Step= 376, Dmax= 4.5e-03 nm, Epot= -1.79891e+03 Fmax= 1.98942e+02, atom= 80\n", + "Step= 377, Dmax= 5.4e-03 nm, Epot= -1.79892e+03 Fmax= 2.76158e+02, atom= 94\n", + "Step= 378, Dmax= 6.5e-03 nm, Epot= -1.79912e+03 Fmax= 3.00731e+02, atom= 80\n", + "Step= 380, Dmax= 3.9e-03 nm, Epot= -1.80066e+03 Fmax= 3.47886e+01, atom= 94\n", + "Step= 381, Dmax= 4.7e-03 nm, Epot= -1.80102e+03 Fmax= 3.61736e+02, atom= 80\n", + "Step= 382, Dmax= 5.6e-03 nm, Epot= -1.80319e+03 Fmax= 1.45041e+02, atom= 94\n", + "Step= 384, Dmax= 3.4e-03 nm, Epot= -1.80357e+03 Fmax= 1.52590e+02, atom= 80\n", + "Step= 385, Dmax= 4.1e-03 nm, Epot= -1.80380e+03 Fmax= 2.03014e+02, atom= 94\n", + "Step= 386, Dmax= 4.9e-03 nm, Epot= -1.80405e+03 Fmax= 2.30176e+02, atom= 80\n", + "Step= 387, Dmax= 5.8e-03 nm, Epot= -1.80415e+03 Fmax= 2.82005e+02, atom= 94\n", + "Step= 389, Dmax= 3.5e-03 nm, Epot= -1.80545e+03 Fmax= 4.36180e+01, atom= 80\n", + "Step= 390, Dmax= 4.2e-03 nm, Epot= -1.80619e+03 Fmax= 2.83402e+02, atom= 94\n", + "Step= 391, Dmax= 5.1e-03 nm, Epot= -1.80713e+03 Fmax= 1.71959e+02, atom= 80\n", + "Step= 393, Dmax= 3.0e-03 nm, Epot= -1.80772e+03 Fmax= 9.10157e+01, atom= 94\n", + "Step= 394, Dmax= 3.6e-03 nm, Epot= -1.80781e+03 Fmax= 2.29411e+02, atom= 80\n", + "Step= 395, Dmax= 4.4e-03 nm, Epot= -1.80856e+03 Fmax= 1.50618e+02, atom= 94\n", + "Step= 397, Dmax= 2.6e-03 nm, Epot= -1.80908e+03 Fmax= 8.92157e+01, atom= 80\n", + "Step= 398, Dmax= 3.1e-03 nm, Epot= -1.80937e+03 Fmax= 1.78434e+02, atom= 94\n", + "Step= 399, Dmax= 3.8e-03 nm, Epot= -1.80983e+03 Fmax= 1.61706e+02, atom= 80\n", + "Step= 400, Dmax= 4.5e-03 nm, Epot= -1.80994e+03 Fmax= 2.31608e+02, atom= 80\n", + "Step= 401, Dmax= 5.4e-03 nm, Epot= -1.81019e+03 Fmax= 2.55573e+02, atom= 80\n", + "Step= 402, Dmax= 6.5e-03 nm, Epot= -1.81019e+03 Fmax= 3.17516e+02, atom= 80\n", + "Step= 404, Dmax= 3.9e-03 nm, Epot= -1.81172e+03 Fmax= 4.73731e+01, atom= 80\n", + "Step= 405, Dmax= 4.7e-03 nm, Epot= -1.81227e+03 Fmax= 3.20210e+02, atom= 80\n", + "Step= 406, Dmax= 5.6e-03 nm, Epot= -1.81336e+03 Fmax= 1.89319e+02, atom= 80\n", + "Step= 408, Dmax= 3.4e-03 nm, Epot= -1.81400e+03 Fmax= 1.03325e+02, atom= 94\n", + "Step= 410, Dmax= 2.0e-03 nm, Epot= -1.81442e+03 Fmax= 8.28590e+01, atom= 80\n", + "Step= 411, Dmax= 2.4e-03 nm, Epot= -1.81483e+03 Fmax= 1.24045e+02, atom= 94\n", + "Step= 412, Dmax= 2.9e-03 nm, Epot= -1.81521e+03 Fmax= 1.39555e+02, atom= 80\n", + "Step= 413, Dmax= 3.5e-03 nm, Epot= -1.81556e+03 Fmax= 1.63175e+02, atom= 94\n", + "Step= 414, Dmax= 4.2e-03 nm, Epot= -1.81578e+03 Fmax= 2.14659e+02, atom= 80\n", + "Step= 415, Dmax= 5.0e-03 nm, Epot= -1.81615e+03 Fmax= 2.24732e+02, atom= 80\n", + "Step= 417, Dmax= 3.0e-03 nm, Epot= -1.81704e+03 Fmax= 5.61231e+01, atom= 80\n", + "Step= 418, Dmax= 3.6e-03 nm, Epot= -1.81757e+03 Fmax= 2.36001e+02, atom= 80\n", + "Step= 419, Dmax= 4.4e-03 nm, Epot= -1.81831e+03 Fmax= 1.59013e+02, atom= 80\n", + "Step= 421, Dmax= 2.6e-03 nm, Epot= -1.81888e+03 Fmax= 6.84069e+01, atom= 94\n", + "Step= 422, Dmax= 3.1e-03 nm, Epot= -1.81925e+03 Fmax= 2.05728e+02, atom= 80\n", + "Step= 423, Dmax= 3.8e-03 nm, Epot= -1.81997e+03 Fmax= 1.21486e+02, atom= 94\n", + "Step= 425, Dmax= 2.3e-03 nm, Epot= -1.82044e+03 Fmax= 8.62634e+01, atom= 80\n", + "Step= 426, Dmax= 2.7e-03 nm, Epot= -1.82087e+03 Fmax= 1.42481e+02, atom= 94\n", + "Step= 427, Dmax= 3.3e-03 nm, Epot= -1.82129e+03 Fmax= 1.51899e+02, atom= 80\n", + "Step= 428, Dmax= 3.9e-03 nm, Epot= -1.82163e+03 Fmax= 1.84924e+02, atom= 80\n", + "Step= 429, Dmax= 4.7e-03 nm, Epot= -1.82186e+03 Fmax= 2.35360e+02, atom= 80\n", + "Step= 430, Dmax= 5.6e-03 nm, Epot= -1.82221e+03 Fmax= 2.54829e+02, atom= 80\n", + "Step= 432, Dmax= 3.4e-03 nm, Epot= -1.82329e+03 Fmax= 5.79886e+01, atom= 80\n", + "Step= 433, Dmax= 4.0e-03 nm, Epot= -1.82384e+03 Fmax= 2.67259e+02, atom= 80\n", + "Step= 434, Dmax= 4.9e-03 nm, Epot= -1.82472e+03 Fmax= 1.71413e+02, atom= 80\n", + "Step= 436, Dmax= 2.9e-03 nm, Epot= -1.82536e+03 Fmax= 7.98972e+01, atom= 94\n", + "Step= 437, Dmax= 3.5e-03 nm, Epot= -1.82567e+03 Fmax= 2.28409e+02, atom= 80\n", + "Step= 438, Dmax= 4.2e-03 nm, Epot= -1.82650e+03 Fmax= 1.32985e+02, atom= 80\n", + "Step= 440, Dmax= 2.5e-03 nm, Epot= -1.82702e+03 Fmax= 9.76965e+01, atom= 80\n", + "Step= 441, Dmax= 3.0e-03 nm, Epot= -1.82746e+03 Fmax= 1.57616e+02, atom= 80\n", + "Step= 442, Dmax= 3.6e-03 nm, Epot= -1.82792e+03 Fmax= 1.68451e+02, atom= 80\n", + "Step= 443, Dmax= 4.3e-03 nm, Epot= -1.82827e+03 Fmax= 2.07622e+02, atom= 80\n", + "Step= 444, Dmax= 5.2e-03 nm, Epot= -1.82852e+03 Fmax= 2.55624e+02, atom= 80\n", + "Step= 445, Dmax= 6.3e-03 nm, Epot= -1.82883e+03 Fmax= 2.90471e+02, atom= 80\n", + "Step= 447, Dmax= 3.8e-03 nm, Epot= -1.83014e+03 Fmax= 5.66583e+01, atom= 80\n", + "Step= 448, Dmax= 4.5e-03 nm, Epot= -1.83078e+03 Fmax= 3.03551e+02, atom= 80\n", + "Step= 449, Dmax= 5.4e-03 nm, Epot= -1.83186e+03 Fmax= 1.81349e+02, atom= 80\n", + "Step= 451, Dmax= 3.2e-03 nm, Epot= -1.83254e+03 Fmax= 9.53221e+01, atom= 80\n", + "Step= 452, Dmax= 3.9e-03 nm, Epot= -1.83273e+03 Fmax= 2.48749e+02, atom= 80\n", + "Step= 453, Dmax= 4.7e-03 nm, Epot= -1.83365e+03 Fmax= 1.52258e+02, atom= 80\n", + "Step= 455, Dmax= 2.8e-03 nm, Epot= -1.83424e+03 Fmax= 1.01018e+02, atom= 80\n", + "Step= 456, Dmax= 3.4e-03 nm, Epot= -1.83465e+03 Fmax= 1.83992e+02, atom= 80\n", + "Step= 457, Dmax= 4.0e-03 nm, Epot= -1.83517e+03 Fmax= 1.74041e+02, atom= 80\n", + "Step= 458, Dmax= 4.8e-03 nm, Epot= -1.83540e+03 Fmax= 2.45168e+02, atom= 80\n", + "Step= 459, Dmax= 5.8e-03 nm, Epot= -1.83576e+03 Fmax= 2.63910e+02, atom= 80\n", + "Step= 460, Dmax= 7.0e-03 nm, Epot= -1.83579e+03 Fmax= 3.44424e+02, atom= 80\n", + "Step= 461, Dmax= 8.4e-03 nm, Epot= -1.83580e+03 Fmax= 3.81364e+02, atom= 80\n", + "Step= 463, Dmax= 5.0e-03 nm, Epot= -1.83803e+03 Fmax= 4.23540e+01, atom= 68\n", + "Step= 464, Dmax= 6.0e-03 nm, Epot= -1.83848e+03 Fmax= 4.17138e+02, atom= 80\n", + "Step= 465, Dmax= 7.2e-03 nm, Epot= -1.84087e+03 Fmax= 2.19194e+02, atom= 80\n", + "Step= 467, Dmax= 4.3e-03 nm, Epot= -1.84154e+03 Fmax= 1.59405e+02, atom= 80\n", + "Step= 469, Dmax= 2.6e-03 nm, Epot= -1.84216e+03 Fmax= 6.27535e+01, atom= 80\n", + "Step= 470, Dmax= 3.1e-03 nm, Epot= -1.84272e+03 Fmax= 2.00178e+02, atom= 80\n", + "Step= 471, Dmax= 3.8e-03 nm, Epot= -1.84345e+03 Fmax= 1.19255e+02, atom= 80\n", + "Step= 472, Dmax= 4.5e-03 nm, Epot= -1.84349e+03 Fmax= 2.61373e+02, atom= 80\n", + "Step= 473, Dmax= 5.4e-03 nm, Epot= -1.84433e+03 Fmax= 1.98353e+02, atom= 80\n", + "Step= 475, Dmax= 3.2e-03 nm, Epot= -1.84507e+03 Fmax= 8.63373e+01, atom= 80\n", + "Step= 476, Dmax= 3.9e-03 nm, Epot= -1.84536e+03 Fmax= 2.42891e+02, atom= 80\n", + "Step= 477, Dmax= 4.7e-03 nm, Epot= -1.84614e+03 Fmax= 1.59814e+02, atom= 80\n", + "Step= 479, Dmax= 2.8e-03 nm, Epot= -1.84675e+03 Fmax= 7.66918e+01, atom= 80\n", + "Step= 480, Dmax= 3.4e-03 nm, Epot= -1.84716e+03 Fmax= 2.01635e+02, atom= 80\n", + "Step= 481, Dmax= 4.0e-03 nm, Epot= -1.84786e+03 Fmax= 1.40153e+02, atom= 80\n", + "Step= 483, Dmax= 2.4e-03 nm, Epot= -1.84839e+03 Fmax= 6.96273e+01, atom= 80\n", + "Step= 484, Dmax= 2.9e-03 nm, Epot= -1.84891e+03 Fmax= 1.73185e+02, atom= 80\n", + "Step= 485, Dmax= 3.5e-03 nm, Epot= -1.84948e+03 Fmax= 1.23526e+02, atom= 80\n", + "Step= 486, Dmax= 4.2e-03 nm, Epot= -1.84968e+03 Fmax= 2.34336e+02, atom= 80\n", + "Step= 487, Dmax= 5.0e-03 nm, Epot= -1.85030e+03 Fmax= 1.89255e+02, atom= 80\n", + "Step= 489, Dmax= 3.0e-03 nm, Epot= -1.85104e+03 Fmax= 6.32265e+01, atom= 80\n", + "Step= 490, Dmax= 3.6e-03 nm, Epot= -1.85153e+03 Fmax= 2.22300e+02, atom= 80\n", + "Step= 491, Dmax= 4.3e-03 nm, Epot= -1.85235e+03 Fmax= 1.43259e+02, atom= 80\n", + "Step= 493, Dmax= 2.6e-03 nm, Epot= -1.85288e+03 Fmax= 7.67165e+01, atom= 80\n", + "Step= 494, Dmax= 3.1e-03 nm, Epot= -1.85331e+03 Fmax= 1.87241e+02, atom= 80\n", + "Step= 495, Dmax= 3.7e-03 nm, Epot= -1.85392e+03 Fmax= 1.25716e+02, atom= 80\n", + "Step= 496, Dmax= 4.5e-03 nm, Epot= -1.85400e+03 Fmax= 2.58745e+02, atom= 80\n", + "Step= 497, Dmax= 5.4e-03 nm, Epot= -1.85473e+03 Fmax= 1.89945e+02, atom= 80\n", + "Step= 499, Dmax= 3.2e-03 nm, Epot= -1.85548e+03 Fmax= 7.92876e+01, atom= 80\n", + "Step= 500, Dmax= 3.9e-03 nm, Epot= -1.85578e+03 Fmax= 2.23888e+02, atom= 80\n", + "Step= 501, Dmax= 4.7e-03 nm, Epot= -1.85654e+03 Fmax= 1.65683e+02, atom= 80\n", + "Step= 503, Dmax= 2.8e-03 nm, Epot= -1.85715e+03 Fmax= 6.78244e+01, atom= 80\n", + "Step= 504, Dmax= 3.4e-03 nm, Epot= -1.85759e+03 Fmax= 2.14056e+02, atom= 80\n", + "Step= 505, Dmax= 4.0e-03 nm, Epot= -1.85832e+03 Fmax= 1.17915e+02, atom= 80\n", + "Step= 507, Dmax= 2.4e-03 nm, Epot= -1.85882e+03 Fmax= 8.50859e+01, atom= 80\n", + "Step= 508, Dmax= 2.9e-03 nm, Epot= -1.85928e+03 Fmax= 1.40423e+02, atom= 80\n", + "Step= 509, Dmax= 3.5e-03 nm, Epot= -1.85974e+03 Fmax= 1.51169e+02, atom= 80\n", + "Step= 510, Dmax= 4.2e-03 nm, Epot= -1.86009e+03 Fmax= 1.80443e+02, atom= 80\n", + "Step= 511, Dmax= 5.0e-03 nm, Epot= -1.86038e+03 Fmax= 2.38707e+02, atom= 80\n", + "Step= 512, Dmax= 6.0e-03 nm, Epot= -1.86073e+03 Fmax= 2.41644e+02, atom= 80\n", + "Step= 514, Dmax= 3.6e-03 nm, Epot= -1.86183e+03 Fmax= 5.26862e+01, atom= 80\n", + "Step= 515, Dmax= 4.3e-03 nm, Epot= -1.86255e+03 Fmax= 2.46202e+02, atom= 80\n", + "Step= 516, Dmax= 5.2e-03 nm, Epot= -1.86345e+03 Fmax= 1.81651e+02, atom= 80\n", + "Step= 518, Dmax= 3.1e-03 nm, Epot= -1.86412e+03 Fmax= 6.98732e+01, atom= 80\n", + "Step= 519, Dmax= 3.7e-03 nm, Epot= -1.86451e+03 Fmax= 2.43452e+02, atom= 80\n", + "Step= 520, Dmax= 4.5e-03 nm, Epot= -1.86541e+03 Fmax= 1.16776e+02, atom= 80\n", + "Step= 522, Dmax= 2.7e-03 nm, Epot= -1.86594e+03 Fmax= 1.06046e+02, atom= 80\n", + "Step= 523, Dmax= 3.2e-03 nm, Epot= -1.86640e+03 Fmax= 1.38050e+02, atom= 80\n", + "Step= 524, Dmax= 3.9e-03 nm, Epot= -1.86683e+03 Fmax= 1.82079e+02, atom= 80\n", + "Step= 525, Dmax= 4.7e-03 nm, Epot= -1.86730e+03 Fmax= 1.77157e+02, atom= 80\n", + "Step= 526, Dmax= 5.6e-03 nm, Epot= -1.86739e+03 Fmax= 2.82852e+02, atom= 80\n", + "Step= 527, Dmax= 6.7e-03 nm, Epot= -1.86803e+03 Fmax= 2.38367e+02, atom= 80\n", + "Step= 529, Dmax= 4.0e-03 nm, Epot= -1.86914e+03 Fmax= 8.18101e+01, atom= 80\n", + "Step= 530, Dmax= 4.8e-03 nm, Epot= -1.86942e+03 Fmax= 2.55930e+02, atom= 80\n", + "Step= 531, Dmax= 5.8e-03 nm, Epot= -1.87033e+03 Fmax= 2.08711e+02, atom= 80\n", + "Step= 533, Dmax= 3.5e-03 nm, Epot= -1.87116e+03 Fmax= 6.50171e+01, atom= 80\n", + "Step= 534, Dmax= 4.2e-03 nm, Epot= -1.87161e+03 Fmax= 2.74296e+02, atom= 80\n", + "Step= 535, Dmax= 5.0e-03 nm, Epot= -1.87273e+03 Fmax= 1.15138e+02, atom= 80\n", + "Step= 537, Dmax= 3.0e-03 nm, Epot= -1.87328e+03 Fmax= 1.28963e+02, atom= 80\n", + "Step= 538, Dmax= 3.6e-03 nm, Epot= -1.87379e+03 Fmax= 1.35137e+02, atom= 80\n", + "Step= 539, Dmax= 4.3e-03 nm, Epot= -1.87418e+03 Fmax= 2.14650e+02, atom= 80\n", + "Step= 540, Dmax= 5.2e-03 nm, Epot= -1.87482e+03 Fmax= 1.73804e+02, atom= 80\n", + "Step= 542, Dmax= 3.1e-03 nm, Epot= -1.87561e+03 Fmax= 7.50648e+01, atom= 80\n", + "Step= 543, Dmax= 3.7e-03 nm, Epot= -1.87630e+03 Fmax= 1.70706e+02, atom= 80\n", + "Step= 544, Dmax= 4.5e-03 nm, Epot= -1.87689e+03 Fmax= 1.85770e+02, atom= 80\n", + "Step= 545, Dmax= 5.4e-03 nm, Epot= -1.87730e+03 Fmax= 2.05719e+02, atom= 80\n", + "Step= 546, Dmax= 6.5e-03 nm, Epot= -1.87745e+03 Fmax= 3.04940e+02, atom= 80\n", + "Step= 547, Dmax= 7.7e-03 nm, Epot= -1.87809e+03 Fmax= 2.67408e+02, atom= 80\n", + "Step= 549, Dmax= 4.6e-03 nm, Epot= -1.87950e+03 Fmax= 8.78489e+01, atom= 80\n", + "Step= 550, Dmax= 5.6e-03 nm, Epot= -1.87977e+03 Fmax= 2.76585e+02, atom= 80\n", + "Step= 551, Dmax= 6.7e-03 nm, Epot= -1.88078e+03 Fmax= 2.39562e+02, atom= 80\n", + "Step= 553, Dmax= 4.0e-03 nm, Epot= -1.88184e+03 Fmax= 6.45684e+01, atom= 94\n", + "Step= 554, Dmax= 4.8e-03 nm, Epot= -1.88235e+03 Fmax= 3.06411e+02, atom= 80\n", + "Step= 555, Dmax= 5.8e-03 nm, Epot= -1.88373e+03 Fmax= 1.23523e+02, atom= 80\n", + "Step= 557, Dmax= 3.5e-03 nm, Epot= -1.88433e+03 Fmax= 1.46191e+02, atom= 80\n", + "Step= 558, Dmax= 4.2e-03 nm, Epot= -1.88489e+03 Fmax= 1.44182e+02, atom= 80\n", + "Step= 559, Dmax= 5.0e-03 nm, Epot= -1.88521e+03 Fmax= 2.41718e+02, atom= 80\n", + "Step= 560, Dmax= 6.0e-03 nm, Epot= -1.88597e+03 Fmax= 1.84754e+02, atom= 80\n", + "Step= 562, Dmax= 3.6e-03 nm, Epot= -1.88686e+03 Fmax= 8.89188e+01, atom= 80\n", + "Step= 563, Dmax= 4.3e-03 nm, Epot= -1.88745e+03 Fmax= 1.83771e+02, atom= 80\n", + "Step= 564, Dmax= 5.2e-03 nm, Epot= -1.88804e+03 Fmax= 2.08128e+02, atom= 80\n", + "Step= 565, Dmax= 6.2e-03 nm, Epot= -1.88847e+03 Fmax= 2.21580e+02, atom= 80\n", + "Step= 567, Dmax= 3.7e-03 nm, Epot= -1.88961e+03 Fmax= 6.09289e+01, atom= 80\n", + "Step= 568, Dmax= 4.5e-03 nm, Epot= -1.89069e+03 Fmax= 1.79435e+02, atom= 80\n", + "Step= 569, Dmax= 5.4e-03 nm, Epot= -1.89119e+03 Fmax= 2.23044e+02, atom= 80\n", + "Step= 570, Dmax= 6.4e-03 nm, Epot= -1.89168e+03 Fmax= 2.18898e+02, atom= 80\n", + "Step= 572, Dmax= 3.9e-03 nm, Epot= -1.89281e+03 Fmax= 6.88319e+01, atom= 80\n", + "Step= 573, Dmax= 4.6e-03 nm, Epot= -1.89364e+03 Fmax= 1.91877e+02, atom= 80\n", + "Step= 574, Dmax= 5.6e-03 nm, Epot= -1.89420e+03 Fmax= 2.17797e+02, atom= 80\n", + "Step= 575, Dmax= 6.7e-03 nm, Epot= -1.89457e+03 Fmax= 2.32782e+02, atom= 80\n", + "Step= 577, Dmax= 4.0e-03 nm, Epot= -1.89582e+03 Fmax= 6.18842e+01, atom= 80\n", + "Step= 578, Dmax= 4.8e-03 nm, Epot= -1.89678e+03 Fmax= 1.91105e+02, atom= 80\n", + "Step= 579, Dmax= 5.8e-03 nm, Epot= -1.89726e+03 Fmax= 2.27435e+02, atom= 80\n", + "Step= 580, Dmax= 6.9e-03 nm, Epot= -1.89763e+03 Fmax= 2.34851e+02, atom= 80\n", + "Step= 582, Dmax= 4.2e-03 nm, Epot= -1.89891e+03 Fmax= 6.49026e+01, atom= 80\n", + "Step= 583, Dmax= 5.0e-03 nm, Epot= -1.89964e+03 Fmax= 2.03357e+02, atom= 80\n", + "Step= 584, Dmax= 6.0e-03 nm, Epot= -1.90017e+03 Fmax= 2.22109e+02, atom= 80\n", + "Step= 585, Dmax= 7.2e-03 nm, Epot= -1.90037e+03 Fmax= 2.49315e+02, atom= 80\n", + "Step= 587, Dmax= 4.3e-03 nm, Epot= -1.90179e+03 Fmax= 5.72050e+01, atom= 80\n", + "Step= 588, Dmax= 5.2e-03 nm, Epot= -1.90260e+03 Fmax= 2.02239e+02, atom= 80\n", + "Step= 589, Dmax= 6.2e-03 nm, Epot= -1.90301e+03 Fmax= 2.31574e+02, atom= 80\n", + "Step= 590, Dmax= 7.4e-03 nm, Epot= -1.90318e+03 Fmax= 2.52859e+02, atom= 80\n", + "Step= 592, Dmax= 4.5e-03 nm, Epot= -1.90466e+03 Fmax= 5.79649e+01, atom= 80\n", + "Step= 593, Dmax= 5.4e-03 nm, Epot= -1.90516e+03 Fmax= 2.19207e+02, atom= 80\n", + "Step= 594, Dmax= 6.4e-03 nm, Epot= -1.90568e+03 Fmax= 2.21179e+02, atom= 80\n", + "Step= 596, Dmax= 3.9e-03 nm, Epot= -1.90678e+03 Fmax= 4.22893e+01, atom= 80\n", + "Step= 597, Dmax= 4.6e-03 nm, Epot= -1.90732e+03 Fmax= 2.38296e+02, atom= 80\n", + "Step= 598, Dmax= 5.6e-03 nm, Epot= -1.90831e+03 Fmax= 1.24856e+02, atom= 80\n", + "Step= 600, Dmax= 3.3e-03 nm, Epot= -1.90879e+03 Fmax= 1.01643e+02, atom= 80\n", + "Step= 601, Dmax= 4.0e-03 nm, Epot= -1.90902e+03 Fmax= 1.43153e+02, atom= 80\n", + "Step= 602, Dmax= 4.8e-03 nm, Epot= -1.90926e+03 Fmax= 1.78307e+02, atom= 80\n", + "Step= 603, Dmax= 5.8e-03 nm, Epot= -1.90949e+03 Fmax= 1.85744e+02, atom= 80\n", + "Step= 605, Dmax= 3.5e-03 nm, Epot= -1.91041e+03 Fmax= 4.80111e+01, atom= 80\n", + "Step= 606, Dmax= 4.1e-03 nm, Epot= -1.91078e+03 Fmax= 1.66292e+02, atom= 80\n", + "Step= 607, Dmax= 5.0e-03 nm, Epot= -1.91118e+03 Fmax= 1.61702e+02, atom= 80\n", + "Step= 609, Dmax= 3.0e-03 nm, Epot= -1.91189e+03 Fmax= 3.61518e+01, atom= 80\n", + "Step= 610, Dmax= 3.6e-03 nm, Epot= -1.91231e+03 Fmax= 1.69479e+02, atom= 80\n", + "Step= 611, Dmax= 4.3e-03 nm, Epot= -1.91291e+03 Fmax= 1.03022e+02, atom= 80\n", + "Step= 613, Dmax= 2.6e-03 nm, Epot= -1.91331e+03 Fmax= 6.70445e+01, atom= 80\n", + "Step= 614, Dmax= 3.1e-03 nm, Epot= -1.91350e+03 Fmax= 1.16016e+02, atom= 80\n", + "Step= 615, Dmax= 3.7e-03 nm, Epot= -1.91378e+03 Fmax= 1.24321e+02, atom= 80\n", + "Step= 616, Dmax= 4.5e-03 nm, Epot= -1.91388e+03 Fmax= 1.50904e+02, atom= 80\n", + "Step= 617, Dmax= 5.4e-03 nm, Epot= -1.91388e+03 Fmax= 1.91850e+02, atom= 80\n", + "Step= 618, Dmax= 6.4e-03 nm, Epot= -1.91394e+03 Fmax= 2.07361e+02, atom= 80\n", + "Step= 620, Dmax= 3.9e-03 nm, Epot= -1.91521e+03 Fmax= 4.03950e+01, atom= 80\n", + "Step= 622, Dmax= 2.3e-03 nm, Epot= -1.91551e+03 Fmax= 8.77072e+01, atom= 80\n", + "Step= 623, Dmax= 2.8e-03 nm, Epot= -1.91579e+03 Fmax= 8.94044e+01, atom= 80\n", + "Step= 624, Dmax= 3.3e-03 nm, Epot= -1.91592e+03 Fmax= 1.14441e+02, atom= 80\n", + "Step= 625, Dmax= 4.0e-03 nm, Epot= -1.91605e+03 Fmax= 1.37937e+02, atom= 80\n", + "Step= 626, Dmax= 4.8e-03 nm, Epot= -1.91610e+03 Fmax= 1.57828e+02, atom= 80\n", + "Step= 628, Dmax= 2.9e-03 nm, Epot= -1.91705e+03 Fmax= 2.85342e+01, atom= 80\n", + "Step= 629, Dmax= 3.5e-03 nm, Epot= -1.91734e+03 Fmax= 1.36322e+02, atom= 80\n", + "Step= 630, Dmax= 4.1e-03 nm, Epot= -1.91772e+03 Fmax= 1.21877e+02, atom= 80\n", + "Step= 632, Dmax= 2.5e-03 nm, Epot= -1.91843e+03 Fmax= 3.93435e+01, atom= 80\n", + "Step= 633, Dmax= 3.0e-03 nm, Epot= -1.91845e+03 Fmax= 1.19798e+02, atom= 80\n", + "Step= 634, Dmax= 3.6e-03 nm, Epot= -1.91885e+03 Fmax= 1.05048e+02, atom= 8\n", + "Step= 636, Dmax= 2.1e-03 nm, Epot= -1.91948e+03 Fmax= 3.03549e+01, atom= 80\n", + "Step= 638, Dmax= 1.3e-03 nm, Epot= -1.91976e+03 Fmax= 6.01867e+01, atom= 8\n", + "Step= 639, Dmax= 1.5e-03 nm, Epot= -1.92003e+03 Fmax= 3.24648e+01, atom= 4\n", + "Step= 640, Dmax= 1.9e-03 nm, Epot= -1.92027e+03 Fmax= 9.38702e+01, atom= 8\n", + "Step= 641, Dmax= 2.2e-03 nm, Epot= -1.92068e+03 Fmax= 4.07342e+01, atom= 8\n", + "Step= 643, Dmax= 1.3e-03 nm, Epot= -1.92094e+03 Fmax= 5.76210e+01, atom= 8\n", + "Step= 644, Dmax= 1.6e-03 nm, Epot= -1.92121e+03 Fmax= 3.55493e+01, atom= 4\n", + "Step= 645, Dmax= 1.9e-03 nm, Epot= -1.92146e+03 Fmax= 9.87100e+01, atom= 8\n", + "Step= 646, Dmax= 2.3e-03 nm, Epot= -1.92186e+03 Fmax= 4.09362e+01, atom= 8\n", + "Step= 648, Dmax= 1.4e-03 nm, Epot= -1.92213e+03 Fmax= 6.09304e+01, atom= 8\n", + "Step= 649, Dmax= 1.7e-03 nm, Epot= -1.92241e+03 Fmax= 3.63382e+01, atom= 4\n", + "Step= 650, Dmax= 2.0e-03 nm, Epot= -1.92267e+03 Fmax= 1.02325e+02, atom= 8\n", + "Step= 651, Dmax= 2.4e-03 nm, Epot= -1.92308e+03 Fmax= 4.25280e+01, atom= 8\n", + "Step= 653, Dmax= 1.4e-03 nm, Epot= -1.92336e+03 Fmax= 6.27646e+01, atom= 8\n", + "Step= 654, Dmax= 1.7e-03 nm, Epot= -1.92364e+03 Fmax= 3.76057e+01, atom= 4\n", + "Step= 655, Dmax= 2.1e-03 nm, Epot= -1.92388e+03 Fmax= 1.07348e+02, atom= 8\n", + "Step= 656, Dmax= 2.5e-03 nm, Epot= -1.92434e+03 Fmax= 4.34368e+01, atom= 8\n", + "Step= 658, Dmax= 1.5e-03 nm, Epot= -1.92463e+03 Fmax= 6.52203e+01, atom= 8\n", + "Step= 659, Dmax= 1.8e-03 nm, Epot= -1.92493e+03 Fmax= 3.92239e+01, atom= 67\n", + "Step= 660, Dmax= 2.1e-03 nm, Epot= -1.92513e+03 Fmax= 1.11688e+02, atom= 8\n", + "Step= 661, Dmax= 2.6e-03 nm, Epot= -1.92566e+03 Fmax= 4.56978e+01, atom= 67\n", + "Step= 663, Dmax= 1.5e-03 nm, Epot= -1.92596e+03 Fmax= 6.59605e+01, atom= 8\n", + "Step= 664, Dmax= 1.9e-03 nm, Epot= -1.92629e+03 Fmax= 4.36022e+01, atom= 67\n", + "Step= 665, Dmax= 2.2e-03 nm, Epot= -1.92643e+03 Fmax= 1.09696e+02, atom= 8\n", + "Step= 666, Dmax= 2.7e-03 nm, Epot= -1.92699e+03 Fmax= 5.57959e+01, atom= 73\n", + "Step= 668, Dmax= 1.6e-03 nm, Epot= -1.92732e+03 Fmax= 5.70265e+01, atom= 83\n", + "Step= 669, Dmax= 1.9e-03 nm, Epot= -1.92763e+03 Fmax= 5.92593e+01, atom= 73\n", + "Step= 670, Dmax= 2.3e-03 nm, Epot= -1.92783e+03 Fmax= 9.53056e+01, atom= 73\n", + "Step= 671, Dmax= 2.8e-03 nm, Epot= -1.92822e+03 Fmax= 8.32827e+01, atom= 73\n", + "Step= 673, Dmax= 1.7e-03 nm, Epot= -1.92870e+03 Fmax= 3.60473e+01, atom= 43\n", + "Step= 674, Dmax= 2.0e-03 nm, Epot= -1.92916e+03 Fmax= 6.66725e+01, atom= 73\n", + "Step= 675, Dmax= 2.4e-03 nm, Epot= -1.92942e+03 Fmax= 9.33698e+01, atom= 73\n", + "Step= 676, Dmax= 2.9e-03 nm, Epot= -1.92975e+03 Fmax= 9.16722e+01, atom= 73\n", + "Step= 677, Dmax= 3.4e-03 nm, Epot= -1.92982e+03 Fmax= 1.37834e+02, atom= 73\n", + "Step= 678, Dmax= 4.1e-03 nm, Epot= -1.93021e+03 Fmax= 1.30635e+02, atom= 73\n", + "Step= 680, Dmax= 2.5e-03 nm, Epot= -1.93099e+03 Fmax= 3.64143e+01, atom= 43\n", + "Step= 681, Dmax= 3.0e-03 nm, Epot= -1.93129e+03 Fmax= 1.41812e+02, atom= 73\n", + "Step= 682, Dmax= 3.6e-03 nm, Epot= -1.93195e+03 Fmax= 9.45319e+01, atom= 73\n", + "Step= 684, Dmax= 2.1e-03 nm, Epot= -1.93242e+03 Fmax= 4.35319e+01, atom= 45\n", + "Step= 685, Dmax= 2.6e-03 nm, Epot= -1.93263e+03 Fmax= 1.30327e+02, atom= 73\n", + "Step= 686, Dmax= 3.1e-03 nm, Epot= -1.93326e+03 Fmax= 7.01076e+01, atom= 73\n", + "Step= 688, Dmax= 1.8e-03 nm, Epot= -1.93363e+03 Fmax= 5.48650e+01, atom= 73\n", + "Step= 689, Dmax= 2.2e-03 nm, Epot= -1.93394e+03 Fmax= 8.58786e+01, atom= 73\n", + "Step= 690, Dmax= 2.7e-03 nm, Epot= -1.93427e+03 Fmax= 9.24230e+01, atom= 73\n", + "Step= 691, Dmax= 3.2e-03 nm, Epot= -1.93452e+03 Fmax= 1.13677e+02, atom= 73\n", + "Step= 692, Dmax= 3.8e-03 nm, Epot= -1.93471e+03 Fmax= 1.41645e+02, atom= 73\n", + "Step= 693, Dmax= 4.6e-03 nm, Epot= -1.93492e+03 Fmax= 1.57637e+02, atom= 73\n", + "Step= 695, Dmax= 2.8e-03 nm, Epot= -1.93581e+03 Fmax= 3.31622e+01, atom= 43\n", + "Step= 696, Dmax= 3.3e-03 nm, Epot= -1.93645e+03 Fmax= 1.34886e+02, atom= 73\n", + "Step= 697, Dmax= 4.0e-03 nm, Epot= -1.93683e+03 Fmax= 1.26959e+02, atom= 73\n", + "Step= 699, Dmax= 2.4e-03 nm, Epot= -1.93742e+03 Fmax= 2.93981e+01, atom= 43\n", + "Step= 700, Dmax= 2.9e-03 nm, Epot= -1.93784e+03 Fmax= 1.57698e+02, atom= 73\n", + "Step= 701, Dmax= 3.4e-03 nm, Epot= -1.93860e+03 Fmax= 6.58372e+01, atom= 73\n", + "Step= 703, Dmax= 2.1e-03 nm, Epot= -1.93892e+03 Fmax= 7.34898e+01, atom= 73\n", + "Step= 704, Dmax= 2.5e-03 nm, Epot= -1.93923e+03 Fmax= 8.41663e+01, atom= 73\n", + "Step= 705, Dmax= 3.0e-03 nm, Epot= -1.93947e+03 Fmax= 1.14354e+02, atom= 73\n", + "Step= 706, Dmax= 3.6e-03 nm, Epot= -1.93977e+03 Fmax= 1.15985e+02, atom= 73\n", + "Step= 707, Dmax= 4.3e-03 nm, Epot= -1.93981e+03 Fmax= 1.68266e+02, atom= 73\n", + "Step= 708, Dmax= 5.1e-03 nm, Epot= -1.94013e+03 Fmax= 1.65476e+02, atom= 73\n", + "Step= 710, Dmax= 3.1e-03 nm, Epot= -1.94098e+03 Fmax= 3.96665e+01, atom= 73\n", + "Step= 711, Dmax= 3.7e-03 nm, Epot= -1.94113e+03 Fmax= 1.89921e+02, atom= 73\n", + "Step= 712, Dmax= 4.4e-03 nm, Epot= -1.94197e+03 Fmax= 1.02348e+02, atom= 73\n", + "Step= 714, Dmax= 2.7e-03 nm, Epot= -1.94235e+03 Fmax= 6.79933e+01, atom= 73\n", + "Step= 715, Dmax= 3.2e-03 nm, Epot= -1.94245e+03 Fmax= 1.46149e+02, atom= 73\n", + "Step= 716, Dmax= 3.8e-03 nm, Epot= -1.94295e+03 Fmax= 1.02122e+02, atom= 73\n", + "Step= 718, Dmax= 2.3e-03 nm, Epot= -1.94337e+03 Fmax= 5.10269e+01, atom= 73\n", + "Step= 719, Dmax= 2.8e-03 nm, Epot= -1.94361e+03 Fmax= 1.23305e+02, atom= 73\n", + "Step= 720, Dmax= 3.3e-03 nm, Epot= -1.94403e+03 Fmax= 9.53611e+01, atom= 73\n", + "Step= 721, Dmax= 4.0e-03 nm, Epot= -1.94406e+03 Fmax= 1.60309e+02, atom= 73\n", + "Step= 722, Dmax= 4.8e-03 nm, Epot= -1.94442e+03 Fmax= 1.53375e+02, atom= 73\n", + "Step= 724, Dmax= 2.9e-03 nm, Epot= -1.94510e+03 Fmax= 3.10758e+01, atom= 40\n", + "Step= 725, Dmax= 3.4e-03 nm, Epot= -1.94529e+03 Fmax= 2.04147e+02, atom= 73\n", + "Step= 726, Dmax= 4.1e-03 nm, Epot= -1.94631e+03 Fmax= 6.55691e+01, atom= 73\n", + "Step= 728, Dmax= 2.5e-03 nm, Epot= -1.94658e+03 Fmax= 9.78274e+01, atom= 73\n", + "Step= 729, Dmax= 3.0e-03 nm, Epot= -1.94689e+03 Fmax= 9.23771e+01, atom= 73\n", + "Step= 730, Dmax= 3.6e-03 nm, Epot= -1.94703e+03 Fmax= 1.42455e+02, atom= 73\n", + "Step= 731, Dmax= 4.3e-03 nm, Epot= -1.94737e+03 Fmax= 1.32802e+02, atom= 73\n", + "Step= 733, Dmax= 2.6e-03 nm, Epot= -1.94792e+03 Fmax= 3.58905e+01, atom= 73\n", + "Step= 734, Dmax= 3.1e-03 nm, Epot= -1.94825e+03 Fmax= 1.57173e+02, atom= 73\n", + "Step= 735, Dmax= 3.7e-03 nm, Epot= -1.94886e+03 Fmax= 8.49004e+01, atom= 73\n", + "Step= 737, Dmax= 2.2e-03 nm, Epot= -1.94919e+03 Fmax= 5.61875e+01, atom= 73\n", + "Step= 738, Dmax= 2.7e-03 nm, Epot= -1.94941e+03 Fmax= 1.20476e+02, atom= 73\n", + "Step= 739, Dmax= 3.2e-03 nm, Epot= -1.94981e+03 Fmax= 8.45400e+01, atom= 73\n", + "Step= 740, Dmax= 3.8e-03 nm, Epot= -1.94982e+03 Fmax= 1.67385e+02, atom= 73\n", + "Step= 741, Dmax= 4.6e-03 nm, Epot= -1.95031e+03 Fmax= 1.28426e+02, atom= 73\n", + "Step= 743, Dmax= 2.8e-03 nm, Epot= -1.95082e+03 Fmax= 5.20341e+01, atom= 73\n", + "Step= 744, Dmax= 3.3e-03 nm, Epot= -1.95096e+03 Fmax= 1.57972e+02, atom= 73\n", + "Step= 745, Dmax= 4.0e-03 nm, Epot= -1.95152e+03 Fmax= 1.00780e+02, atom= 73\n", + "Step= 747, Dmax= 2.4e-03 nm, Epot= -1.95189e+03 Fmax= 5.08946e+01, atom= 73\n", + "Step= 748, Dmax= 2.9e-03 nm, Epot= -1.95208e+03 Fmax= 1.38563e+02, atom= 73\n", + "Step= 749, Dmax= 3.4e-03 nm, Epot= -1.95256e+03 Fmax= 8.17923e+01, atom= 73\n", + "Step= 751, Dmax= 2.1e-03 nm, Epot= -1.95289e+03 Fmax= 5.27576e+01, atom= 73\n", + "Step= 752, Dmax= 2.5e-03 nm, Epot= -1.95315e+03 Fmax= 1.03122e+02, atom= 73\n", + "Step= 753, Dmax= 3.0e-03 nm, Epot= -1.95348e+03 Fmax= 8.99841e+01, atom= 73\n", + "Step= 754, Dmax= 3.5e-03 nm, Epot= -1.95362e+03 Fmax= 1.36905e+02, atom= 73\n", + "Step= 755, Dmax= 4.3e-03 nm, Epot= -1.95390e+03 Fmax= 1.40274e+02, atom= 73\n", + "Step= 757, Dmax= 2.6e-03 nm, Epot= -1.95446e+03 Fmax= 3.14169e+01, atom= 50\n", + "Step= 758, Dmax= 3.1e-03 nm, Epot= -1.95502e+03 Fmax= 1.29954e+02, atom= 73\n", + "Step= 759, Dmax= 3.7e-03 nm, Epot= -1.95539e+03 Fmax= 1.07106e+02, atom= 73\n", + "Step= 761, Dmax= 2.2e-03 nm, Epot= -1.95579e+03 Fmax= 3.67246e+01, atom= 73\n", + "Step= 762, Dmax= 2.6e-03 nm, Epot= -1.95612e+03 Fmax= 1.29366e+02, atom= 73\n", + "Step= 763, Dmax= 3.2e-03 nm, Epot= -1.95658e+03 Fmax= 7.70396e+01, atom= 73\n", + "Step= 765, Dmax= 1.9e-03 nm, Epot= -1.95688e+03 Fmax= 4.35906e+01, atom= 73\n", + "Step= 766, Dmax= 2.3e-03 nm, Epot= -1.95715e+03 Fmax= 1.07219e+02, atom= 73\n", + "Step= 767, Dmax= 2.7e-03 nm, Epot= -1.95752e+03 Fmax= 6.77190e+01, atom= 73\n", + "Step= 768, Dmax= 3.3e-03 nm, Epot= -1.95759e+03 Fmax= 1.47101e+02, atom= 73\n", + "Step= 769, Dmax= 4.0e-03 nm, Epot= -1.95804e+03 Fmax= 1.05269e+02, atom= 73\n", + "Step= 771, Dmax= 2.4e-03 nm, Epot= -1.95844e+03 Fmax= 4.87556e+01, atom= 73\n", + "Step= 772, Dmax= 2.8e-03 nm, Epot= -1.95862e+03 Fmax= 1.30266e+02, atom= 73\n", + "Step= 773, Dmax= 3.4e-03 nm, Epot= -1.95905e+03 Fmax= 9.03279e+01, atom= 73\n", + "Step= 775, Dmax= 2.1e-03 nm, Epot= -1.95938e+03 Fmax= 3.89895e+01, atom= 73\n", + "Step= 776, Dmax= 2.5e-03 nm, Epot= -1.95962e+03 Fmax= 1.23243e+02, atom= 73\n", + "Step= 777, Dmax= 3.0e-03 nm, Epot= -1.96006e+03 Fmax= 6.43717e+01, atom= 73\n", + "Step= 779, Dmax= 1.8e-03 nm, Epot= -1.96034e+03 Fmax= 5.06886e+01, atom= 73\n", + "Step= 780, Dmax= 2.1e-03 nm, Epot= -1.96059e+03 Fmax= 8.24033e+01, atom= 73\n", + "Step= 781, Dmax= 2.6e-03 nm, Epot= -1.96086e+03 Fmax= 8.24685e+01, atom= 73\n", + "Step= 782, Dmax= 3.1e-03 nm, Epot= -1.96104e+03 Fmax= 1.10610e+02, atom= 73\n", + "Step= 783, Dmax= 3.7e-03 nm, Epot= -1.96124e+03 Fmax= 1.25870e+02, atom= 73\n", + "Step= 784, Dmax= 4.4e-03 nm, Epot= -1.96134e+03 Fmax= 1.53505e+02, atom= 73\n", + "Step= 785, Dmax= 5.3e-03 nm, Epot= -1.96137e+03 Fmax= 1.85916e+02, atom= 73\n", + "Step= 787, Dmax= 3.2e-03 nm, Epot= -1.96232e+03 Fmax= 2.88161e+01, atom= 50\n", + "Step= 788, Dmax= 3.8e-03 nm, Epot= -1.96301e+03 Fmax= 1.18516e+02, atom= 73\n", + "Step= 790, Dmax= 2.3e-03 nm, Epot= -1.96353e+03 Fmax= 3.09638e+01, atom= 45\n", + "Step= 791, Dmax= 2.7e-03 nm, Epot= -1.96377e+03 Fmax= 1.33223e+02, atom= 73\n", + "Step= 792, Dmax= 3.3e-03 nm, Epot= -1.96429e+03 Fmax= 7.14067e+01, atom= 73\n", + "Step= 794, Dmax= 2.0e-03 nm, Epot= -1.96458e+03 Fmax= 5.71279e+01, atom= 73\n", + "Step= 795, Dmax= 2.4e-03 nm, Epot= -1.96473e+03 Fmax= 9.03485e+01, atom= 73\n", + "Step= 796, Dmax= 2.8e-03 nm, Epot= -1.96497e+03 Fmax= 9.24984e+01, atom= 73\n", + "Step= 797, Dmax= 3.4e-03 nm, Epot= -1.96501e+03 Fmax= 1.21386e+02, atom= 73\n", + "Step= 798, Dmax= 4.1e-03 nm, Epot= -1.96507e+03 Fmax= 1.40550e+02, atom= 73\n", + "Step= 800, Dmax= 2.5e-03 nm, Epot= -1.96593e+03 Fmax= 2.79959e+01, atom= 50\n", + "Step= 801, Dmax= 2.9e-03 nm, Epot= -1.96636e+03 Fmax= 9.86573e+01, atom= 11\n", + "Step= 803, Dmax= 1.8e-03 nm, Epot= -1.96687e+03 Fmax= 2.85317e+01, atom= 50\n", + "Step= 804, Dmax= 2.1e-03 nm, Epot= -1.96729e+03 Fmax= 6.99878e+01, atom= 11\n", + "Step= 805, Dmax= 2.5e-03 nm, Epot= -1.96743e+03 Fmax= 8.90188e+01, atom= 23\n", + "Step= 806, Dmax= 3.1e-03 nm, Epot= -1.96753e+03 Fmax= 1.18734e+02, atom= 11\n", + "Step= 807, Dmax= 3.7e-03 nm, Epot= -1.96775e+03 Fmax= 1.14648e+02, atom= 11\n", + "Step= 809, Dmax= 2.2e-03 nm, Epot= -1.96829e+03 Fmax= 3.65236e+01, atom= 11\n", + "Step= 810, Dmax= 2.6e-03 nm, Epot= -1.96842e+03 Fmax= 1.19265e+02, atom= 23\n", + "Step= 811, Dmax= 3.2e-03 nm, Epot= -1.96878e+03 Fmax= 9.39507e+01, atom= 11\n", + "Step= 813, Dmax= 1.9e-03 nm, Epot= -1.96912e+03 Fmax= 3.04313e+01, atom= 23\n", + "Step= 814, Dmax= 2.3e-03 nm, Epot= -1.96931e+03 Fmax= 1.17416e+02, atom= 11\n", + "Step= 815, Dmax= 2.7e-03 nm, Epot= -1.96971e+03 Fmax= 5.97281e+01, atom= 23\n", + "Step= 817, Dmax= 1.6e-03 nm, Epot= -1.96993e+03 Fmax= 5.28330e+01, atom= 11\n", + "Step= 818, Dmax= 2.0e-03 nm, Epot= -1.97010e+03 Fmax= 7.03846e+01, atom= 23\n", + "Step= 819, Dmax= 2.4e-03 nm, Epot= -1.97026e+03 Fmax= 8.88194e+01, atom= 11\n", + "Step= 820, Dmax= 2.8e-03 nm, Epot= -1.97043e+03 Fmax= 9.20270e+01, atom= 23\n", + "Step= 821, Dmax= 3.4e-03 nm, Epot= -1.97044e+03 Fmax= 1.36377e+02, atom= 11\n", + "Step= 822, Dmax= 4.1e-03 nm, Epot= -1.97066e+03 Fmax= 1.25197e+02, atom= 23\n", + "Step= 824, Dmax= 2.5e-03 nm, Epot= -1.97116e+03 Fmax= 4.20069e+01, atom= 11\n", + "Step= 825, Dmax= 2.9e-03 nm, Epot= -1.97118e+03 Fmax= 1.36733e+02, atom= 23\n", + "Step= 826, Dmax= 3.5e-03 nm, Epot= -1.97156e+03 Fmax= 9.88405e+01, atom= 11\n", + "Step= 828, Dmax= 2.1e-03 nm, Epot= -1.97187e+03 Fmax= 3.90612e+01, atom= 23\n", + "Step= 829, Dmax= 2.5e-03 nm, Epot= -1.97192e+03 Fmax= 1.26153e+02, atom= 11\n", + "Step= 830, Dmax= 3.1e-03 nm, Epot= -1.97231e+03 Fmax= 7.11990e+01, atom= 23\n", + "Step= 832, Dmax= 1.8e-03 nm, Epot= -1.97252e+03 Fmax= 5.30064e+01, atom= 11\n", + "Step= 833, Dmax= 2.2e-03 nm, Epot= -1.97264e+03 Fmax= 8.47563e+01, atom= 23\n", + "Step= 834, Dmax= 2.6e-03 nm, Epot= -1.97280e+03 Fmax= 9.10007e+01, atom= 11\n", + "Step= 835, Dmax= 3.2e-03 nm, Epot= -1.97287e+03 Fmax= 1.11470e+02, atom= 23\n", + "Step= 836, Dmax= 3.8e-03 nm, Epot= -1.97290e+03 Fmax= 1.39098e+02, atom= 11\n", + "Step= 837, Dmax= 4.6e-03 nm, Epot= -1.97294e+03 Fmax= 1.54658e+02, atom= 23\n", + "Step= 839, Dmax= 2.7e-03 nm, Epot= -1.97361e+03 Fmax= 3.00050e+01, atom= 11\n", + "Step= 841, Dmax= 1.6e-03 nm, Epot= -1.97380e+03 Fmax= 6.97811e+01, atom= 23\n", + "Step= 842, Dmax= 2.0e-03 nm, Epot= -1.97398e+03 Fmax= 5.97237e+01, atom= 11\n", + "Step= 843, Dmax= 2.4e-03 nm, Epot= -1.97406e+03 Fmax= 9.08769e+01, atom= 23\n", + "Step= 844, Dmax= 2.8e-03 nm, Epot= -1.97420e+03 Fmax= 9.50209e+01, atom= 11\n", + "Step= 845, Dmax= 3.4e-03 nm, Epot= -1.97421e+03 Fmax= 1.24097e+02, atom= 23\n", + "Step= 846, Dmax= 4.1e-03 nm, Epot= -1.97425e+03 Fmax= 1.43640e+02, atom= 11\n", + "Step= 848, Dmax= 2.4e-03 nm, Epot= -1.97481e+03 Fmax= 2.14815e+01, atom= 50\n", + "Step= 849, Dmax= 2.9e-03 nm, Epot= -1.97512e+03 Fmax= 1.18182e+02, atom= 11\n", + "Step= 850, Dmax= 3.5e-03 nm, Epot= -1.97529e+03 Fmax= 1.09331e+02, atom= 23\n", + "Step= 852, Dmax= 2.1e-03 nm, Epot= -1.97566e+03 Fmax= 3.25021e+01, atom= 11\n", + "Step= 854, Dmax= 1.3e-03 nm, Epot= -1.97580e+03 Fmax= 4.87049e+01, atom= 23\n", + "Step= 855, Dmax= 1.5e-03 nm, Epot= -1.97593e+03 Fmax= 4.93154e+01, atom= 11\n", + "Step= 856, Dmax= 1.8e-03 nm, Epot= -1.97603e+03 Fmax= 6.87956e+01, atom= 23\n", + "Step= 857, Dmax= 2.2e-03 nm, Epot= -1.97615e+03 Fmax= 7.32493e+01, atom= 11\n", + "Step= 858, Dmax= 2.6e-03 nm, Epot= -1.97620e+03 Fmax= 9.72041e+01, atom= 23\n", + "Step= 859, Dmax= 3.2e-03 nm, Epot= -1.97627e+03 Fmax= 1.07860e+02, atom= 11\n", + "Step= 861, Dmax= 1.9e-03 nm, Epot= -1.97662e+03 Fmax= 1.91887e+01, atom= 50\n", + "Step= 862, Dmax= 2.3e-03 nm, Epot= -1.97687e+03 Fmax= 9.34073e+01, atom= 11\n", + "Step= 863, Dmax= 2.7e-03 nm, Epot= -1.97703e+03 Fmax= 8.54148e+01, atom= 23\n", + "Step= 865, Dmax= 1.6e-03 nm, Epot= -1.97727e+03 Fmax= 2.48764e+01, atom= 11\n", + "Step= 866, Dmax= 2.0e-03 nm, Epot= -1.97737e+03 Fmax= 9.27157e+01, atom= 23\n", + "Step= 867, Dmax= 2.4e-03 nm, Epot= -1.97758e+03 Fmax= 6.14610e+01, atom= 11\n", + "Step= 869, Dmax= 1.4e-03 nm, Epot= -1.97773e+03 Fmax= 3.21721e+01, atom= 23\n", + "Step= 870, Dmax= 1.7e-03 nm, Epot= -1.97781e+03 Fmax= 7.12656e+01, atom= 11\n", + "Step= 871, Dmax= 2.0e-03 nm, Epot= -1.97795e+03 Fmax= 6.19605e+01, atom= 23\n", + "Step= 872, Dmax= 2.4e-03 nm, Epot= -1.97796e+03 Fmax= 9.30125e+01, atom= 11\n", + "Step= 873, Dmax= 2.9e-03 nm, Epot= -1.97805e+03 Fmax= 9.77378e+01, atom= 23\n", + "Step= 875, Dmax= 1.8e-03 nm, Epot= -1.97834e+03 Fmax= 2.05468e+01, atom= 11\n", + "Step= 876, Dmax= 2.1e-03 nm, Epot= -1.97847e+03 Fmax= 1.01388e+02, atom= 23\n", + "Step= 877, Dmax= 2.5e-03 nm, Epot= -1.97869e+03 Fmax= 6.27675e+01, atom= 11\n", + "Step= 879, Dmax= 1.5e-03 nm, Epot= -1.97884e+03 Fmax= 3.76683e+01, atom= 23\n", + "Step= 880, Dmax= 1.8e-03 nm, Epot= -1.97889e+03 Fmax= 7.46273e+01, atom= 11\n", + "Step= 881, Dmax= 2.2e-03 nm, Epot= -1.97901e+03 Fmax= 6.83851e+01, atom= 23\n", + "Step= 883, Dmax= 1.3e-03 nm, Epot= -1.97918e+03 Fmax= 1.94359e+01, atom= 11\n", + "Step= 884, Dmax= 1.6e-03 nm, Epot= -1.97932e+03 Fmax= 7.35281e+01, atom= 23\n", + "Step= 885, Dmax= 1.9e-03 nm, Epot= -1.97948e+03 Fmax= 4.86883e+01, atom= 11\n", + "Step= 887, Dmax= 1.1e-03 nm, Epot= -1.97959e+03 Fmax= 2.74833e+01, atom= 23\n", + "Step= 888, Dmax= 1.4e-03 nm, Epot= -1.97969e+03 Fmax= 5.33395e+01, atom= 11\n", + "Step= 889, Dmax= 1.6e-03 nm, Epot= -1.97979e+03 Fmax= 5.36107e+01, atom= 23\n", + "Step= 890, Dmax= 2.0e-03 nm, Epot= -1.97985e+03 Fmax= 6.99175e+01, atom= 11\n", + "Step= 891, Dmax= 2.4e-03 nm, Epot= -1.97991e+03 Fmax= 8.32195e+01, atom= 23\n", + "Step= 892, Dmax= 2.8e-03 nm, Epot= -1.97994e+03 Fmax= 9.62321e+01, atom= 11\n", + "Step= 894, Dmax= 1.7e-03 nm, Epot= -1.98024e+03 Fmax= 1.70546e+01, atom= 23\n", + "Step= 895, Dmax= 2.0e-03 nm, Epot= -1.98042e+03 Fmax= 8.17866e+01, atom= 11\n", + "Step= 896, Dmax= 2.4e-03 nm, Epot= -1.98054e+03 Fmax= 7.87549e+01, atom= 23\n", + "Step= 898, Dmax= 1.5e-03 nm, Epot= -1.98074e+03 Fmax= 1.82801e+01, atom= 11\n", + "Step= 899, Dmax= 1.8e-03 nm, Epot= -1.98086e+03 Fmax= 8.60070e+01, atom= 23\n", + "Step= 900, Dmax= 2.1e-03 nm, Epot= -1.98105e+03 Fmax= 4.89054e+01, atom= 11\n", + "Step= 902, Dmax= 1.3e-03 nm, Epot= -1.98116e+03 Fmax= 3.55580e+01, atom= 23\n", + "Step= 903, Dmax= 1.5e-03 nm, Epot= -1.98123e+03 Fmax= 5.57065e+01, atom= 11\n", + "Step= 904, Dmax= 1.8e-03 nm, Epot= -1.98131e+03 Fmax= 6.39843e+01, atom= 23\n", + "Step= 905, Dmax= 2.2e-03 nm, Epot= -1.98136e+03 Fmax= 7.24722e+01, atom= 11\n", + "Step= 907, Dmax= 1.3e-03 nm, Epot= -1.98155e+03 Fmax= 1.69570e+01, atom= 23\n", + "Step= 908, Dmax= 1.6e-03 nm, Epot= -1.98174e+03 Fmax= 5.63275e+01, atom= 11\n", + "Step= 909, Dmax= 1.9e-03 nm, Epot= -1.98181e+03 Fmax= 6.83987e+01, atom= 23\n", + "Step= 910, Dmax= 2.3e-03 nm, Epot= -1.98187e+03 Fmax= 7.27648e+01, atom= 11\n", + "Step= 912, Dmax= 1.4e-03 nm, Epot= -1.98207e+03 Fmax= 1.95786e+01, atom= 23\n", + "Step= 913, Dmax= 1.6e-03 nm, Epot= -1.98221e+03 Fmax= 6.06944e+01, atom= 11\n", + "Step= 914, Dmax= 2.0e-03 nm, Epot= -1.98229e+03 Fmax= 6.88629e+01, atom= 23\n", + "Step= 915, Dmax= 2.4e-03 nm, Epot= -1.98233e+03 Fmax= 7.64097e+01, atom= 11\n", + "Step= 917, Dmax= 1.4e-03 nm, Epot= -1.98256e+03 Fmax= 1.92869e+01, atom= 23\n", + "Step= 918, Dmax= 1.7e-03 nm, Epot= -1.98270e+03 Fmax= 6.15076e+01, atom= 11\n", + "Step= 919, Dmax= 2.0e-03 nm, Epot= -1.98277e+03 Fmax= 7.30581e+01, atom= 23\n", + "Step= 920, Dmax= 2.4e-03 nm, Epot= -1.98283e+03 Fmax= 7.70883e+01, atom= 11\n", + "Step= 922, Dmax= 1.5e-03 nm, Epot= -1.98307e+03 Fmax= 2.17414e+01, atom= 23\n", + "Step= 923, Dmax= 1.8e-03 nm, Epot= -1.98318e+03 Fmax= 6.53928e+01, atom= 11\n", + "Step= 924, Dmax= 2.1e-03 nm, Epot= -1.98326e+03 Fmax= 7.44452e+01, atom= 23\n", + "Step= 925, Dmax= 2.5e-03 nm, Epot= -1.98330e+03 Fmax= 8.00918e+01, atom= 11\n", + "Step= 927, Dmax= 1.5e-03 nm, Epot= -1.98357e+03 Fmax= 2.23403e+01, atom= 23\n", + "Step= 928, Dmax= 1.8e-03 nm, Epot= -1.98366e+03 Fmax= 6.67667e+01, atom= 11\n", + "Step= 929, Dmax= 2.2e-03 nm, Epot= -1.98373e+03 Fmax= 7.85324e+01, atom= 23\n", + "Step= 930, Dmax= 2.6e-03 nm, Epot= -1.98378e+03 Fmax= 8.06128e+01, atom= 11\n", + "Step= 932, Dmax= 1.6e-03 nm, Epot= -1.98408e+03 Fmax= 2.40798e+01, atom= 23\n", + "Step= 933, Dmax= 1.9e-03 nm, Epot= -1.98412e+03 Fmax= 7.05713e+01, atom= 11\n", + "Step= 934, Dmax= 2.3e-03 nm, Epot= -1.98421e+03 Fmax= 7.84777e+01, atom= 23\n", + "Step= 935, Dmax= 2.7e-03 nm, Epot= -1.98421e+03 Fmax= 8.57801e+01, atom= 11\n", + "Step= 937, Dmax= 1.6e-03 nm, Epot= -1.98460e+03 Fmax= 2.50888e+01, atom= 23\n", + "Step= 938, Dmax= 2.0e-03 nm, Epot= -1.98463e+03 Fmax= 6.73701e+01, atom= 11\n", + "Step= 940, Dmax= 1.2e-03 nm, Epot= -1.98493e+03 Fmax= 1.87958e+01, atom= 34\n", + "Step= 941, Dmax= 1.4e-03 nm, Epot= -1.98514e+03 Fmax= 3.19280e+01, atom= 34\n", + "Step= 943, Dmax= 8.4e-04 nm, Epot= -1.98525e+03 Fmax= 2.54590e+01, atom= 23\n", + "Step= 944, Dmax= 1.0e-03 nm, Epot= -1.98536e+03 Fmax= 3.60196e+01, atom= 34\n", + "Step= 945, Dmax= 1.2e-03 nm, Epot= -1.98545e+03 Fmax= 3.79993e+01, atom= 23\n", + "Step= 946, Dmax= 1.5e-03 nm, Epot= -1.98550e+03 Fmax= 5.81890e+01, atom= 34\n", + "Step= 947, Dmax= 1.8e-03 nm, Epot= -1.98562e+03 Fmax= 5.25112e+01, atom= 34\n", + "Step= 949, Dmax= 1.1e-03 nm, Epot= -1.98582e+03 Fmax= 2.73786e+01, atom= 34\n", + "Step= 950, Dmax= 1.3e-03 nm, Epot= -1.98595e+03 Fmax= 3.64981e+01, atom= 34\n", + "Step= 951, Dmax= 1.5e-03 nm, Epot= -1.98601e+03 Fmax= 6.33636e+01, atom= 34\n", + "Step= 952, Dmax= 1.8e-03 nm, Epot= -1.98615e+03 Fmax= 5.25118e+01, atom= 34\n", + "Step= 954, Dmax= 1.1e-03 nm, Epot= -1.98631e+03 Fmax= 2.95759e+01, atom= 34\n", + "Step= 955, Dmax= 1.3e-03 nm, Epot= -1.98644e+03 Fmax= 3.90494e+01, atom= 34\n", + "Step= 956, Dmax= 1.6e-03 nm, Epot= -1.98652e+03 Fmax= 6.51853e+01, atom= 34\n", + "Step= 957, Dmax= 1.9e-03 nm, Epot= -1.98665e+03 Fmax= 5.48532e+01, atom= 34\n", + "Step= 959, Dmax= 1.1e-03 nm, Epot= -1.98681e+03 Fmax= 3.02958e+01, atom= 34\n", + "Step= 960, Dmax= 1.4e-03 nm, Epot= -1.98695e+03 Fmax= 4.04982e+01, atom= 34\n", + "Step= 961, Dmax= 1.6e-03 nm, Epot= -1.98704e+03 Fmax= 6.77057e+01, atom= 34\n", + "Step= 962, Dmax= 2.0e-03 nm, Epot= -1.98717e+03 Fmax= 5.70320e+01, atom= 34\n", + "Step= 963, Dmax= 2.3e-03 nm, Epot= -1.98718e+03 Fmax= 1.00063e+02, atom= 34\n", + "Step= 964, Dmax= 2.8e-03 nm, Epot= -1.98736e+03 Fmax= 8.14156e+01, atom= 34\n", + "Step= 966, Dmax= 1.7e-03 nm, Epot= -1.98758e+03 Fmax= 3.95078e+01, atom= 34\n", + "Step= 967, Dmax= 2.0e-03 nm, Epot= -1.98769e+03 Fmax= 7.13563e+01, atom= 34\n", + "Step= 968, Dmax= 2.4e-03 nm, Epot= -1.98777e+03 Fmax= 9.34324e+01, atom= 34\n", + "Step= 969, Dmax= 2.9e-03 nm, Epot= -1.98788e+03 Fmax= 9.26256e+01, atom= 34\n", + "Step= 971, Dmax= 1.7e-03 nm, Epot= -1.98814e+03 Fmax= 3.52017e+01, atom= 34\n", + "Step= 972, Dmax= 2.1e-03 nm, Epot= -1.98830e+03 Fmax= 6.84221e+01, atom= 34\n", + "Step= 973, Dmax= 2.5e-03 nm, Epot= -1.98835e+03 Fmax= 1.02324e+02, atom= 34\n", + "Step= 974, Dmax= 3.0e-03 nm, Epot= -1.98850e+03 Fmax= 9.14942e+01, atom= 34\n", + "Step= 976, Dmax= 1.8e-03 nm, Epot= -1.98875e+03 Fmax= 3.92685e+01, atom= 34\n", + "Step= 977, Dmax= 2.2e-03 nm, Epot= -1.98889e+03 Fmax= 7.54753e+01, atom= 34\n", + "Step= 978, Dmax= 2.6e-03 nm, Epot= -1.98896e+03 Fmax= 1.03195e+02, atom= 34\n", + "Step= 979, Dmax= 3.1e-03 nm, Epot= -1.98909e+03 Fmax= 9.77337e+01, atom= 34\n", + "Step= 981, Dmax= 1.9e-03 nm, Epot= -1.98936e+03 Fmax= 3.91313e+01, atom= 34\n", + "Step= 982, Dmax= 2.3e-03 nm, Epot= -1.98951e+03 Fmax= 7.66818e+01, atom= 34\n", + "Step= 983, Dmax= 2.7e-03 nm, Epot= -1.98958e+03 Fmax= 1.08347e+02, atom= 34\n", + "Step= 984, Dmax= 3.2e-03 nm, Epot= -1.98972e+03 Fmax= 9.96009e+01, atom= 34\n", + "Step= 986, Dmax= 1.9e-03 nm, Epot= -1.99000e+03 Fmax= 4.17852e+01, atom= 34\n", + "Step= 987, Dmax= 2.3e-03 nm, Epot= -1.99013e+03 Fmax= 8.13009e+01, atom= 34\n", + "Step= 988, Dmax= 2.8e-03 nm, Epot= -1.99020e+03 Fmax= 1.11223e+02, atom= 34\n", + "Step= 989, Dmax= 3.4e-03 nm, Epot= -1.99034e+03 Fmax= 1.04203e+02, atom= 34\n", + "Step= 991, Dmax= 2.0e-03 nm, Epot= -1.99063e+03 Fmax= 4.24564e+01, atom= 34\n", + "Step= 992, Dmax= 2.4e-03 nm, Epot= -1.99077e+03 Fmax= 8.35069e+01, atom= 34\n", + "Step= 993, Dmax= 2.9e-03 nm, Epot= -1.99083e+03 Fmax= 1.16341e+02, atom= 34\n", + "Step= 994, Dmax= 3.5e-03 nm, Epot= -1.99098e+03 Fmax= 1.07817e+02, atom= 34\n", + "Step= 996, Dmax= 2.1e-03 nm, Epot= -1.99128e+03 Fmax= 4.45800e+01, atom= 34\n", + "Step= 997, Dmax= 2.5e-03 nm, Epot= -1.99141e+03 Fmax= 8.71914e+01, atom= 34\n", + "Step= 998, Dmax= 3.0e-03 nm, Epot= -1.99147e+03 Fmax= 1.20368e+02, atom= 34\n", + "Step= 999, Dmax= 3.6e-03 nm, Epot= -1.99161e+03 Fmax= 1.11740e+02, atom= 34\n", + "Step= 1000, Dmax= 4.3e-03 nm, Epot= -1.99140e+03 Fmax= 1.84451e+02, atom= 34\n", + "Energy minimization reached the maximum number of steps before the forces\n", + "reached the requested precision Fmax < 10.\n", + "\n", + "writing lowest energy coordinates.\n", + "\n", + "Back Off! I just backed up em.pdb to ./#em.pdb.3#\n", + "\n", + "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n", + "Potential Energy = -1.9916112e+03\n", + "Maximum force = 1.1173969e+02 on atom 34\n", + "Norm of force = 1.9757371e+01\n", + "\n", + "GROMACS reminds you: \"Have a Nice Day\" (R. McDonald)\n", + "\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.2#\n", + "Number of degrees of freedom in T-Coupling group System is 291.00\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.2#\n", + "\n", + "GROMACS reminds you: \"I have a hunch that the unknown sequences of DNA will decode into copyright notices and patent protections.\" (Donald Knuth)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] All files set up for a run time of 5000 ps (dt=0.0001, nsteps=5e+07)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1873764311\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.100 nm, buffer size 0.000 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.100 nm, buffer size 0.000 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 224 Mb of data\n" + ] + }, + { + "data": { + "text/plain": [ + "{'struct': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.gro',\n", + " 'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top',\n", + " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx',\n", + " 'qscript': ['./local.sh'],\n", + " 'mainselection': None,\n", + " 'deffnm': 'md',\n", + " 'includes': ['/home/awsm/MDPOW/mdpow/top',\n", + " '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top']}" + ] + }, + "execution_count": 30, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ "from mdpow.equil import WaterSimulation\n", "\n", - "sim = WaterSimulation(molecule=\"BENZ\", ff_class=MARTINI)\n", + "sim = WaterSimulation(\n", + " molecule=\"BENZ\",\n", + " ff_class=MARTINI,\n", + " mdp={\n", + " \"energy_minimize\": str(EM_FILE.absolute()),\n", + " \"MD_relaxed\": str(EQ_FILE.absolute()),\n", + " \"MD_NPT\": str(RUN_FILE.absolute()),\n", + " \"MD_restrained\": str(RUN_FILE.absolute()),\n", + " },\n", + ")\n", "sim.topology(str(BENZENE_ITP))\n", - "print(sim.solvent)\n", - "# sim.solvate(struct=MARTINI_BENZENE)\n", - "# sim.energy_minimize()\n", - "# sim.MD_relaxed(runtime=5) # should be at least 1e3 ps for production not just 5 ps" + "sim.solvate(struct=MARTINI_BENZENE, maxwarn=1)\n", + "sim.energy_minimize(maxwarn=1)\n", + "sim.MD_relaxed(runtime=5e3) # should be at least 1e3 ps for production not just 5 ps" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "metadata": { + "vscode": { + "languageId": "shellscript" + } + }, + "outputs": [ + { + "ename": "CalledProcessError", + "evalue": "Command 'b'MD_PATH=./Equilibrium/water/MD_relaxed\\nchmod +x $MD_PATH/local.sh\\n$MD_PATH/local.sh >> mdrun.log\\n'' returned non-zero exit status 66.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[41], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m get_ipython()\u001b[39m.\u001b[39;49mrun_cell_magic(\u001b[39m'\u001b[39;49m\u001b[39mscript\u001b[39;49m\u001b[39m'\u001b[39;49m, \u001b[39m'\u001b[39;49m\u001b[39mbash\u001b[39;49m\u001b[39m'\u001b[39;49m, \u001b[39m'\u001b[39;49m\u001b[39mMD_PATH=./Equilibrium/water/MD_relaxed\u001b[39;49m\u001b[39m\\n\u001b[39;49;00m\u001b[39mchmod +x $MD_PATH/local.sh\u001b[39;49m\u001b[39m\\n\u001b[39;49;00m\u001b[39m$MD_PATH/local.sh >> mdrun.log\u001b[39;49m\u001b[39m\\n\u001b[39;49;00m\u001b[39m'\u001b[39;49m)\n", + "File \u001b[0;32m~/mambaforge/envs/mdpow/lib/python3.11/site-packages/IPython/core/interactiveshell.py:2478\u001b[0m, in \u001b[0;36mInteractiveShell.run_cell_magic\u001b[0;34m(self, magic_name, line, cell)\u001b[0m\n\u001b[1;32m 2476\u001b[0m \u001b[39mwith\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mbuiltin_trap:\n\u001b[1;32m 2477\u001b[0m args \u001b[39m=\u001b[39m (magic_arg_s, cell)\n\u001b[0;32m-> 2478\u001b[0m result \u001b[39m=\u001b[39m fn(\u001b[39m*\u001b[39;49margs, \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mkwargs)\n\u001b[1;32m 2480\u001b[0m \u001b[39m# The code below prevents the output from being displayed\u001b[39;00m\n\u001b[1;32m 2481\u001b[0m \u001b[39m# when using magics with decodator @output_can_be_silenced\u001b[39;00m\n\u001b[1;32m 2482\u001b[0m \u001b[39m# when the last Python token in the expression is a ';'.\u001b[39;00m\n\u001b[1;32m 2483\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mgetattr\u001b[39m(fn, magic\u001b[39m.\u001b[39mMAGIC_OUTPUT_CAN_BE_SILENCED, \u001b[39mFalse\u001b[39;00m):\n", + "File \u001b[0;32m~/mambaforge/envs/mdpow/lib/python3.11/site-packages/IPython/core/magics/script.py:314\u001b[0m, in \u001b[0;36mScriptMagics.shebang\u001b[0;34m(self, line, cell)\u001b[0m\n\u001b[1;32m 309\u001b[0m \u001b[39mif\u001b[39;00m args\u001b[39m.\u001b[39mraise_error \u001b[39mand\u001b[39;00m p\u001b[39m.\u001b[39mreturncode \u001b[39m!=\u001b[39m \u001b[39m0\u001b[39m:\n\u001b[1;32m 310\u001b[0m \u001b[39m# If we get here and p.returncode is still None, we must have\u001b[39;00m\n\u001b[1;32m 311\u001b[0m \u001b[39m# killed it but not yet seen its return code. We don't wait for it,\u001b[39;00m\n\u001b[1;32m 312\u001b[0m \u001b[39m# in case it's stuck in uninterruptible sleep. -9 = SIGKILL\u001b[39;00m\n\u001b[1;32m 313\u001b[0m rc \u001b[39m=\u001b[39m p\u001b[39m.\u001b[39mreturncode \u001b[39mor\u001b[39;00m \u001b[39m-\u001b[39m\u001b[39m9\u001b[39m\n\u001b[0;32m--> 314\u001b[0m \u001b[39mraise\u001b[39;00m CalledProcessError(rc, cell)\n", + "\u001b[0;31mCalledProcessError\u001b[0m: Command 'b'MD_PATH=./Equilibrium/water/MD_relaxed\\nchmod +x $MD_PATH/local.sh\\n$MD_PATH/local.sh >> mdrun.log\\n'' returned non-zero exit status 66." + ] + } + ], + "source": [ + "%%script bash\n", + "MD_PATH=./Equilibrium/water/MD_relaxed\n", + "chmod +x $MD_PATH/local.sh\n", + "$MD_PATH/local.sh >> mdrun.log" ] }, { diff --git a/doc/examples/martini/run.mdp b/doc/examples/martini/run.mdp index aed06872..3b1f95ed 100644 --- a/doc/examples/martini/run.mdp +++ b/doc/examples/martini/run.mdp @@ -1,3 +1,4 @@ +include = integrator = sd ; start time and timestep in ps = tinit = 0 diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index d922ef37..ae28bf5b 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -60,11 +60,12 @@ from dataclasses import dataclass from collections import defaultdict from pathlib import Path -from typing import Dict, List, Union +from typing import Dict, List, Union, Optional import logging logger = logging.getLogger("mdpow.forecefields") +Pathy = Union[str, os.PathLike] HERE = Path(__file__).parent TOP_DIR = HERE / "top" @@ -76,26 +77,25 @@ @dataclass -class GromacsSolventModel(object): +class GromacsSolventModel: """Data for a solvent model in Gromacs.""" - def __init__( + identifier: str + name: Optional[str] = None + itp: Optional[Pathy] = None + coordinates: Optional[Pathy] = None + description: Optional[str] = None + forcefield: str = "OPLS-AA" + + def __post_init__( self, - identifier, - name=None, - itp=None, - coordinates=None, - description=None, - forcefield="OPLS-AA", ): - self.identifier = identifier - self.name = name if name is not None else str(identifier).upper() - self.itp = itp if itp is not None else self.guess_filename("itp") - self.coordinates = ( - coordinates if coordinates is not None else self.guess_filename("gro") - ) - self.description = description - self.forcefield = forcefield + if self.name is None: + self.name = str(self.identifier).upper() + if self.itp is None: + self.itp = self.guess_filename("itp") + if self.coordinates is None: + self.coordinates = self.guess_filename("gro") def guess_filename(self, extension): """Guess the filename for the model and add *extension*""" @@ -239,6 +239,7 @@ class Forcefield: ions_itp: Path default_water_itp: Path default_water_model: str = "tip4p" + water_models: Optional[Dict[str, GromacsSolventModel]] = None def __post_init__(self): """Check that the provided paths exist and populate the :attr:`water_models`.""" @@ -246,9 +247,10 @@ def __post_init__(self): if not path_.exists(): raise ValueError(f"Could not find required forcefield files: {path_}") - self.water_models: Dict[str, GromacsSolventModel] = _create_water_models( - self.forcefield_dir / "watermodels.dat" - ) + if self.water_models is None: + self.water_models = _create_water_models( + self.forcefield_dir / "watermodels.dat" + ) @property def ff_paths(self) -> List[Path]: From c03b4e597cd1ac6cd6d641a38b92c05539331fc5 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 4 Sep 2023 14:15:12 +0100 Subject: [PATCH 26/38] Test _get_forcefield() --- mdpow/forcefields.py | 14 +++++++------- mdpow/tests/test_forcefields.py | 20 ++++++++++++++++++++ 2 files changed, 27 insertions(+), 7 deletions(-) diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index d922ef37..75d7465c 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -358,12 +358,14 @@ def __repr__(self) -> str: } -def _get_forcefield(ff_name: str) -> Forcefield: +def _get_forcefield(ff: Union[str, Forcefield]) -> Forcefield: """Get the :class:`Forcefield` instance corresponding to a given name.""" + if isinstance(ff, Forcefield): + return ff try: - return ALL_FORCEFIELDS[ff_name] + return ALL_FORCEFIELDS[ff] except KeyError: - raise ValueError(f"Forcefield `{ff_name}` not found.") + raise ValueError(f"Forcefield `{ff}` not found.") def get_solvent_identifier( @@ -392,8 +394,7 @@ def get_solvent_identifier( :Returns: An identifier """ - if isinstance(forcefield, str): - forcefield = _get_forcefield(forcefield) + forcefield = _get_forcefield(forcefield) if solvent_type == "water": identifier = ( @@ -424,8 +425,7 @@ def get_solvent_model(identifier, forcefield: Union[Forcefield, str] = OPLS_AA): If identifier is "water" then the default water model for the :class:`Forcefield` is assumed. """ - if isinstance(forcefield, str): - forcefield = _get_forcefield(forcefield) + forcefield = _get_forcefield(forcefield) if identifier == "water": identifier = forcefield.default_water_model diff --git a/mdpow/tests/test_forcefields.py b/mdpow/tests/test_forcefields.py index 6d361a94..e2f70746 100644 --- a/mdpow/tests/test_forcefields.py +++ b/mdpow/tests/test_forcefields.py @@ -9,6 +9,8 @@ WATERMODELS = ("tip4p", "tip3p", "tip5p", "spc", "spce", "m24", "tip4pd") SOLVENTMODELS = ("water", "cyclohexane", "octanol", "toluene") +forcefields = mdpow.forcefields + class TestIncludedForcefiels(object): @staticmethod @@ -29,6 +31,24 @@ def test_oplsaa_ff(): os.path.join("mdpow", "top", "oplsaa.ff") ) + @pytest.mark.parametrize( + "ff_str,ff_instance", + [ + ("OPLS-AA", forcefields.OPLS_AA), + ("CHARMM", forcefields.CHARMM), + ("AMBER", forcefields.AMBER), + ("Violet Parr", None), + ], + ) + def test_get_forcefield(self, ff_str, ff_instance): + """Check that we can correctly cast a `Forcefield`.""" + if ff_instance is not None: + assert forcefields._get_forcefield(ff_str) == ff_instance + assert forcefields._get_forcefield(ff_instance) == ff_instance + else: + with pytest.raises(ValueError): + forcefields._get_forcefield(ff_str) + class TestIncludedSolvents(object): solvents = { From a3edfb5fc12fb6d389682c7b77d8c18a801c38ab Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 4 Sep 2023 14:17:43 +0100 Subject: [PATCH 27/38] Better error handling for ff_class --- mdpow/equil.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mdpow/equil.py b/mdpow/equil.py index 3bdc4a92..761e9076 100644 --- a/mdpow/equil.py +++ b/mdpow/equil.py @@ -192,7 +192,8 @@ def __init__( dirname = kwargs.pop("dirname", self.dirname_default) if ff_class is not None: - assert isinstance(ff_class, forcefields.Forcefield) + if not isinstance(ff_class, forcefields.Forcefield): + raise TypeError(f"`ff_class` must be a `forcefields.Forcefield` instance.") forcefield: forcefields.Forcefield = ff_class else: forcefield_name = kwargs.pop("forcefield", "OPLS-AA") From d38f4ab67133a325e45630cef0ea60dd42f17c70 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 4 Sep 2023 14:26:59 +0100 Subject: [PATCH 28/38] Use `.config` and add docstrings --- mdpow/forcefields.py | 37 ++++++++++++++++++++++++------------- 1 file changed, 24 insertions(+), 13 deletions(-) diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index 75d7465c..d311ec3b 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -64,10 +64,9 @@ import logging -logger = logging.getLogger("mdpow.forecefields") +from . import config -HERE = Path(__file__).parent -TOP_DIR = HERE / "top" +logger = logging.getLogger("mdpow.forecefields") #: Default force field. At the moment, OPLS-AA, CHARMM/CGENFF, and AMBER/GAFF #: are directly supported. However, it is not recommended to change the @@ -231,7 +230,11 @@ def get_water_model(watermodel="tip4p"): @dataclass class Forcefield: - """Contains information about files corresponding to a forcefield.""" + """Contains information about files corresponding to a forcefield. + + .. versionadded: 0.9.0 + + """ name: str solvent_models: Dict[str, GromacsSolventModel] @@ -263,7 +266,7 @@ def __repr__(self) -> str: #: Other solvents (not water, see :data:`GROMACS_WATER_MODELS` for those). NEW_OCTANOL_DESC = "Zangi R (2018) Refinement of the OPLSAA force-field for liquid alcohols.; ACS Omega 3(12):18089-18099. doi: 10.1021/acsomega.8b03132" -OPLS_AA_FF_DIR = TOP_DIR / "oplsaa.ff" +OPLS_AA_FF_DIR = Path(config.topfiles["oplsaa.ff"]) OPLS_AA = Forcefield( "OPLS-AA", { @@ -297,7 +300,7 @@ def __repr__(self) -> str: OPLS_AA_FF_DIR / "tip4p.itp", ) -CHARMM_FF_DIR = TOP_DIR / "charmm36-mar2019.ff" +CHARMM_FF_DIR = Path(config.topfiles["charmm36-mar2019.ff"]) CHARMM = Forcefield( "CHARMM", { @@ -320,7 +323,7 @@ def __repr__(self) -> str: default_water_model="tip3p", ) -AMBER_FF_DIR = TOP_DIR / "amber99sb.ff" +AMBER_FF_DIR = Path(config.topfiles["amber99sb.ff"]) AMBER = Forcefield( "AMBER", { @@ -374,13 +377,14 @@ def get_solvent_identifier( """Get the identifier for a solvent model. The identifier is needed to access a water model (i.e., a - :class:`GromacsSolventModel`) through :func:`get_solvent_model`. Because we - have multiple water models but only limited other solvents, the organization - of these models is a bit convoluted and it is best to obtain the desired - water model in these two steps:: + :class:`GromacsSolventModel`) through + :func:`get_solvent_model`. Because we have multiple water models + but only limited other solvents, the organization of these models + is a bit convoluted and it is best to obtain the desired water + model in these two steps:: - identifier = get_solvent_identifier("water", model="tip3p") model = - get_solvent_model(identifier) + identifier = get_solvent_identifier("water", model="tip3p") + model = get_solvent_model(identifier) For ``solvent_type`` *water*: either provide ``None`` or "water" for the @@ -393,6 +397,10 @@ def get_solvent_identifier( :Raises ValueError: If there is no identifier found for the combination. :Returns: An identifier + + .. versionchanged:: 0.9.0 + Raises :exc:`ValueError` instead of returning ``None``. + """ forcefield = _get_forcefield(forcefield) @@ -424,6 +432,9 @@ def get_solvent_model(identifier, forcefield: Union[Forcefield, str] = OPLS_AA): If identifier is "water" then the default water model for the :class:`Forcefield` is assumed. + .. versionchanged:: 0.9.0 + Function can now also accept a :class:`Forcefield` for the ``forcefield`` argument. + """ forcefield = _get_forcefield(forcefield) From 6b3df4d0d92099b54ccca3add2ca084cb857fae3 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 4 Sep 2023 14:42:08 +0100 Subject: [PATCH 29/38] Add Forcefield changes --- CHANGES | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/CHANGES b/CHANGES index d9cc73f0..ce289198 100644 --- a/CHANGES +++ b/CHANGES @@ -25,6 +25,17 @@ Changes EnsembleAnalysis.run() method, no longer needed (per comments, #199) * internal log_banner() now uses logger as argument (PR #247) * use `black` formatter for codebase (#271) +* implemented `forcefields.Forcefield` class (#267) + - facilitates users using non-default forcefields without changing package code + - `equil.Simulation` has new `ff_class` argument + - each `Forcefield` has unique `default_water_model`, replacing global `DEFAULT_WATER_MODEL` + - `get_solvent_model()` and `get_solvent_identifier()` take either `str` or `Forcefield` type for the `forcefield` argument + - both functions also use the `Forcefield`-specific `default_water_model` (fixes #112) +* `forcefields.DEFAULT_WATER_MODEL` removed (#267) +* changed `system.top` and `system_octwet.top` to act as templates and added `.template` suffix (#267) +* removed `forcefields.get_ff_paths()` (#267) +* changed `forcefields.get_solvent_identifier()`: will raise `ValueError` instead of returning `None` (#267) + Enhancements From 256b76bb6b02d5d362f3f7fabba187f727eb66f1 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 4 Sep 2023 14:45:56 +0100 Subject: [PATCH 30/38] Formatting --- mdpow/equil.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/mdpow/equil.py b/mdpow/equil.py index 761e9076..0f0ca3ae 100644 --- a/mdpow/equil.py +++ b/mdpow/equil.py @@ -193,7 +193,9 @@ def __init__( if ff_class is not None: if not isinstance(ff_class, forcefields.Forcefield): - raise TypeError(f"`ff_class` must be a `forcefields.Forcefield` instance.") + raise TypeError( + f"`ff_class` must be a `forcefields.Forcefield` instance." + ) forcefield: forcefields.Forcefield = ff_class else: forcefield_name = kwargs.pop("forcefield", "OPLS-AA") From e92ffd888c20a8b05d4b1c779b311f3b5f93ee77 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 4 Sep 2023 20:52:11 +0100 Subject: [PATCH 31/38] [WIP] Martini example --- doc/examples/martini/martini-benzene.ipynb | 9357 +++++++++++++++++--- doc/examples/martini/run.mdp | 21 +- 2 files changed, 8360 insertions(+), 1018 deletions(-) diff --git a/doc/examples/martini/martini-benzene.ipynb b/doc/examples/martini/martini-benzene.ipynb index 132fbc64..f8478852 100644 --- a/doc/examples/martini/martini-benzene.ipynb +++ b/doc/examples/martini/martini-benzene.ipynb @@ -19,7 +19,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -27,7 +27,6 @@ "from typing import Optional\n", "\n", "import requests as req\n", - "from zipfile import ZipFile\n", "\n", "\n", "HERE = Path(\".\")\n", @@ -89,7 +88,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 2, "metadata": {}, "outputs": [ { @@ -98,7 +97,7 @@ "56" ] }, - "execution_count": 20, + "execution_count": 2, "metadata": {}, "output_type": "execute_result" } @@ -118,7 +117,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 15, "metadata": {}, "outputs": [], "source": [ @@ -130,7 +129,7 @@ " \"octanol\": GromacsSolventModel(\n", " identifier=\"octanol\",\n", " itp=MARTINI_SOLVENTS.absolute(),\n", - " coordinates=MARTINI_OCTANOL.absolute(),\n", + " coordinates=str(MARTINI_OCTANOL.absolute()),\n", " forcefield=\"Martini\",\n", " ),\n", " },\n", @@ -151,7 +150,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 4, "metadata": {}, "outputs": [ { @@ -173,7 +172,7 @@ }, { "cell_type": "code", - "execution_count": 30, + "execution_count": 5, "metadata": {}, "outputs": [ { @@ -188,12 +187,12 @@ "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n", "Command line:\n", - " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 1.0\n", + " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 3.0\n", "\n", "\n", - "Back Off! I just backed up boxed.gro to ./#boxed.gro.13#\n", + "Back Off! I just backed up boxed.gro to ./#boxed.gro.11#\n", "\n", - "GROMACS reminds you: \"That Was Really Cool\" (Butthead)\n", + "GROMACS reminds you: \"The loveliest theories are being overthrown by these damned experiments; it is no fun being a chemist any more.\" (Justus von Liebig, letter to J.J. Berzelius 1834)\n", "\n", " :-) GROMACS - gmx solvate, 2023.2 (-:\n", "\n", @@ -209,27 +208,27 @@ "Initialising inter-atomic distances...\n", "Generating solvent configuration\n", "Will generate new solvent configuration of 1x1x1 boxes\n", - "Solvent box contains 107 atoms in 107 residues\n", - "Removed 10 solvent atoms due to solvent-solvent overlap\n", - "Removed 1 solvent atoms due to solute-solvent overlap\n", + "Solvent box contains 1731 atoms in 1731 residues\n", + "Removed 98 solvent atoms due to solvent-solvent overlap\n", + "Removed 0 solvent atoms due to solute-solvent overlap\n", "Sorting configuration\n", "Found 1 molecule type:\n", - " W ( 1 atoms): 96 residues\n", - "Generated solvent containing 96 atoms in 96 residues\n", + " W ( 1 atoms): 1633 residues\n", + "Generated solvent containing 1633 atoms in 1633 residues\n", "Writing generated configuration to solvated.gro\n", "\n", - "Back Off! I just backed up solvated.gro to ./#solvated.gro.13#\n", + "Back Off! I just backed up solvated.gro to ./#solvated.gro.11#\n", "\n", - "Output configuration contains 99 atoms in 97 residues\n", - "Volume : 8.2737 (nm^3)\n", - "Density : 3549.33 (g/l)\n", - "Number of solvent molecules: 96 \n", + "Output configuration contains 1636 atoms in 1634 residues\n", + "Volume : 174.316 (nm^3)\n", + "Density : 2860.16 (g/l)\n", + "Number of solvent molecules: 1633 \n", "\n", "Processing topology\n", "\n", - "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#system.top.14#\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#system.top.12#\n", "\n", - "GROMACS reminds you: \"It Just Tastes Better\" (Burger King)\n", + "GROMACS reminds you: \"The loveliest theories are being overthrown by these damned experiments; it is no fun being a chemist any more.\" (Justus von Liebig, letter to J.J. Berzelius 1834)\n", "\n", "gromacs.setup: INFO Solvated system with /home/awsm/MDPOW/doc/examples/martini/water.gro\n" ] @@ -248,11 +247,11 @@ " box vectors : 15.000 15.000 18.000 (nm)\n", " box angles : 90.00 90.00 90.00 (degrees)\n", " box volume :4050.00 (nm^3)\n", - " shift : -1.284 1.097 -1.512 (nm)\n", - "new center : 1.703 1.703 0.803 (nm)\n", - "new box vectors : 2.270 2.270 2.270 (nm)\n", + " shift : 1.716 4.097 -0.098 (nm)\n", + "new center : 4.703 4.703 2.217 (nm)\n", + "new box vectors : 6.270 6.270 6.270 (nm)\n", "new box angles : 60.00 60.00 90.00 (degrees)\n", - "new box volume : 8.27 (nm^3)\n", + "new box volume : 174.32 (nm^3)\n", "\n", "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n", " based on residue and atom names, since they could not be\n", @@ -273,7 +272,7 @@ "J. Phys. Chem. 68 (1964) pp. 441-451\n", "-------- -------- --- Thank You --- -------- --------\n", "\n", - "Adding line for 96 solvent molecules with resname (W) to topology file (/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top)\n" + "Adding line for 1633 solvent molecules with resname (W) to topology file (/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top)\n" ] }, { @@ -297,9 +296,9 @@ "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "\n", - "Back Off! I just backed up main.ndx to ./#main.ndx.26#\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.22#\n", "\n", - "GROMACS reminds you: \"It Just Tastes Better\" (Burger King)\n", + "GROMACS reminds you: \"You still have to climb to the shoulders of the giants\" (Vedran Miletic)\n", "\n", " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", "\n", @@ -314,9 +313,9 @@ "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "\n", - "Back Off! I just backed up main.ndx to ./#main.ndx.27#\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.23#\n", "\n", - "GROMACS reminds you: \"It Just Tastes Better\" (Burger King)\n", + "GROMACS reminds you: \"You still have to climb to the shoulders of the giants\" (Vedran Miletic)\n", "\n", " :-) GROMACS - gmx trjconv, 2023.2 (-:\n", "\n", @@ -329,29 +328,29 @@ "Will write pdb: Protein data bank file\n", "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", - "Group 0 ( System) has 99 elements\n", - "Group 1 ( Other) has 99 elements\n", + "Group 0 ( System) has 1636 elements\n", + "Group 1 ( Other) has 1636 elements\n", "Group 2 ( BENZ) has 3 elements\n", - "Group 3 ( W) has 96 elements\n", + "Group 3 ( W) has 1633 elements\n", "Group 4 ( __main__) has 3 elements\n", - "Group 5 (__environment__) has 96 elements\n", - "Select a group: Group 0 ( System) has 99 elements\n", - "Group 1 ( Other) has 99 elements\n", + "Group 5 (__environment__) has 1633 elements\n", + "Select a group: Group 0 ( System) has 1636 elements\n", + "Group 1 ( Other) has 1636 elements\n", "Group 2 ( BENZ) has 3 elements\n", - "Group 3 ( W) has 96 elements\n", + "Group 3 ( W) has 1633 elements\n", "Group 4 ( __main__) has 3 elements\n", - "Group 5 (__environment__) has 96 elements\n", - "Select a group: Reading frames from gro file 'This is an auto generated system', 99 atoms.\n", + "Group 5 (__environment__) has 1633 elements\n", + "Select a group: Reading frames from gro file 'This is an auto generated system', 1636 atoms.\n", "Reading frame 0 time 0.000 \n", "Precision of ionized.gro is 0.001 (nm)\n", "\n", - "Back Off! I just backed up compact.pdb to ./#compact.pdb.13#\n", + "Back Off! I just backed up compact.pdb to ./#compact.pdb.11#\n", "Last frame 0 time 0.000 \n", " -> frame 0 time 0.000 \n", "Last written: frame 0 time 0.000\n", "\n", "\n", - "GROMACS reminds you: \"It Just Tastes Better\" (Burger King)\n", + "GROMACS reminds you: \"You still have to climb to the shoulders of the giants\" (Vedran Miletic)\n", "\n", " :-) GROMACS - gmx grompp, 2023.2 (-:\n", "\n", @@ -359,15 +358,15 @@ "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -f /tmp/tmpbri3j0j8.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -nov\n", + " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -f /tmp/tmpev4lqv00.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -nov\n", "\n", "\n", - "NOTE 1 [file /tmp/tmpbri3j0j8.mdp]:\n", + "NOTE 1 [file /tmp/tmpev4lqv00.mdp]:\n", " For a correct single-point energy evaluation with nsteps = 0, use\n", " continuation = yes to avoid constraining the input coordinates.\n", "\n", "\n", - "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#pp_system.top.13#\n" + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#pp_system.top.11#\n" ] }, { @@ -385,50 +384,50 @@ "name": "stderr", "output_type": "stream", "text": [ - "atom name 46 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 47 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 48 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 49 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 50 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 51 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 52 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 53 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 54 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 55 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 56 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 57 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 58 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 59 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 60 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 61 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 62 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 63 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 64 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 65 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", "(more than 20 non-matching atom names)\n", "\n", "WARNING 1 [file system.top, line 28]:\n", - " 54 non-matching atom names\n", + " 999 non-matching atom names\n", " atom names from\n", " /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top\n", " will be used\n", @@ -442,10 +441,10 @@ " For energy conservation with LINCS, lincs_iter should be 2 or larger.\n", "\n", "\n", - "Number of degrees of freedom in T-Coupling group rest is 291.00\n", + "Number of degrees of freedom in T-Coupling group rest is 4902.00\n", "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", "\n", - "NOTE 3 [file /tmp/tmpbri3j0j8.mdp]:\n", + "NOTE 3 [file /tmp/tmpev4lqv00.mdp]:\n", " NVE simulation with an initial temperature of zero: will use a Verlet\n", " buffer of 10%. Check your energy drift!\n", "\n", @@ -454,7 +453,7 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"This simulation is not as the former.\" (Malvolio, Act II, scene V of Shaphespeare's Twelfth Night)\n", + "GROMACS reminds you: \"You still have to climb to the shoulders of the giants\" (Vedran Miletic)\n", "\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top', mdp='em.mdp' ...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n", @@ -475,14 +474,14 @@ "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", "\n", - "Back Off! I just backed up processed.top to ./#processed.top.7#\n" + "Back Off! I just backed up processed.top to ./#processed.top.11#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1526199919\n", + "Setting the LD random seed to 1853841179\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -490,49 +489,49 @@ "\n", "Excluding 1 bonded neighbours molecule type 'W'\n", "\n", - "atom name 46 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 47 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 48 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 49 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 50 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 51 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 52 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 53 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 54 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 55 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 56 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 57 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 58 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 59 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 60 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 61 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 62 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 63 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 64 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 65 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", "(more than 20 non-matching atom names)\n", "Analysing residue names:\n", - "There are: 97 Other residues\n", + "There are: 1634 Other residues\n", "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", "\n", "This run will generate roughly 0 Mb of data\n" @@ -542,50 +541,50 @@ "name": "stderr", "output_type": "stream", "text": [ - "atom name 46 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 47 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 48 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 49 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 50 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 51 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 52 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 53 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 54 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 55 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 56 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 57 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 58 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 59 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 60 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 61 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 62 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 63 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 64 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 65 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", "(more than 20 non-matching atom names)\n", "\n", "WARNING 1 [file system.top, line 28]:\n", - " 54 non-matching atom names\n", + " 999 non-matching atom names\n", " atom names from\n", " /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top\n", " will be used\n", @@ -594,14 +593,14 @@ " will be ignored\n", "\n", "\n", - "Number of degrees of freedom in T-Coupling group rest is 291.00\n", + "Number of degrees of freedom in T-Coupling group rest is 4902.00\n", "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up em.tpr to ./#em.tpr.3#\n", + "Back Off! I just backed up em.tpr to ./#em.tpr.11#\n", "\n", - "GROMACS reminds you: \"This simulation is not as the former.\" (Malvolio, Act II, scene V of Shaphespeare's Twelfth Night)\n", + "GROMACS reminds you: \"I'm Only Faking When I Get It Right\" (Soundgarden)\n", "\n", "gromacs.run : WARNING No 'mdrun_d' binary found so trying 'mdrun' instead.\n", "(Note that energy minimization runs better with mdrun_d.)\n", @@ -622,7 +621,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -219464132\n", + "Setting the LD random seed to -561519253\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -630,49 +629,49 @@ "\n", "Excluding 1 bonded neighbours molecule type 'W'\n", "\n", - "atom name 46 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 47 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 48 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 49 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 50 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 51 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 52 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 53 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 54 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 55 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 56 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 57 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 58 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 59 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 60 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 61 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 62 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 63 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 64 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", - "atom name 65 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", + "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n", "\n", "(more than 20 non-matching atom names)\n", "Analysing residue names:\n", - "There are: 97 Other residues\n", + "There are: 1634 Other residues\n", "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", "\n", "This run will generate roughly 0 Mb of data\n" @@ -683,13 +682,8 @@ "output_type": "stream", "text": [ "\n", - "Back Off! I just backed up em.log to ./#em.log.3#\n", + "Back Off! I just backed up em.log to ./#em.log.11#\n", "Reading file em.tpr, VERSION 2023.2 (single precision)\n", - "\n", - "NOTE: Parallelization is limited by the small number of atoms,\n", - " only starting 1 thread-MPI ranks.\n", - " You can use the -nt and/or -ntmpi option to optimize the number of threads.\n", - "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", " PP:0\n", @@ -699,818 +693,819 @@ "Using 4 OpenMP threads \n", "\n", "\n", - "Back Off! I just backed up em.trr to ./#em.trr.3#\n", + "Back Off! I just backed up em.trr to ./#em.trr.11#\n", "\n", - "Back Off! I just backed up em.edr to ./#em.edr.3#\n", + "Back Off! I just backed up em.edr to ./#em.edr.11#\n", "\n", "Steepest Descents:\n", " Tolerance (Fmax) = 1.00000e+01\n", " Number of steps = 1000\n", - "Step= 0, Dmax= 1.0e-02 nm, Epot= 1.23531e+06 Fmax= 1.48149e+07, atom= 4\n", - "Step= 1, Dmax= 1.0e-02 nm, Epot= 7.70813e+05 Fmax= 5.61453e+06, atom= 86\n", - "Step= 2, Dmax= 1.2e-02 nm, Epot= 4.81154e+05 Fmax= 2.27826e+06, atom= 86\n", - "Step= 3, Dmax= 1.4e-02 nm, Epot= 3.05902e+05 Fmax= 8.26141e+05, atom= 86\n", - "Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88718e+05 Fmax= 3.05413e+05, atom= 91\n", - "Step= 5, Dmax= 2.1e-02 nm, Epot= 1.14388e+05 Fmax= 1.57159e+05, atom= 27\n", - "Step= 6, Dmax= 2.5e-02 nm, Epot= 7.08726e+04 Fmax= 9.21310e+04, atom= 38\n", - "Step= 7, Dmax= 3.0e-02 nm, Epot= 4.49159e+04 Fmax= 8.27843e+04, atom= 48\n", - "Step= 8, Dmax= 3.6e-02 nm, Epot= 3.34613e+04 Fmax= 6.48167e+04, atom= 94\n", - "Step= 9, Dmax= 4.3e-02 nm, Epot= 2.52637e+04 Fmax= 8.72701e+04, atom= 48\n", - "Step= 10, Dmax= 5.2e-02 nm, Epot= 2.04773e+04 Fmax= 2.73106e+04, atom= 91\n", - "Step= 11, Dmax= 6.2e-02 nm, Epot= 1.41021e+04 Fmax= 9.10967e+04, atom= 48\n", - "Step= 12, Dmax= 7.4e-02 nm, Epot= 1.10696e+04 Fmax= 1.60415e+04, atom= 48\n", - "Step= 13, Dmax= 8.9e-02 nm, Epot= 7.72396e+03 Fmax= 4.26140e+04, atom= 48\n", - "Step= 14, Dmax= 1.1e-01 nm, Epot= 5.96311e+03 Fmax= 8.74381e+03, atom= 86\n", - "Step= 16, Dmax= 6.4e-02 nm, Epot= 4.68375e+03 Fmax= 1.05593e+04, atom= 28\n", - "Step= 17, Dmax= 7.7e-02 nm, Epot= 4.47625e+03 Fmax= 2.86871e+04, atom= 62\n", - "Step= 18, Dmax= 9.2e-02 nm, Epot= 3.49467e+03 Fmax= 1.84483e+04, atom= 34\n", - "Step= 19, Dmax= 1.1e-01 nm, Epot= 3.05704e+03 Fmax= 1.57467e+04, atom= 50\n", - "Step= 21, Dmax= 6.7e-02 nm, Epot= 2.48774e+03 Fmax= 8.35716e+03, atom= 93\n", - "Step= 22, Dmax= 8.0e-02 nm, Epot= 1.98686e+03 Fmax= 5.53022e+03, atom= 93\n", - "Step= 23, Dmax= 9.6e-02 nm, Epot= 1.72792e+03 Fmax= 7.55378e+03, atom= 50\n", - "Step= 25, Dmax= 5.8e-02 nm, Epot= 1.19236e+03 Fmax= 4.54330e+03, atom= 53\n", - "Step= 26, Dmax= 6.9e-02 nm, Epot= 1.18750e+03 Fmax= 7.87388e+03, atom= 30\n", - "Step= 27, Dmax= 8.3e-02 nm, Epot= 1.17387e+03 Fmax= 1.21579e+04, atom= 30\n", - "Step= 29, Dmax= 5.0e-02 nm, Epot= 6.19271e+02 Fmax= 3.14347e+03, atom= 99\n", - "Step= 30, Dmax= 6.0e-02 nm, Epot= 5.13212e+02 Fmax= 5.61843e+03, atom= 99\n", - "Step= 31, Dmax= 7.2e-02 nm, Epot= 3.89048e+02 Fmax= 4.97197e+03, atom= 99\n", - "Step= 33, Dmax= 4.3e-02 nm, Epot= 1.51418e+02 Fmax= 1.37543e+03, atom= 63\n", - "Step= 34, Dmax= 5.2e-02 nm, Epot= 2.70003e+01 Fmax= 5.00114e+03, atom= 63\n", - "Step= 35, Dmax= 6.2e-02 nm, Epot= -7.81142e+01 Fmax= 3.32794e+03, atom= 99\n", - "Step= 37, Dmax= 3.7e-02 nm, Epot= -2.16465e+02 Fmax= 1.01594e+03, atom= 59\n", - "Step= 39, Dmax= 2.2e-02 nm, Epot= -2.91331e+02 Fmax= 1.56361e+03, atom= 73\n", - "Step= 40, Dmax= 2.7e-02 nm, Epot= -3.18646e+02 Fmax= 2.12704e+03, atom= 73\n", - "Step= 41, Dmax= 3.2e-02 nm, Epot= -3.34565e+02 Fmax= 3.10421e+03, atom= 73\n", - "Step= 42, Dmax= 3.8e-02 nm, Epot= -3.95506e+02 Fmax= 1.98314e+03, atom= 73\n", - "Step= 44, Dmax= 2.3e-02 nm, Epot= -4.58630e+02 Fmax= 8.56395e+02, atom= 38\n", - "Step= 46, Dmax= 1.4e-02 nm, Epot= -4.94776e+02 Fmax= 6.96671e+02, atom= 45\n", - "Step= 47, Dmax= 1.7e-02 nm, Epot= -5.09859e+02 Fmax= 1.51727e+03, atom= 73\n", - "Step= 48, Dmax= 2.0e-02 nm, Epot= -5.55774e+02 Fmax= 8.37062e+02, atom= 45\n", - "Step= 50, Dmax= 1.2e-02 nm, Epot= -5.86000e+02 Fmax= 5.55214e+02, atom= 73\n", - "Step= 51, Dmax= 1.4e-02 nm, Epot= -6.08029e+02 Fmax= 9.46368e+02, atom= 38\n", - "Step= 52, Dmax= 1.7e-02 nm, Epot= -6.29567e+02 Fmax= 1.10282e+03, atom= 73\n", - "Step= 53, Dmax= 2.1e-02 nm, Epot= -6.49759e+02 Fmax= 1.07976e+03, atom= 38\n", - "Step= 55, Dmax= 1.2e-02 nm, Epot= -6.94500e+02 Fmax= 3.55241e+02, atom= 73\n", - "Step= 56, Dmax= 1.5e-02 nm, Epot= -7.16639e+02 Fmax= 1.25705e+03, atom= 63\n", - "Step= 57, Dmax= 1.8e-02 nm, Epot= -7.57033e+02 Fmax= 7.75228e+02, atom= 63\n", - "Step= 59, Dmax= 1.1e-02 nm, Epot= -7.84539e+02 Fmax= 3.70427e+02, atom= 63\n", - "Step= 60, Dmax= 1.3e-02 nm, Epot= -8.10124e+02 Fmax= 9.55604e+02, atom= 63\n", - "Step= 61, Dmax= 1.5e-02 nm, Epot= -8.39097e+02 Fmax= 6.57462e+02, atom= 63\n", - "Step= 62, Dmax= 1.9e-02 nm, Epot= -8.49229e+02 Fmax= 1.20918e+03, atom= 63\n", - "Step= 63, Dmax= 2.2e-02 nm, Epot= -8.77608e+02 Fmax= 1.01717e+03, atom= 63\n", - "Step= 65, Dmax= 1.3e-02 nm, Epot= -9.10259e+02 Fmax= 3.59827e+02, atom= 63\n", - "Step= 66, Dmax= 1.6e-02 nm, Epot= -9.34776e+02 Fmax= 1.04464e+03, atom= 15\n", - "Step= 67, Dmax= 1.9e-02 nm, Epot= -9.59352e+02 Fmax= 7.90866e+02, atom= 63\n", - "Step= 68, Dmax= 2.3e-02 nm, Epot= -9.59384e+02 Fmax= 1.36825e+03, atom= 15\n", - "Step= 69, Dmax= 2.8e-02 nm, Epot= -9.80644e+02 Fmax= 1.12403e+03, atom= 15\n", - "Step= 71, Dmax= 1.7e-02 nm, Epot= -1.02460e+03 Fmax= 4.27435e+02, atom= 88\n", - "Step= 72, Dmax= 2.0e-02 nm, Epot= -1.03181e+03 Fmax= 1.05550e+03, atom= 88\n", - "Step= 73, Dmax= 2.4e-02 nm, Epot= -1.04573e+03 Fmax= 1.21505e+03, atom= 88\n", - "Step= 74, Dmax= 2.9e-02 nm, Epot= -1.05552e+03 Fmax= 1.18349e+03, atom= 88\n", - "Step= 76, Dmax= 1.7e-02 nm, Epot= -1.10137e+03 Fmax= 3.32521e+02, atom= 44\n", - "Step= 78, Dmax= 1.0e-02 nm, Epot= -1.11650e+03 Fmax= 5.03713e+02, atom= 14\n", - "Step= 79, Dmax= 1.2e-02 nm, Epot= -1.12894e+03 Fmax= 4.89832e+02, atom= 14\n", - "Step= 80, Dmax= 1.5e-02 nm, Epot= -1.13128e+03 Fmax= 8.31786e+02, atom= 14\n", - "Step= 81, Dmax= 1.8e-02 nm, Epot= -1.14755e+03 Fmax= 6.72474e+02, atom= 46\n", - "Step= 83, Dmax= 1.1e-02 nm, Epot= -1.17210e+03 Fmax= 2.97577e+02, atom= 46\n", - "Step= 84, Dmax= 1.3e-02 nm, Epot= -1.17536e+03 Fmax= 9.14939e+02, atom= 46\n", - "Step= 85, Dmax= 1.5e-02 nm, Epot= -1.19793e+03 Fmax= 5.24850e+02, atom= 46\n", - "Step= 87, Dmax= 9.2e-03 nm, Epot= -1.20948e+03 Fmax= 3.28243e+02, atom= 46\n", - "Step= 88, Dmax= 1.1e-02 nm, Epot= -1.21731e+03 Fmax= 6.92502e+02, atom= 46\n", - "Step= 89, Dmax= 1.3e-02 nm, Epot= -1.22834e+03 Fmax= 5.56511e+02, atom= 46\n", - "Step= 90, Dmax= 1.6e-02 nm, Epot= -1.23074e+03 Fmax= 9.32022e+02, atom= 46\n", - "Step= 91, Dmax= 1.9e-02 nm, Epot= -1.24063e+03 Fmax= 8.60424e+02, atom= 46\n", - "Step= 93, Dmax= 1.1e-02 nm, Epot= -1.25583e+03 Fmax= 2.07618e+02, atom= 30\n", - "Step= 94, Dmax= 1.4e-02 nm, Epot= -1.26051e+03 Fmax= 1.26640e+03, atom= 46\n", - "Step= 95, Dmax= 1.7e-02 nm, Epot= -1.28203e+03 Fmax= 3.99836e+02, atom= 46\n", - "Step= 97, Dmax= 9.9e-03 nm, Epot= -1.28888e+03 Fmax= 5.17173e+02, atom= 46\n", - "Step= 98, Dmax= 1.2e-02 nm, Epot= -1.29499e+03 Fmax= 5.82943e+02, atom= 46\n", - "Step= 99, Dmax= 1.4e-02 nm, Epot= -1.29985e+03 Fmax= 7.82873e+02, atom= 46\n", - "Step= 100, Dmax= 1.7e-02 nm, Epot= -1.30525e+03 Fmax= 8.13948e+02, atom= 46\n", - "Step= 101, Dmax= 2.1e-02 nm, Epot= -1.30580e+03 Fmax= 1.16789e+03, atom= 46\n", - "Step= 102, Dmax= 2.5e-02 nm, Epot= -1.31098e+03 Fmax= 1.12892e+03, atom= 46\n", - "Step= 104, Dmax= 1.5e-02 nm, Epot= -1.33203e+03 Fmax= 2.01087e+02, atom= 46\n", - "Step= 106, Dmax= 8.9e-03 nm, Epot= -1.34061e+03 Fmax= 6.26878e+02, atom= 46\n", - "Step= 107, Dmax= 1.1e-02 nm, Epot= -1.34988e+03 Fmax= 4.26997e+02, atom= 46\n", - "Step= 108, Dmax= 1.3e-02 nm, Epot= -1.35419e+03 Fmax= 7.14250e+02, atom= 46\n", - "Step= 109, Dmax= 1.5e-02 nm, Epot= -1.36088e+03 Fmax= 7.60130e+02, atom= 46\n", - "Step= 110, Dmax= 1.8e-02 nm, Epot= -1.36367e+03 Fmax= 9.08721e+02, atom= 46\n", - "Step= 111, Dmax= 2.2e-02 nm, Epot= -1.36485e+03 Fmax= 1.22558e+03, atom= 46\n", - "Step= 112, Dmax= 2.7e-02 nm, Epot= -1.36898e+03 Fmax= 1.17562e+03, atom= 46\n", - "Step= 114, Dmax= 1.6e-02 nm, Epot= -1.39228e+03 Fmax= 2.36480e+02, atom= 46\n", - "Step= 116, Dmax= 9.6e-03 nm, Epot= -1.39959e+03 Fmax= 5.78072e+02, atom= 46\n", - "Step= 117, Dmax= 1.1e-02 nm, Epot= -1.40737e+03 Fmax= 5.47191e+02, atom= 46\n", - "Step= 118, Dmax= 1.4e-02 nm, Epot= -1.41186e+03 Fmax= 6.38350e+02, atom= 46\n", - "Step= 119, Dmax= 1.7e-02 nm, Epot= -1.41413e+03 Fmax= 9.57934e+02, atom= 46\n", - "Step= 120, Dmax= 2.0e-02 nm, Epot= -1.42141e+03 Fmax= 7.80371e+02, atom= 46\n", - "Step= 122, Dmax= 1.2e-02 nm, Epot= -1.43407e+03 Fmax= 2.81777e+02, atom= 46\n", - "Step= 123, Dmax= 1.4e-02 nm, Epot= -1.43572e+03 Fmax= 8.72953e+02, atom= 46\n", - "Step= 124, Dmax= 1.7e-02 nm, Epot= -1.44639e+03 Fmax= 7.29953e+02, atom= 46\n", - "Step= 126, Dmax= 1.0e-02 nm, Epot= -1.45629e+03 Fmax= 1.85111e+02, atom= 30\n", - "Step= 127, Dmax= 1.2e-02 nm, Epot= -1.46028e+03 Fmax= 1.04938e+03, atom= 46\n", - "Step= 128, Dmax= 1.5e-02 nm, Epot= -1.47469e+03 Fmax= 2.83085e+02, atom= 46\n", - "Step= 130, Dmax= 8.9e-03 nm, Epot= -1.47935e+03 Fmax= 5.61673e+02, atom= 46\n", - "Step= 131, Dmax= 1.1e-02 nm, Epot= -1.48561e+03 Fmax= 3.03875e+02, atom= 46\n", - "Step= 133, Dmax= 6.4e-03 nm, Epot= -1.49090e+03 Fmax= 2.85057e+02, atom= 46\n", - "Step= 134, Dmax= 7.7e-03 nm, Epot= -1.49596e+03 Fmax= 2.88499e+02, atom= 46\n", - "Step= 135, Dmax= 9.2e-03 nm, Epot= -1.49959e+03 Fmax= 5.89020e+02, atom= 46\n", - "Step= 136, Dmax= 1.1e-02 nm, Epot= -1.50638e+03 Fmax= 2.94146e+02, atom= 46\n", - "Step= 138, Dmax= 6.6e-03 nm, Epot= -1.51145e+03 Fmax= 3.05515e+02, atom= 46\n", - "Step= 139, Dmax= 8.0e-03 nm, Epot= -1.51616e+03 Fmax= 2.78040e+02, atom= 46\n", - "Step= 140, Dmax= 9.6e-03 nm, Epot= -1.51886e+03 Fmax= 6.15229e+02, atom= 46\n", - "Step= 141, Dmax= 1.1e-02 nm, Epot= -1.52638e+03 Fmax= 2.84333e+02, atom= 30\n", - "Step= 143, Dmax= 6.9e-03 nm, Epot= -1.53121e+03 Fmax= 3.18607e+02, atom= 46\n", - "Step= 144, Dmax= 8.3e-03 nm, Epot= -1.53569e+03 Fmax= 2.78624e+02, atom= 30\n", - "Step= 145, Dmax= 9.9e-03 nm, Epot= -1.53753e+03 Fmax= 6.07045e+02, atom= 46\n", - "Step= 146, Dmax= 1.2e-02 nm, Epot= -1.54532e+03 Fmax= 2.98561e+02, atom= 30\n", - "Step= 148, Dmax= 7.1e-03 nm, Epot= -1.55019e+03 Fmax= 3.00360e+02, atom= 46\n", - "Step= 149, Dmax= 8.6e-03 nm, Epot= -1.55414e+03 Fmax= 3.00495e+02, atom= 30\n", - "Step= 150, Dmax= 1.0e-02 nm, Epot= -1.55495e+03 Fmax= 5.71855e+02, atom= 46\n", - "Step= 151, Dmax= 1.2e-02 nm, Epot= -1.56241e+03 Fmax= 3.35835e+02, atom= 30\n", - "Step= 153, Dmax= 7.4e-03 nm, Epot= -1.56823e+03 Fmax= 2.56194e+02, atom= 46\n", - "Step= 154, Dmax= 8.9e-03 nm, Epot= -1.57018e+03 Fmax= 3.84893e+02, atom= 95\n", - "Step= 155, Dmax= 1.1e-02 nm, Epot= -1.57306e+03 Fmax= 4.55866e+02, atom= 95\n", - "Step= 156, Dmax= 1.3e-02 nm, Epot= -1.57432e+03 Fmax= 5.59437e+02, atom= 95\n", - "Step= 157, Dmax= 1.5e-02 nm, Epot= -1.57665e+03 Fmax= 6.60315e+02, atom= 95\n", - "Step= 159, Dmax= 9.2e-03 nm, Epot= -1.59074e+03 Fmax= 1.27129e+02, atom= 95\n", - "Step= 160, Dmax= 1.1e-02 nm, Epot= -1.59725e+03 Fmax= 6.63711e+02, atom= 65\n", - "Step= 161, Dmax= 1.3e-02 nm, Epot= -1.60372e+03 Fmax= 4.06029e+02, atom= 95\n", - "Step= 163, Dmax= 7.9e-03 nm, Epot= -1.60863e+03 Fmax= 1.94396e+02, atom= 65\n", - "Step= 164, Dmax= 9.5e-03 nm, Epot= -1.61065e+03 Fmax= 5.21003e+02, atom= 95\n", - "Step= 165, Dmax= 1.1e-02 nm, Epot= -1.61651e+03 Fmax= 3.72184e+02, atom= 65\n", - "Step= 167, Dmax= 6.9e-03 nm, Epot= -1.62090e+03 Fmax= 1.83671e+02, atom= 95\n", - "Step= 168, Dmax= 8.2e-03 nm, Epot= -1.62404e+03 Fmax= 4.55366e+02, atom= 65\n", - "Step= 169, Dmax= 9.9e-03 nm, Epot= -1.62830e+03 Fmax= 3.16952e+02, atom= 95\n", - "Step= 170, Dmax= 1.2e-02 nm, Epot= -1.62842e+03 Fmax= 6.45156e+02, atom= 65\n", - "Step= 171, Dmax= 1.4e-02 nm, Epot= -1.63357e+03 Fmax= 4.58465e+02, atom= 95\n", - "Step= 173, Dmax= 8.5e-03 nm, Epot= -1.63939e+03 Fmax= 1.79413e+02, atom= 65\n", - "Step= 174, Dmax= 1.0e-02 nm, Epot= -1.63977e+03 Fmax= 5.76793e+02, atom= 65\n", - "Step= 175, Dmax= 1.2e-02 nm, Epot= -1.64675e+03 Fmax= 3.92461e+02, atom= 65\n", - "Step= 177, Dmax= 7.4e-03 nm, Epot= -1.65116e+03 Fmax= 1.79598e+02, atom= 95\n", - "Step= 178, Dmax= 8.9e-03 nm, Epot= -1.65245e+03 Fmax= 5.45644e+02, atom= 65\n", - "Step= 179, Dmax= 1.1e-02 nm, Epot= -1.65816e+03 Fmax= 2.85069e+02, atom= 65\n", - "Step= 181, Dmax= 6.4e-03 nm, Epot= -1.66154e+03 Fmax= 2.02405e+02, atom= 65\n", - "Step= 182, Dmax= 7.7e-03 nm, Epot= -1.66363e+03 Fmax= 3.70369e+02, atom= 65\n", - "Step= 183, Dmax= 9.2e-03 nm, Epot= -1.66692e+03 Fmax= 3.42580e+02, atom= 65\n", - "Step= 184, Dmax= 1.1e-02 nm, Epot= -1.66748e+03 Fmax= 4.92426e+02, atom= 65\n", - "Step= 185, Dmax= 1.3e-02 nm, Epot= -1.66979e+03 Fmax= 5.35548e+02, atom= 65\n", - "Step= 187, Dmax= 7.9e-03 nm, Epot= -1.67671e+03 Fmax= 1.02893e+02, atom= 95\n", - "Step= 188, Dmax= 9.5e-03 nm, Epot= -1.67961e+03 Fmax= 6.22062e+02, atom= 65\n", - "Step= 189, Dmax= 1.1e-02 nm, Epot= -1.68615e+03 Fmax= 2.93349e+02, atom= 65\n", - "Step= 191, Dmax= 6.9e-03 nm, Epot= -1.68891e+03 Fmax= 2.20704e+02, atom= 65\n", - "Step= 192, Dmax= 8.2e-03 nm, Epot= -1.68979e+03 Fmax= 4.06780e+02, atom= 65\n", - "Step= 193, Dmax= 9.9e-03 nm, Epot= -1.69276e+03 Fmax= 3.47940e+02, atom= 65\n", - "Step= 195, Dmax= 5.9e-03 nm, Epot= -1.69632e+03 Fmax= 1.15212e+02, atom= 65\n", - "Step= 196, Dmax= 7.1e-03 nm, Epot= -1.69782e+03 Fmax= 4.42169e+02, atom= 65\n", - "Step= 197, Dmax= 8.5e-03 nm, Epot= -1.70194e+03 Fmax= 2.30295e+02, atom= 65\n", - "Step= 199, Dmax= 5.1e-03 nm, Epot= -1.70411e+03 Fmax= 1.56805e+02, atom= 65\n", - "Step= 200, Dmax= 6.1e-03 nm, Epot= -1.70533e+03 Fmax= 3.20711e+02, atom= 65\n", - "Step= 201, Dmax= 7.4e-03 nm, Epot= -1.70776e+03 Fmax= 2.43531e+02, atom= 65\n", - "Step= 203, Dmax= 4.4e-03 nm, Epot= -1.71000e+03 Fmax= 1.06450e+02, atom= 59\n", - "Step= 204, Dmax= 5.3e-03 nm, Epot= -1.71168e+03 Fmax= 2.91243e+02, atom= 65\n", - "Step= 205, Dmax= 6.4e-03 nm, Epot= -1.71386e+03 Fmax= 2.09332e+02, atom= 65\n", - "Step= 206, Dmax= 7.6e-03 nm, Epot= -1.71392e+03 Fmax= 3.82881e+02, atom= 65\n", - "Step= 207, Dmax= 9.2e-03 nm, Epot= -1.71592e+03 Fmax= 3.34820e+02, atom= 65\n", - "Step= 209, Dmax= 5.5e-03 nm, Epot= -1.71896e+03 Fmax= 1.01078e+02, atom= 59\n", - "Step= 210, Dmax= 6.6e-03 nm, Epot= -1.71976e+03 Fmax= 3.60549e+02, atom= 65\n", - "Step= 211, Dmax= 7.9e-03 nm, Epot= -1.72212e+03 Fmax= 2.54754e+02, atom= 65\n", - "Step= 213, Dmax= 4.8e-03 nm, Epot= -1.72412e+03 Fmax= 1.16027e+02, atom= 65\n", - "Step= 214, Dmax= 5.7e-03 nm, Epot= -1.72419e+03 Fmax= 3.30170e+02, atom= 65\n", - "Step= 215, Dmax= 6.8e-03 nm, Epot= -1.72647e+03 Fmax= 2.09114e+02, atom= 65\n", - "Step= 217, Dmax= 4.1e-03 nm, Epot= -1.72793e+03 Fmax= 1.09336e+02, atom= 65\n", - "Step= 218, Dmax= 4.9e-03 nm, Epot= -1.72823e+03 Fmax= 2.76009e+02, atom= 65\n", - "Step= 219, Dmax= 5.9e-03 nm, Epot= -1.72989e+03 Fmax= 1.84592e+02, atom= 65\n", - "Step= 221, Dmax= 3.5e-03 nm, Epot= -1.73112e+03 Fmax= 9.15048e+01, atom= 65\n", - "Step= 222, Dmax= 4.3e-03 nm, Epot= -1.73148e+03 Fmax= 2.43456e+02, atom= 65\n", - "Step= 223, Dmax= 5.1e-03 nm, Epot= -1.73290e+03 Fmax= 1.56505e+02, atom= 65\n", - "Step= 225, Dmax= 3.1e-03 nm, Epot= -1.73389e+03 Fmax= 8.39731e+01, atom= 65\n", - "Step= 226, Dmax= 3.7e-03 nm, Epot= -1.73434e+03 Fmax= 1.99155e+02, atom= 65\n", - "Step= 227, Dmax= 4.4e-03 nm, Epot= -1.73537e+03 Fmax= 1.47313e+02, atom= 65\n", - "Step= 229, Dmax= 2.6e-03 nm, Epot= -1.73627e+03 Fmax= 5.81890e+01, atom= 59\n", - "Step= 230, Dmax= 3.2e-03 nm, Epot= -1.73677e+03 Fmax= 1.95169e+02, atom= 65\n", - "Step= 231, Dmax= 3.8e-03 nm, Epot= -1.73789e+03 Fmax= 1.01485e+02, atom= 65\n", - "Step= 233, Dmax= 2.3e-03 nm, Epot= -1.73851e+03 Fmax= 8.04922e+01, atom= 65\n", - "Step= 234, Dmax= 2.7e-03 nm, Epot= -1.73895e+03 Fmax= 1.27947e+02, atom= 65\n", - "Step= 235, Dmax= 3.3e-03 nm, Epot= -1.73946e+03 Fmax= 1.33032e+02, atom= 65\n", - "Step= 236, Dmax= 4.0e-03 nm, Epot= -1.73967e+03 Fmax= 1.71057e+02, atom= 65\n", - "Step= 237, Dmax= 4.7e-03 nm, Epot= -1.73986e+03 Fmax= 2.03708e+02, atom= 65\n", - "Step= 238, Dmax= 5.7e-03 nm, Epot= -1.73986e+03 Fmax= 2.36179e+02, atom= 65\n", - "Step= 240, Dmax= 3.4e-03 nm, Epot= -1.74177e+03 Fmax= 4.15057e+01, atom= 59\n", - "Step= 241, Dmax= 4.1e-03 nm, Epot= -1.74187e+03 Fmax= 2.32512e+02, atom= 80\n", - "Step= 242, Dmax= 4.9e-03 nm, Epot= -1.74305e+03 Fmax= 1.67802e+02, atom= 80\n", - "Step= 244, Dmax= 3.0e-03 nm, Epot= -1.74397e+03 Fmax= 6.03771e+01, atom= 94\n", - "Step= 246, Dmax= 1.8e-03 nm, Epot= -1.74432e+03 Fmax= 8.91181e+01, atom= 80\n", - "Step= 247, Dmax= 2.1e-03 nm, Epot= -1.74471e+03 Fmax= 7.21345e+01, atom= 80\n", - "Step= 248, Dmax= 2.6e-03 nm, Epot= -1.74489e+03 Fmax= 1.40228e+02, atom= 80\n", - "Step= 249, Dmax= 3.1e-03 nm, Epot= -1.74542e+03 Fmax= 9.65080e+01, atom= 80\n", - "Step= 251, Dmax= 1.8e-03 nm, Epot= -1.74586e+03 Fmax= 5.76928e+01, atom= 80\n", - "Step= 252, Dmax= 2.2e-03 nm, Epot= -1.74618e+03 Fmax= 1.04045e+02, atom= 80\n", - "Step= 253, Dmax= 2.6e-03 nm, Epot= -1.74650e+03 Fmax= 1.14614e+02, atom= 80\n", - "Step= 254, Dmax= 3.2e-03 nm, Epot= -1.74675e+03 Fmax= 1.30348e+02, atom= 80\n", - "Step= 255, Dmax= 3.8e-03 nm, Epot= -1.74683e+03 Fmax= 1.81353e+02, atom= 80\n", - "Step= 256, Dmax= 4.6e-03 nm, Epot= -1.74716e+03 Fmax= 1.76935e+02, atom= 80\n", - "Step= 258, Dmax= 2.7e-03 nm, Epot= -1.74798e+03 Fmax= 5.10490e+01, atom= 80\n", - "Step= 259, Dmax= 3.3e-03 nm, Epot= -1.74815e+03 Fmax= 1.88293e+02, atom= 80\n", - "Step= 260, Dmax= 3.9e-03 nm, Epot= -1.74875e+03 Fmax= 1.35292e+02, atom= 80\n", - "Step= 262, Dmax= 2.4e-03 nm, Epot= -1.74924e+03 Fmax= 5.20099e+01, atom= 94\n", - "Step= 263, Dmax= 2.8e-03 nm, Epot= -1.74940e+03 Fmax= 1.76078e+02, atom= 80\n", - "Step= 264, Dmax= 3.4e-03 nm, Epot= -1.75002e+03 Fmax= 9.18823e+01, atom= 80\n", - "Step= 266, Dmax= 2.0e-03 nm, Epot= -1.75035e+03 Fmax= 7.99091e+01, atom= 80\n", - "Step= 267, Dmax= 2.5e-03 nm, Epot= -1.75060e+03 Fmax= 1.08156e+02, atom= 80\n", - "Step= 268, Dmax= 2.9e-03 nm, Epot= -1.75084e+03 Fmax= 1.36140e+02, atom= 80\n", - "Step= 269, Dmax= 3.5e-03 nm, Epot= -1.75110e+03 Fmax= 1.41605e+02, atom= 80\n", - "Step= 271, Dmax= 2.1e-03 nm, Epot= -1.75162e+03 Fmax= 3.73844e+01, atom= 80\n", - "Step= 272, Dmax= 2.5e-03 nm, Epot= -1.75213e+03 Fmax= 1.40692e+02, atom= 80\n", - "Step= 273, Dmax= 3.1e-03 nm, Epot= -1.75253e+03 Fmax= 1.12604e+02, atom= 80\n", - "Step= 274, Dmax= 3.7e-03 nm, Epot= -1.75260e+03 Fmax= 1.76181e+02, atom= 80\n", - "Step= 275, Dmax= 4.4e-03 nm, Epot= -1.75286e+03 Fmax= 1.85809e+02, atom= 80\n", - "Step= 277, Dmax= 2.6e-03 nm, Epot= -1.75358e+03 Fmax= 3.03199e+01, atom= 94\n", - "Step= 278, Dmax= 3.2e-03 nm, Epot= -1.75428e+03 Fmax= 1.86278e+02, atom= 80\n", - "Step= 279, Dmax= 3.8e-03 nm, Epot= -1.75487e+03 Fmax= 1.19407e+02, atom= 80\n", - "Step= 281, Dmax= 2.3e-03 nm, Epot= -1.75528e+03 Fmax= 7.31812e+01, atom= 80\n", - "Step= 282, Dmax= 2.7e-03 nm, Epot= -1.75551e+03 Fmax= 1.38715e+02, atom= 80\n", - "Step= 283, Dmax= 3.3e-03 nm, Epot= -1.75584e+03 Fmax= 1.35888e+02, atom= 80\n", - "Step= 284, Dmax= 3.9e-03 nm, Epot= -1.75597e+03 Fmax= 1.79115e+02, atom= 80\n", - "Step= 285, Dmax= 4.7e-03 nm, Epot= -1.75611e+03 Fmax= 2.12816e+02, atom= 80\n", - "Step= 286, Dmax= 5.7e-03 nm, Epot= -1.75621e+03 Fmax= 2.46678e+02, atom= 80\n", - "Step= 288, Dmax= 3.4e-03 nm, Epot= -1.75735e+03 Fmax= 4.35506e+01, atom= 80\n", - "Step= 289, Dmax= 4.1e-03 nm, Epot= -1.75764e+03 Fmax= 2.55520e+02, atom= 80\n", - "Step= 290, Dmax= 4.9e-03 nm, Epot= -1.75852e+03 Fmax= 1.54277e+02, atom= 80\n", - "Step= 292, Dmax= 2.9e-03 nm, Epot= -1.75904e+03 Fmax= 8.29253e+01, atom= 94\n", - "Step= 293, Dmax= 3.5e-03 nm, Epot= -1.75905e+03 Fmax= 2.08779e+02, atom= 80\n", - "Step= 294, Dmax= 4.2e-03 nm, Epot= -1.75973e+03 Fmax= 1.33541e+02, atom= 94\n", - "Step= 296, Dmax= 2.5e-03 nm, Epot= -1.76021e+03 Fmax= 8.37206e+01, atom= 80\n", - "Step= 297, Dmax= 3.1e-03 nm, Epot= -1.76043e+03 Fmax= 1.57650e+02, atom= 94\n", - "Step= 298, Dmax= 3.7e-03 nm, Epot= -1.76083e+03 Fmax= 1.50947e+02, atom= 80\n", - "Step= 299, Dmax= 4.4e-03 nm, Epot= -1.76093e+03 Fmax= 2.06243e+02, atom= 80\n", - "Step= 300, Dmax= 5.3e-03 nm, Epot= -1.76112e+03 Fmax= 2.34984e+02, atom= 80\n", - "Step= 301, Dmax= 6.3e-03 nm, Epot= -1.76112e+03 Fmax= 2.86036e+02, atom= 80\n", - "Step= 303, Dmax= 3.8e-03 nm, Epot= -1.76260e+03 Fmax= 4.27467e+01, atom= 80\n", - "Step= 304, Dmax= 4.6e-03 nm, Epot= -1.76305e+03 Fmax= 2.94402e+02, atom= 94\n", - "Step= 305, Dmax= 5.5e-03 nm, Epot= -1.76417e+03 Fmax= 1.67546e+02, atom= 80\n", - "Step= 307, Dmax= 3.3e-03 nm, Epot= -1.76475e+03 Fmax= 1.00350e+02, atom= 94\n", - "Step= 309, Dmax= 2.0e-03 nm, Epot= -1.76517e+03 Fmax= 6.91986e+01, atom= 80\n", - "Step= 310, Dmax= 2.4e-03 nm, Epot= -1.76558e+03 Fmax= 1.20130e+02, atom= 94\n", - "Step= 311, Dmax= 2.8e-03 nm, Epot= -1.76598e+03 Fmax= 1.20165e+02, atom= 80\n", - "Step= 312, Dmax= 3.4e-03 nm, Epot= -1.76628e+03 Fmax= 1.59300e+02, atom= 94\n", - "Step= 313, Dmax= 4.1e-03 nm, Epot= -1.76657e+03 Fmax= 1.85532e+02, atom= 80\n", - "Step= 314, Dmax= 4.9e-03 nm, Epot= -1.76680e+03 Fmax= 2.20684e+02, atom= 94\n", - "Step= 315, Dmax= 5.9e-03 nm, Epot= -1.76681e+03 Fmax= 2.74426e+02, atom= 80\n", - "Step= 316, Dmax= 7.0e-03 nm, Epot= -1.76691e+03 Fmax= 3.14860e+02, atom= 94\n", - "Step= 318, Dmax= 4.2e-03 nm, Epot= -1.76869e+03 Fmax= 5.57988e+01, atom= 80\n", - "Step= 319, Dmax= 5.1e-03 nm, Epot= -1.76872e+03 Fmax= 3.44266e+02, atom= 94\n", - "Step= 320, Dmax= 6.1e-03 nm, Epot= -1.77022e+03 Fmax= 1.76829e+02, atom= 80\n", - "Step= 322, Dmax= 3.7e-03 nm, Epot= -1.77083e+03 Fmax= 1.26146e+02, atom= 94\n", - "Step= 324, Dmax= 2.2e-03 nm, Epot= -1.77135e+03 Fmax= 6.51935e+01, atom= 80\n", - "Step= 325, Dmax= 2.6e-03 nm, Epot= -1.77184e+03 Fmax= 1.47039e+02, atom= 94\n", - "Step= 326, Dmax= 3.2e-03 nm, Epot= -1.77235e+03 Fmax= 1.23268e+02, atom= 80\n", - "Step= 327, Dmax= 3.8e-03 nm, Epot= -1.77259e+03 Fmax= 1.93876e+02, atom= 94\n", - "Step= 328, Dmax= 4.5e-03 nm, Epot= -1.77304e+03 Fmax= 1.94069e+02, atom= 80\n", - "Step= 329, Dmax= 5.5e-03 nm, Epot= -1.77307e+03 Fmax= 2.67682e+02, atom= 94\n", - "Step= 330, Dmax= 6.5e-03 nm, Epot= -1.77331e+03 Fmax= 2.89155e+02, atom= 80\n", - "Step= 332, Dmax= 3.9e-03 nm, Epot= -1.77491e+03 Fmax= 3.91085e+01, atom= 94\n", - "Step= 333, Dmax= 4.7e-03 nm, Epot= -1.77533e+03 Fmax= 3.31564e+02, atom= 80\n", - "Step= 334, Dmax= 5.7e-03 nm, Epot= -1.77731e+03 Fmax= 1.63203e+02, atom= 94\n", - "Step= 336, Dmax= 3.4e-03 nm, Epot= -1.77789e+03 Fmax= 1.28061e+02, atom= 80\n", - "Step= 337, Dmax= 4.1e-03 nm, Epot= -1.77807e+03 Fmax= 2.20862e+02, atom= 94\n", - "Step= 338, Dmax= 4.9e-03 nm, Epot= -1.77865e+03 Fmax= 1.99452e+02, atom= 80\n", - "Step= 340, Dmax= 2.9e-03 nm, Epot= -1.77954e+03 Fmax= 4.95994e+01, atom= 94\n", - "Step= 341, Dmax= 3.5e-03 nm, Epot= -1.78015e+03 Fmax= 2.37474e+02, atom= 80\n", - "Step= 342, Dmax= 4.2e-03 nm, Epot= -1.78122e+03 Fmax= 1.26553e+02, atom= 94\n", - "Step= 344, Dmax= 2.5e-03 nm, Epot= -1.78176e+03 Fmax= 9.38963e+01, atom= 80\n", - "Step= 345, Dmax= 3.0e-03 nm, Epot= -1.78217e+03 Fmax= 1.64874e+02, atom= 94\n", - "Step= 346, Dmax= 3.6e-03 nm, Epot= -1.78271e+03 Fmax= 1.50207e+02, atom= 80\n", - "Step= 347, Dmax= 4.4e-03 nm, Epot= -1.78290e+03 Fmax= 2.26860e+02, atom= 94\n", - "Step= 348, Dmax= 5.3e-03 nm, Epot= -1.78337e+03 Fmax= 2.26253e+02, atom= 80\n", - "Step= 350, Dmax= 3.2e-03 nm, Epot= -1.78443e+03 Fmax= 4.25156e+01, atom= 94\n", - "Step= 351, Dmax= 3.8e-03 nm, Epot= -1.78520e+03 Fmax= 2.60945e+02, atom= 80\n", - "Step= 352, Dmax= 4.5e-03 nm, Epot= -1.78645e+03 Fmax= 1.35998e+02, atom= 94\n", - "Step= 354, Dmax= 2.7e-03 nm, Epot= -1.78699e+03 Fmax= 1.02894e+02, atom= 80\n", - "Step= 355, Dmax= 3.3e-03 nm, Epot= -1.78736e+03 Fmax= 1.77904e+02, atom= 94\n", - "Step= 356, Dmax= 3.9e-03 nm, Epot= -1.78789e+03 Fmax= 1.64462e+02, atom= 80\n", - "Step= 357, Dmax= 4.7e-03 nm, Epot= -1.78803e+03 Fmax= 2.43316e+02, atom= 94\n", - "Step= 358, Dmax= 5.6e-03 nm, Epot= -1.78845e+03 Fmax= 2.48512e+02, atom= 80\n", - "Step= 360, Dmax= 3.4e-03 nm, Epot= -1.78965e+03 Fmax= 4.07283e+01, atom= 94\n", - "Step= 361, Dmax= 4.1e-03 nm, Epot= -1.79033e+03 Fmax= 2.95734e+02, atom= 80\n", - "Step= 362, Dmax= 4.9e-03 nm, Epot= -1.79187e+03 Fmax= 1.33302e+02, atom= 94\n", - "Step= 364, Dmax= 2.9e-03 nm, Epot= -1.79236e+03 Fmax= 1.23954e+02, atom= 80\n", - "Step= 365, Dmax= 3.5e-03 nm, Epot= -1.79270e+03 Fmax= 1.80543e+02, atom= 94\n", - "Step= 366, Dmax= 4.2e-03 nm, Epot= -1.79313e+03 Fmax= 1.89348e+02, atom= 80\n", - "Step= 367, Dmax= 5.1e-03 nm, Epot= -1.79330e+03 Fmax= 2.50611e+02, atom= 94\n", - "Step= 368, Dmax= 6.1e-03 nm, Epot= -1.79351e+03 Fmax= 2.80963e+02, atom= 80\n", - "Step= 370, Dmax= 3.6e-03 nm, Epot= -1.79494e+03 Fmax= 3.15234e+01, atom= 68\n", - "Step= 371, Dmax= 4.4e-03 nm, Epot= -1.79602e+03 Fmax= 3.18779e+02, atom= 80\n", - "Step= 372, Dmax= 5.2e-03 nm, Epot= -1.79775e+03 Fmax= 1.52025e+02, atom= 94\n", - "Step= 374, Dmax= 3.1e-03 nm, Epot= -1.79825e+03 Fmax= 1.25696e+02, atom= 80\n", - "Step= 375, Dmax= 3.8e-03 nm, Epot= -1.79847e+03 Fmax= 2.03004e+02, atom= 94\n", - "Step= 376, Dmax= 4.5e-03 nm, Epot= -1.79891e+03 Fmax= 1.98942e+02, atom= 80\n", - "Step= 377, Dmax= 5.4e-03 nm, Epot= -1.79892e+03 Fmax= 2.76158e+02, atom= 94\n", - "Step= 378, Dmax= 6.5e-03 nm, Epot= -1.79912e+03 Fmax= 3.00731e+02, atom= 80\n", - "Step= 380, Dmax= 3.9e-03 nm, Epot= -1.80066e+03 Fmax= 3.47886e+01, atom= 94\n", - "Step= 381, Dmax= 4.7e-03 nm, Epot= -1.80102e+03 Fmax= 3.61736e+02, atom= 80\n", - "Step= 382, Dmax= 5.6e-03 nm, Epot= -1.80319e+03 Fmax= 1.45041e+02, atom= 94\n", - "Step= 384, Dmax= 3.4e-03 nm, Epot= -1.80357e+03 Fmax= 1.52590e+02, atom= 80\n", - "Step= 385, Dmax= 4.1e-03 nm, Epot= -1.80380e+03 Fmax= 2.03014e+02, atom= 94\n", - "Step= 386, Dmax= 4.9e-03 nm, Epot= -1.80405e+03 Fmax= 2.30176e+02, atom= 80\n", - "Step= 387, Dmax= 5.8e-03 nm, Epot= -1.80415e+03 Fmax= 2.82005e+02, atom= 94\n", - "Step= 389, Dmax= 3.5e-03 nm, Epot= -1.80545e+03 Fmax= 4.36180e+01, atom= 80\n", - "Step= 390, Dmax= 4.2e-03 nm, Epot= -1.80619e+03 Fmax= 2.83402e+02, atom= 94\n", - "Step= 391, Dmax= 5.1e-03 nm, Epot= -1.80713e+03 Fmax= 1.71959e+02, atom= 80\n", - "Step= 393, Dmax= 3.0e-03 nm, Epot= -1.80772e+03 Fmax= 9.10157e+01, atom= 94\n", - "Step= 394, Dmax= 3.6e-03 nm, Epot= -1.80781e+03 Fmax= 2.29411e+02, atom= 80\n", - "Step= 395, Dmax= 4.4e-03 nm, Epot= -1.80856e+03 Fmax= 1.50618e+02, atom= 94\n", - "Step= 397, Dmax= 2.6e-03 nm, Epot= -1.80908e+03 Fmax= 8.92157e+01, atom= 80\n", - "Step= 398, Dmax= 3.1e-03 nm, Epot= -1.80937e+03 Fmax= 1.78434e+02, atom= 94\n", - "Step= 399, Dmax= 3.8e-03 nm, Epot= -1.80983e+03 Fmax= 1.61706e+02, atom= 80\n", - "Step= 400, Dmax= 4.5e-03 nm, Epot= -1.80994e+03 Fmax= 2.31608e+02, atom= 80\n", - "Step= 401, Dmax= 5.4e-03 nm, Epot= -1.81019e+03 Fmax= 2.55573e+02, atom= 80\n", - "Step= 402, Dmax= 6.5e-03 nm, Epot= -1.81019e+03 Fmax= 3.17516e+02, atom= 80\n", - "Step= 404, Dmax= 3.9e-03 nm, Epot= -1.81172e+03 Fmax= 4.73731e+01, atom= 80\n", - "Step= 405, Dmax= 4.7e-03 nm, Epot= -1.81227e+03 Fmax= 3.20210e+02, atom= 80\n", - "Step= 406, Dmax= 5.6e-03 nm, Epot= -1.81336e+03 Fmax= 1.89319e+02, atom= 80\n", - "Step= 408, Dmax= 3.4e-03 nm, Epot= -1.81400e+03 Fmax= 1.03325e+02, atom= 94\n", - "Step= 410, Dmax= 2.0e-03 nm, Epot= -1.81442e+03 Fmax= 8.28590e+01, atom= 80\n", - "Step= 411, Dmax= 2.4e-03 nm, Epot= -1.81483e+03 Fmax= 1.24045e+02, atom= 94\n", - "Step= 412, Dmax= 2.9e-03 nm, Epot= -1.81521e+03 Fmax= 1.39555e+02, atom= 80\n", - "Step= 413, Dmax= 3.5e-03 nm, Epot= -1.81556e+03 Fmax= 1.63175e+02, atom= 94\n", - "Step= 414, Dmax= 4.2e-03 nm, Epot= -1.81578e+03 Fmax= 2.14659e+02, atom= 80\n", - "Step= 415, Dmax= 5.0e-03 nm, Epot= -1.81615e+03 Fmax= 2.24732e+02, atom= 80\n", - "Step= 417, Dmax= 3.0e-03 nm, Epot= -1.81704e+03 Fmax= 5.61231e+01, atom= 80\n", - "Step= 418, Dmax= 3.6e-03 nm, Epot= -1.81757e+03 Fmax= 2.36001e+02, atom= 80\n", - "Step= 419, Dmax= 4.4e-03 nm, Epot= -1.81831e+03 Fmax= 1.59013e+02, atom= 80\n", - "Step= 421, Dmax= 2.6e-03 nm, Epot= -1.81888e+03 Fmax= 6.84069e+01, atom= 94\n", - "Step= 422, Dmax= 3.1e-03 nm, Epot= -1.81925e+03 Fmax= 2.05728e+02, atom= 80\n", - "Step= 423, Dmax= 3.8e-03 nm, Epot= -1.81997e+03 Fmax= 1.21486e+02, atom= 94\n", - "Step= 425, Dmax= 2.3e-03 nm, Epot= -1.82044e+03 Fmax= 8.62634e+01, atom= 80\n", - "Step= 426, Dmax= 2.7e-03 nm, Epot= -1.82087e+03 Fmax= 1.42481e+02, atom= 94\n", - "Step= 427, Dmax= 3.3e-03 nm, Epot= -1.82129e+03 Fmax= 1.51899e+02, atom= 80\n", - "Step= 428, Dmax= 3.9e-03 nm, Epot= -1.82163e+03 Fmax= 1.84924e+02, atom= 80\n", - "Step= 429, Dmax= 4.7e-03 nm, Epot= -1.82186e+03 Fmax= 2.35360e+02, atom= 80\n", - "Step= 430, Dmax= 5.6e-03 nm, Epot= -1.82221e+03 Fmax= 2.54829e+02, atom= 80\n", - "Step= 432, Dmax= 3.4e-03 nm, Epot= -1.82329e+03 Fmax= 5.79886e+01, atom= 80\n", - "Step= 433, Dmax= 4.0e-03 nm, Epot= -1.82384e+03 Fmax= 2.67259e+02, atom= 80\n", - "Step= 434, Dmax= 4.9e-03 nm, Epot= -1.82472e+03 Fmax= 1.71413e+02, atom= 80\n", - "Step= 436, Dmax= 2.9e-03 nm, Epot= -1.82536e+03 Fmax= 7.98972e+01, atom= 94\n", - "Step= 437, Dmax= 3.5e-03 nm, Epot= -1.82567e+03 Fmax= 2.28409e+02, atom= 80\n", - "Step= 438, Dmax= 4.2e-03 nm, Epot= -1.82650e+03 Fmax= 1.32985e+02, atom= 80\n", - "Step= 440, Dmax= 2.5e-03 nm, Epot= -1.82702e+03 Fmax= 9.76965e+01, atom= 80\n", - "Step= 441, Dmax= 3.0e-03 nm, Epot= -1.82746e+03 Fmax= 1.57616e+02, atom= 80\n", - "Step= 442, Dmax= 3.6e-03 nm, Epot= -1.82792e+03 Fmax= 1.68451e+02, atom= 80\n", - "Step= 443, Dmax= 4.3e-03 nm, Epot= -1.82827e+03 Fmax= 2.07622e+02, atom= 80\n", - "Step= 444, Dmax= 5.2e-03 nm, Epot= -1.82852e+03 Fmax= 2.55624e+02, atom= 80\n", - "Step= 445, Dmax= 6.3e-03 nm, Epot= -1.82883e+03 Fmax= 2.90471e+02, atom= 80\n", - "Step= 447, Dmax= 3.8e-03 nm, Epot= -1.83014e+03 Fmax= 5.66583e+01, atom= 80\n", - "Step= 448, Dmax= 4.5e-03 nm, Epot= -1.83078e+03 Fmax= 3.03551e+02, atom= 80\n", - "Step= 449, Dmax= 5.4e-03 nm, Epot= -1.83186e+03 Fmax= 1.81349e+02, atom= 80\n", - "Step= 451, Dmax= 3.2e-03 nm, Epot= -1.83254e+03 Fmax= 9.53221e+01, atom= 80\n", - "Step= 452, Dmax= 3.9e-03 nm, Epot= -1.83273e+03 Fmax= 2.48749e+02, atom= 80\n", - "Step= 453, Dmax= 4.7e-03 nm, Epot= -1.83365e+03 Fmax= 1.52258e+02, atom= 80\n", - "Step= 455, Dmax= 2.8e-03 nm, Epot= -1.83424e+03 Fmax= 1.01018e+02, atom= 80\n", - "Step= 456, Dmax= 3.4e-03 nm, Epot= -1.83465e+03 Fmax= 1.83992e+02, atom= 80\n", - "Step= 457, Dmax= 4.0e-03 nm, Epot= -1.83517e+03 Fmax= 1.74041e+02, atom= 80\n", - "Step= 458, Dmax= 4.8e-03 nm, Epot= -1.83540e+03 Fmax= 2.45168e+02, atom= 80\n", - "Step= 459, Dmax= 5.8e-03 nm, Epot= -1.83576e+03 Fmax= 2.63910e+02, atom= 80\n", - "Step= 460, Dmax= 7.0e-03 nm, Epot= -1.83579e+03 Fmax= 3.44424e+02, atom= 80\n", - "Step= 461, Dmax= 8.4e-03 nm, Epot= -1.83580e+03 Fmax= 3.81364e+02, atom= 80\n", - "Step= 463, Dmax= 5.0e-03 nm, Epot= -1.83803e+03 Fmax= 4.23540e+01, atom= 68\n", - "Step= 464, Dmax= 6.0e-03 nm, Epot= -1.83848e+03 Fmax= 4.17138e+02, atom= 80\n", - "Step= 465, Dmax= 7.2e-03 nm, Epot= -1.84087e+03 Fmax= 2.19194e+02, atom= 80\n", - "Step= 467, Dmax= 4.3e-03 nm, Epot= -1.84154e+03 Fmax= 1.59405e+02, atom= 80\n", - "Step= 469, Dmax= 2.6e-03 nm, Epot= -1.84216e+03 Fmax= 6.27535e+01, atom= 80\n", - "Step= 470, Dmax= 3.1e-03 nm, Epot= -1.84272e+03 Fmax= 2.00178e+02, atom= 80\n", - "Step= 471, Dmax= 3.8e-03 nm, Epot= -1.84345e+03 Fmax= 1.19255e+02, atom= 80\n", - "Step= 472, Dmax= 4.5e-03 nm, Epot= -1.84349e+03 Fmax= 2.61373e+02, atom= 80\n", - "Step= 473, Dmax= 5.4e-03 nm, Epot= -1.84433e+03 Fmax= 1.98353e+02, atom= 80\n", - "Step= 475, Dmax= 3.2e-03 nm, Epot= -1.84507e+03 Fmax= 8.63373e+01, atom= 80\n", - "Step= 476, Dmax= 3.9e-03 nm, Epot= -1.84536e+03 Fmax= 2.42891e+02, atom= 80\n", - "Step= 477, Dmax= 4.7e-03 nm, Epot= -1.84614e+03 Fmax= 1.59814e+02, atom= 80\n", - "Step= 479, Dmax= 2.8e-03 nm, Epot= -1.84675e+03 Fmax= 7.66918e+01, atom= 80\n", - "Step= 480, Dmax= 3.4e-03 nm, Epot= -1.84716e+03 Fmax= 2.01635e+02, atom= 80\n", - "Step= 481, Dmax= 4.0e-03 nm, Epot= -1.84786e+03 Fmax= 1.40153e+02, atom= 80\n", - "Step= 483, Dmax= 2.4e-03 nm, Epot= -1.84839e+03 Fmax= 6.96273e+01, atom= 80\n", - "Step= 484, Dmax= 2.9e-03 nm, Epot= -1.84891e+03 Fmax= 1.73185e+02, atom= 80\n", - "Step= 485, Dmax= 3.5e-03 nm, Epot= -1.84948e+03 Fmax= 1.23526e+02, atom= 80\n", - "Step= 486, Dmax= 4.2e-03 nm, Epot= -1.84968e+03 Fmax= 2.34336e+02, atom= 80\n", - "Step= 487, Dmax= 5.0e-03 nm, Epot= -1.85030e+03 Fmax= 1.89255e+02, atom= 80\n", - "Step= 489, Dmax= 3.0e-03 nm, Epot= -1.85104e+03 Fmax= 6.32265e+01, atom= 80\n", - "Step= 490, Dmax= 3.6e-03 nm, Epot= -1.85153e+03 Fmax= 2.22300e+02, atom= 80\n", - "Step= 491, Dmax= 4.3e-03 nm, Epot= -1.85235e+03 Fmax= 1.43259e+02, atom= 80\n", - "Step= 493, Dmax= 2.6e-03 nm, Epot= -1.85288e+03 Fmax= 7.67165e+01, atom= 80\n", - "Step= 494, Dmax= 3.1e-03 nm, Epot= -1.85331e+03 Fmax= 1.87241e+02, atom= 80\n", - "Step= 495, Dmax= 3.7e-03 nm, Epot= -1.85392e+03 Fmax= 1.25716e+02, atom= 80\n", - "Step= 496, Dmax= 4.5e-03 nm, Epot= -1.85400e+03 Fmax= 2.58745e+02, atom= 80\n", - "Step= 497, Dmax= 5.4e-03 nm, Epot= -1.85473e+03 Fmax= 1.89945e+02, atom= 80\n", - "Step= 499, Dmax= 3.2e-03 nm, Epot= -1.85548e+03 Fmax= 7.92876e+01, atom= 80\n", - "Step= 500, Dmax= 3.9e-03 nm, Epot= -1.85578e+03 Fmax= 2.23888e+02, atom= 80\n", - "Step= 501, Dmax= 4.7e-03 nm, Epot= -1.85654e+03 Fmax= 1.65683e+02, atom= 80\n", - "Step= 503, Dmax= 2.8e-03 nm, Epot= -1.85715e+03 Fmax= 6.78244e+01, atom= 80\n", - "Step= 504, Dmax= 3.4e-03 nm, Epot= -1.85759e+03 Fmax= 2.14056e+02, atom= 80\n", - "Step= 505, Dmax= 4.0e-03 nm, Epot= -1.85832e+03 Fmax= 1.17915e+02, atom= 80\n", - "Step= 507, Dmax= 2.4e-03 nm, Epot= -1.85882e+03 Fmax= 8.50859e+01, atom= 80\n", - "Step= 508, Dmax= 2.9e-03 nm, Epot= -1.85928e+03 Fmax= 1.40423e+02, atom= 80\n", - "Step= 509, Dmax= 3.5e-03 nm, Epot= -1.85974e+03 Fmax= 1.51169e+02, atom= 80\n", - "Step= 510, Dmax= 4.2e-03 nm, Epot= -1.86009e+03 Fmax= 1.80443e+02, atom= 80\n", - "Step= 511, Dmax= 5.0e-03 nm, Epot= -1.86038e+03 Fmax= 2.38707e+02, atom= 80\n", - "Step= 512, Dmax= 6.0e-03 nm, Epot= -1.86073e+03 Fmax= 2.41644e+02, atom= 80\n", - "Step= 514, Dmax= 3.6e-03 nm, Epot= -1.86183e+03 Fmax= 5.26862e+01, atom= 80\n", - "Step= 515, Dmax= 4.3e-03 nm, Epot= -1.86255e+03 Fmax= 2.46202e+02, atom= 80\n", - "Step= 516, Dmax= 5.2e-03 nm, Epot= -1.86345e+03 Fmax= 1.81651e+02, atom= 80\n", - "Step= 518, Dmax= 3.1e-03 nm, Epot= -1.86412e+03 Fmax= 6.98732e+01, atom= 80\n", - "Step= 519, Dmax= 3.7e-03 nm, Epot= -1.86451e+03 Fmax= 2.43452e+02, atom= 80\n", - "Step= 520, Dmax= 4.5e-03 nm, Epot= -1.86541e+03 Fmax= 1.16776e+02, atom= 80\n", - "Step= 522, Dmax= 2.7e-03 nm, Epot= -1.86594e+03 Fmax= 1.06046e+02, atom= 80\n", - "Step= 523, Dmax= 3.2e-03 nm, Epot= -1.86640e+03 Fmax= 1.38050e+02, atom= 80\n", - "Step= 524, Dmax= 3.9e-03 nm, Epot= -1.86683e+03 Fmax= 1.82079e+02, atom= 80\n", - "Step= 525, Dmax= 4.7e-03 nm, Epot= -1.86730e+03 Fmax= 1.77157e+02, atom= 80\n", - "Step= 526, Dmax= 5.6e-03 nm, Epot= -1.86739e+03 Fmax= 2.82852e+02, atom= 80\n", - "Step= 527, Dmax= 6.7e-03 nm, Epot= -1.86803e+03 Fmax= 2.38367e+02, atom= 80\n", - "Step= 529, Dmax= 4.0e-03 nm, Epot= -1.86914e+03 Fmax= 8.18101e+01, atom= 80\n", - "Step= 530, Dmax= 4.8e-03 nm, Epot= -1.86942e+03 Fmax= 2.55930e+02, atom= 80\n", - "Step= 531, Dmax= 5.8e-03 nm, Epot= -1.87033e+03 Fmax= 2.08711e+02, atom= 80\n", - "Step= 533, Dmax= 3.5e-03 nm, Epot= -1.87116e+03 Fmax= 6.50171e+01, atom= 80\n", - "Step= 534, Dmax= 4.2e-03 nm, Epot= -1.87161e+03 Fmax= 2.74296e+02, atom= 80\n", - "Step= 535, Dmax= 5.0e-03 nm, Epot= -1.87273e+03 Fmax= 1.15138e+02, atom= 80\n", - "Step= 537, Dmax= 3.0e-03 nm, Epot= -1.87328e+03 Fmax= 1.28963e+02, atom= 80\n", - "Step= 538, Dmax= 3.6e-03 nm, Epot= -1.87379e+03 Fmax= 1.35137e+02, atom= 80\n", - "Step= 539, Dmax= 4.3e-03 nm, Epot= -1.87418e+03 Fmax= 2.14650e+02, atom= 80\n", - "Step= 540, Dmax= 5.2e-03 nm, Epot= -1.87482e+03 Fmax= 1.73804e+02, atom= 80\n", - "Step= 542, Dmax= 3.1e-03 nm, Epot= -1.87561e+03 Fmax= 7.50648e+01, atom= 80\n", - "Step= 543, Dmax= 3.7e-03 nm, Epot= -1.87630e+03 Fmax= 1.70706e+02, atom= 80\n", - "Step= 544, Dmax= 4.5e-03 nm, Epot= -1.87689e+03 Fmax= 1.85770e+02, atom= 80\n", - "Step= 545, Dmax= 5.4e-03 nm, Epot= -1.87730e+03 Fmax= 2.05719e+02, atom= 80\n", - "Step= 546, Dmax= 6.5e-03 nm, Epot= -1.87745e+03 Fmax= 3.04940e+02, atom= 80\n", - "Step= 547, Dmax= 7.7e-03 nm, Epot= -1.87809e+03 Fmax= 2.67408e+02, atom= 80\n", - "Step= 549, Dmax= 4.6e-03 nm, Epot= -1.87950e+03 Fmax= 8.78489e+01, atom= 80\n", - "Step= 550, Dmax= 5.6e-03 nm, Epot= -1.87977e+03 Fmax= 2.76585e+02, atom= 80\n", - "Step= 551, Dmax= 6.7e-03 nm, Epot= -1.88078e+03 Fmax= 2.39562e+02, atom= 80\n", - "Step= 553, Dmax= 4.0e-03 nm, Epot= -1.88184e+03 Fmax= 6.45684e+01, atom= 94\n", - "Step= 554, Dmax= 4.8e-03 nm, Epot= -1.88235e+03 Fmax= 3.06411e+02, atom= 80\n", - "Step= 555, Dmax= 5.8e-03 nm, Epot= -1.88373e+03 Fmax= 1.23523e+02, atom= 80\n", - "Step= 557, Dmax= 3.5e-03 nm, Epot= -1.88433e+03 Fmax= 1.46191e+02, atom= 80\n", - "Step= 558, Dmax= 4.2e-03 nm, Epot= -1.88489e+03 Fmax= 1.44182e+02, atom= 80\n", - "Step= 559, Dmax= 5.0e-03 nm, Epot= -1.88521e+03 Fmax= 2.41718e+02, atom= 80\n", - "Step= 560, Dmax= 6.0e-03 nm, Epot= -1.88597e+03 Fmax= 1.84754e+02, atom= 80\n", - "Step= 562, Dmax= 3.6e-03 nm, Epot= -1.88686e+03 Fmax= 8.89188e+01, atom= 80\n", - "Step= 563, Dmax= 4.3e-03 nm, Epot= -1.88745e+03 Fmax= 1.83771e+02, atom= 80\n", - "Step= 564, Dmax= 5.2e-03 nm, Epot= -1.88804e+03 Fmax= 2.08128e+02, atom= 80\n", - "Step= 565, Dmax= 6.2e-03 nm, Epot= -1.88847e+03 Fmax= 2.21580e+02, atom= 80\n", - "Step= 567, Dmax= 3.7e-03 nm, Epot= -1.88961e+03 Fmax= 6.09289e+01, atom= 80\n", - "Step= 568, Dmax= 4.5e-03 nm, Epot= -1.89069e+03 Fmax= 1.79435e+02, atom= 80\n", - "Step= 569, Dmax= 5.4e-03 nm, Epot= -1.89119e+03 Fmax= 2.23044e+02, atom= 80\n", - "Step= 570, Dmax= 6.4e-03 nm, Epot= -1.89168e+03 Fmax= 2.18898e+02, atom= 80\n", - "Step= 572, Dmax= 3.9e-03 nm, Epot= -1.89281e+03 Fmax= 6.88319e+01, atom= 80\n", - "Step= 573, Dmax= 4.6e-03 nm, Epot= -1.89364e+03 Fmax= 1.91877e+02, atom= 80\n", - "Step= 574, Dmax= 5.6e-03 nm, Epot= -1.89420e+03 Fmax= 2.17797e+02, atom= 80\n", - "Step= 575, Dmax= 6.7e-03 nm, Epot= -1.89457e+03 Fmax= 2.32782e+02, atom= 80\n", - "Step= 577, Dmax= 4.0e-03 nm, Epot= -1.89582e+03 Fmax= 6.18842e+01, atom= 80\n", - "Step= 578, Dmax= 4.8e-03 nm, Epot= -1.89678e+03 Fmax= 1.91105e+02, atom= 80\n", - "Step= 579, Dmax= 5.8e-03 nm, Epot= -1.89726e+03 Fmax= 2.27435e+02, atom= 80\n", - "Step= 580, Dmax= 6.9e-03 nm, Epot= -1.89763e+03 Fmax= 2.34851e+02, atom= 80\n", - "Step= 582, Dmax= 4.2e-03 nm, Epot= -1.89891e+03 Fmax= 6.49026e+01, atom= 80\n", - "Step= 583, Dmax= 5.0e-03 nm, Epot= -1.89964e+03 Fmax= 2.03357e+02, atom= 80\n", - "Step= 584, Dmax= 6.0e-03 nm, Epot= -1.90017e+03 Fmax= 2.22109e+02, atom= 80\n", - "Step= 585, Dmax= 7.2e-03 nm, Epot= -1.90037e+03 Fmax= 2.49315e+02, atom= 80\n", - "Step= 587, Dmax= 4.3e-03 nm, Epot= -1.90179e+03 Fmax= 5.72050e+01, atom= 80\n", - "Step= 588, Dmax= 5.2e-03 nm, Epot= -1.90260e+03 Fmax= 2.02239e+02, atom= 80\n", - "Step= 589, Dmax= 6.2e-03 nm, Epot= -1.90301e+03 Fmax= 2.31574e+02, atom= 80\n", - "Step= 590, Dmax= 7.4e-03 nm, Epot= -1.90318e+03 Fmax= 2.52859e+02, atom= 80\n", - "Step= 592, Dmax= 4.5e-03 nm, Epot= -1.90466e+03 Fmax= 5.79649e+01, atom= 80\n", - "Step= 593, Dmax= 5.4e-03 nm, Epot= -1.90516e+03 Fmax= 2.19207e+02, atom= 80\n", - "Step= 594, Dmax= 6.4e-03 nm, Epot= -1.90568e+03 Fmax= 2.21179e+02, atom= 80\n", - "Step= 596, Dmax= 3.9e-03 nm, Epot= -1.90678e+03 Fmax= 4.22893e+01, atom= 80\n", - "Step= 597, Dmax= 4.6e-03 nm, Epot= -1.90732e+03 Fmax= 2.38296e+02, atom= 80\n", - "Step= 598, Dmax= 5.6e-03 nm, Epot= -1.90831e+03 Fmax= 1.24856e+02, atom= 80\n", - "Step= 600, Dmax= 3.3e-03 nm, Epot= -1.90879e+03 Fmax= 1.01643e+02, atom= 80\n", - "Step= 601, Dmax= 4.0e-03 nm, Epot= -1.90902e+03 Fmax= 1.43153e+02, atom= 80\n", - "Step= 602, Dmax= 4.8e-03 nm, Epot= -1.90926e+03 Fmax= 1.78307e+02, atom= 80\n", - "Step= 603, Dmax= 5.8e-03 nm, Epot= -1.90949e+03 Fmax= 1.85744e+02, atom= 80\n", - "Step= 605, Dmax= 3.5e-03 nm, Epot= -1.91041e+03 Fmax= 4.80111e+01, atom= 80\n", - "Step= 606, Dmax= 4.1e-03 nm, Epot= -1.91078e+03 Fmax= 1.66292e+02, atom= 80\n", - "Step= 607, Dmax= 5.0e-03 nm, Epot= -1.91118e+03 Fmax= 1.61702e+02, atom= 80\n", - "Step= 609, Dmax= 3.0e-03 nm, Epot= -1.91189e+03 Fmax= 3.61518e+01, atom= 80\n", - "Step= 610, Dmax= 3.6e-03 nm, Epot= -1.91231e+03 Fmax= 1.69479e+02, atom= 80\n", - "Step= 611, Dmax= 4.3e-03 nm, Epot= -1.91291e+03 Fmax= 1.03022e+02, atom= 80\n", - "Step= 613, Dmax= 2.6e-03 nm, Epot= -1.91331e+03 Fmax= 6.70445e+01, atom= 80\n", - "Step= 614, Dmax= 3.1e-03 nm, Epot= -1.91350e+03 Fmax= 1.16016e+02, atom= 80\n", - "Step= 615, Dmax= 3.7e-03 nm, Epot= -1.91378e+03 Fmax= 1.24321e+02, atom= 80\n", - "Step= 616, Dmax= 4.5e-03 nm, Epot= -1.91388e+03 Fmax= 1.50904e+02, atom= 80\n", - "Step= 617, Dmax= 5.4e-03 nm, Epot= -1.91388e+03 Fmax= 1.91850e+02, atom= 80\n", - "Step= 618, Dmax= 6.4e-03 nm, Epot= -1.91394e+03 Fmax= 2.07361e+02, atom= 80\n", - "Step= 620, Dmax= 3.9e-03 nm, Epot= -1.91521e+03 Fmax= 4.03950e+01, atom= 80\n", - "Step= 622, Dmax= 2.3e-03 nm, Epot= -1.91551e+03 Fmax= 8.77072e+01, atom= 80\n", - "Step= 623, Dmax= 2.8e-03 nm, Epot= -1.91579e+03 Fmax= 8.94044e+01, atom= 80\n", - "Step= 624, Dmax= 3.3e-03 nm, Epot= -1.91592e+03 Fmax= 1.14441e+02, atom= 80\n", - "Step= 625, Dmax= 4.0e-03 nm, Epot= -1.91605e+03 Fmax= 1.37937e+02, atom= 80\n", - "Step= 626, Dmax= 4.8e-03 nm, Epot= -1.91610e+03 Fmax= 1.57828e+02, atom= 80\n", - "Step= 628, Dmax= 2.9e-03 nm, Epot= -1.91705e+03 Fmax= 2.85342e+01, atom= 80\n", - "Step= 629, Dmax= 3.5e-03 nm, Epot= -1.91734e+03 Fmax= 1.36322e+02, atom= 80\n", - "Step= 630, Dmax= 4.1e-03 nm, Epot= -1.91772e+03 Fmax= 1.21877e+02, atom= 80\n", - "Step= 632, Dmax= 2.5e-03 nm, Epot= -1.91843e+03 Fmax= 3.93435e+01, atom= 80\n", - "Step= 633, Dmax= 3.0e-03 nm, Epot= -1.91845e+03 Fmax= 1.19798e+02, atom= 80\n", - "Step= 634, Dmax= 3.6e-03 nm, Epot= -1.91885e+03 Fmax= 1.05048e+02, atom= 8\n", - "Step= 636, Dmax= 2.1e-03 nm, Epot= -1.91948e+03 Fmax= 3.03549e+01, atom= 80\n", - "Step= 638, Dmax= 1.3e-03 nm, Epot= -1.91976e+03 Fmax= 6.01867e+01, atom= 8\n", - "Step= 639, Dmax= 1.5e-03 nm, Epot= -1.92003e+03 Fmax= 3.24648e+01, atom= 4\n", - "Step= 640, Dmax= 1.9e-03 nm, Epot= -1.92027e+03 Fmax= 9.38702e+01, atom= 8\n", - "Step= 641, Dmax= 2.2e-03 nm, Epot= -1.92068e+03 Fmax= 4.07342e+01, atom= 8\n", - "Step= 643, Dmax= 1.3e-03 nm, Epot= -1.92094e+03 Fmax= 5.76210e+01, atom= 8\n", - "Step= 644, Dmax= 1.6e-03 nm, Epot= -1.92121e+03 Fmax= 3.55493e+01, atom= 4\n", - "Step= 645, Dmax= 1.9e-03 nm, Epot= -1.92146e+03 Fmax= 9.87100e+01, atom= 8\n", - "Step= 646, Dmax= 2.3e-03 nm, Epot= -1.92186e+03 Fmax= 4.09362e+01, atom= 8\n", - "Step= 648, Dmax= 1.4e-03 nm, Epot= -1.92213e+03 Fmax= 6.09304e+01, atom= 8\n", - "Step= 649, Dmax= 1.7e-03 nm, Epot= -1.92241e+03 Fmax= 3.63382e+01, atom= 4\n", - "Step= 650, Dmax= 2.0e-03 nm, Epot= -1.92267e+03 Fmax= 1.02325e+02, atom= 8\n", - "Step= 651, Dmax= 2.4e-03 nm, Epot= -1.92308e+03 Fmax= 4.25280e+01, atom= 8\n", - "Step= 653, Dmax= 1.4e-03 nm, Epot= -1.92336e+03 Fmax= 6.27646e+01, atom= 8\n", - "Step= 654, Dmax= 1.7e-03 nm, Epot= -1.92364e+03 Fmax= 3.76057e+01, atom= 4\n", - "Step= 655, Dmax= 2.1e-03 nm, Epot= -1.92388e+03 Fmax= 1.07348e+02, atom= 8\n", - "Step= 656, Dmax= 2.5e-03 nm, Epot= -1.92434e+03 Fmax= 4.34368e+01, atom= 8\n", - "Step= 658, Dmax= 1.5e-03 nm, Epot= -1.92463e+03 Fmax= 6.52203e+01, atom= 8\n", - "Step= 659, Dmax= 1.8e-03 nm, Epot= -1.92493e+03 Fmax= 3.92239e+01, atom= 67\n", - "Step= 660, Dmax= 2.1e-03 nm, Epot= -1.92513e+03 Fmax= 1.11688e+02, atom= 8\n", - "Step= 661, Dmax= 2.6e-03 nm, Epot= -1.92566e+03 Fmax= 4.56978e+01, atom= 67\n", - "Step= 663, Dmax= 1.5e-03 nm, Epot= -1.92596e+03 Fmax= 6.59605e+01, atom= 8\n", - "Step= 664, Dmax= 1.9e-03 nm, Epot= -1.92629e+03 Fmax= 4.36022e+01, atom= 67\n", - "Step= 665, Dmax= 2.2e-03 nm, Epot= -1.92643e+03 Fmax= 1.09696e+02, atom= 8\n", - "Step= 666, Dmax= 2.7e-03 nm, Epot= -1.92699e+03 Fmax= 5.57959e+01, atom= 73\n", - "Step= 668, Dmax= 1.6e-03 nm, Epot= -1.92732e+03 Fmax= 5.70265e+01, atom= 83\n", - "Step= 669, Dmax= 1.9e-03 nm, Epot= -1.92763e+03 Fmax= 5.92593e+01, atom= 73\n", - "Step= 670, Dmax= 2.3e-03 nm, Epot= -1.92783e+03 Fmax= 9.53056e+01, atom= 73\n", - "Step= 671, Dmax= 2.8e-03 nm, Epot= -1.92822e+03 Fmax= 8.32827e+01, atom= 73\n", - "Step= 673, Dmax= 1.7e-03 nm, Epot= -1.92870e+03 Fmax= 3.60473e+01, atom= 43\n", - "Step= 674, Dmax= 2.0e-03 nm, Epot= -1.92916e+03 Fmax= 6.66725e+01, atom= 73\n", - "Step= 675, Dmax= 2.4e-03 nm, Epot= -1.92942e+03 Fmax= 9.33698e+01, atom= 73\n", - "Step= 676, Dmax= 2.9e-03 nm, Epot= -1.92975e+03 Fmax= 9.16722e+01, atom= 73\n", - "Step= 677, Dmax= 3.4e-03 nm, Epot= -1.92982e+03 Fmax= 1.37834e+02, atom= 73\n", - "Step= 678, Dmax= 4.1e-03 nm, Epot= -1.93021e+03 Fmax= 1.30635e+02, atom= 73\n", - "Step= 680, Dmax= 2.5e-03 nm, Epot= -1.93099e+03 Fmax= 3.64143e+01, atom= 43\n", - "Step= 681, Dmax= 3.0e-03 nm, Epot= -1.93129e+03 Fmax= 1.41812e+02, atom= 73\n", - "Step= 682, Dmax= 3.6e-03 nm, Epot= -1.93195e+03 Fmax= 9.45319e+01, atom= 73\n", - "Step= 684, Dmax= 2.1e-03 nm, Epot= -1.93242e+03 Fmax= 4.35319e+01, atom= 45\n", - "Step= 685, Dmax= 2.6e-03 nm, Epot= -1.93263e+03 Fmax= 1.30327e+02, atom= 73\n", - "Step= 686, Dmax= 3.1e-03 nm, Epot= -1.93326e+03 Fmax= 7.01076e+01, atom= 73\n", - "Step= 688, Dmax= 1.8e-03 nm, Epot= -1.93363e+03 Fmax= 5.48650e+01, atom= 73\n", - "Step= 689, Dmax= 2.2e-03 nm, Epot= -1.93394e+03 Fmax= 8.58786e+01, atom= 73\n", - "Step= 690, Dmax= 2.7e-03 nm, Epot= -1.93427e+03 Fmax= 9.24230e+01, atom= 73\n", - "Step= 691, Dmax= 3.2e-03 nm, Epot= -1.93452e+03 Fmax= 1.13677e+02, atom= 73\n", - "Step= 692, Dmax= 3.8e-03 nm, Epot= -1.93471e+03 Fmax= 1.41645e+02, atom= 73\n", - "Step= 693, Dmax= 4.6e-03 nm, Epot= -1.93492e+03 Fmax= 1.57637e+02, atom= 73\n", - "Step= 695, Dmax= 2.8e-03 nm, Epot= -1.93581e+03 Fmax= 3.31622e+01, atom= 43\n", - "Step= 696, Dmax= 3.3e-03 nm, Epot= -1.93645e+03 Fmax= 1.34886e+02, atom= 73\n", - "Step= 697, Dmax= 4.0e-03 nm, Epot= -1.93683e+03 Fmax= 1.26959e+02, atom= 73\n", - "Step= 699, Dmax= 2.4e-03 nm, Epot= -1.93742e+03 Fmax= 2.93981e+01, atom= 43\n", - "Step= 700, Dmax= 2.9e-03 nm, Epot= -1.93784e+03 Fmax= 1.57698e+02, atom= 73\n", - "Step= 701, Dmax= 3.4e-03 nm, Epot= -1.93860e+03 Fmax= 6.58372e+01, atom= 73\n", - "Step= 703, Dmax= 2.1e-03 nm, Epot= -1.93892e+03 Fmax= 7.34898e+01, atom= 73\n", - "Step= 704, Dmax= 2.5e-03 nm, Epot= -1.93923e+03 Fmax= 8.41663e+01, atom= 73\n", - "Step= 705, Dmax= 3.0e-03 nm, Epot= -1.93947e+03 Fmax= 1.14354e+02, atom= 73\n", - "Step= 706, Dmax= 3.6e-03 nm, Epot= -1.93977e+03 Fmax= 1.15985e+02, atom= 73\n", - "Step= 707, Dmax= 4.3e-03 nm, Epot= -1.93981e+03 Fmax= 1.68266e+02, atom= 73\n", - "Step= 708, Dmax= 5.1e-03 nm, Epot= -1.94013e+03 Fmax= 1.65476e+02, atom= 73\n", - "Step= 710, Dmax= 3.1e-03 nm, Epot= -1.94098e+03 Fmax= 3.96665e+01, atom= 73\n", - "Step= 711, Dmax= 3.7e-03 nm, Epot= -1.94113e+03 Fmax= 1.89921e+02, atom= 73\n", - "Step= 712, Dmax= 4.4e-03 nm, Epot= -1.94197e+03 Fmax= 1.02348e+02, atom= 73\n", - "Step= 714, Dmax= 2.7e-03 nm, Epot= -1.94235e+03 Fmax= 6.79933e+01, atom= 73\n", - "Step= 715, Dmax= 3.2e-03 nm, Epot= -1.94245e+03 Fmax= 1.46149e+02, atom= 73\n", - "Step= 716, Dmax= 3.8e-03 nm, Epot= -1.94295e+03 Fmax= 1.02122e+02, atom= 73\n", - "Step= 718, Dmax= 2.3e-03 nm, Epot= -1.94337e+03 Fmax= 5.10269e+01, atom= 73\n", - "Step= 719, Dmax= 2.8e-03 nm, Epot= -1.94361e+03 Fmax= 1.23305e+02, atom= 73\n", - "Step= 720, Dmax= 3.3e-03 nm, Epot= -1.94403e+03 Fmax= 9.53611e+01, atom= 73\n", - "Step= 721, Dmax= 4.0e-03 nm, Epot= -1.94406e+03 Fmax= 1.60309e+02, atom= 73\n", - "Step= 722, Dmax= 4.8e-03 nm, Epot= -1.94442e+03 Fmax= 1.53375e+02, atom= 73\n", - "Step= 724, Dmax= 2.9e-03 nm, Epot= -1.94510e+03 Fmax= 3.10758e+01, atom= 40\n", - "Step= 725, Dmax= 3.4e-03 nm, Epot= -1.94529e+03 Fmax= 2.04147e+02, atom= 73\n", - "Step= 726, Dmax= 4.1e-03 nm, Epot= -1.94631e+03 Fmax= 6.55691e+01, atom= 73\n", - "Step= 728, Dmax= 2.5e-03 nm, Epot= -1.94658e+03 Fmax= 9.78274e+01, atom= 73\n", - "Step= 729, Dmax= 3.0e-03 nm, Epot= -1.94689e+03 Fmax= 9.23771e+01, atom= 73\n", - "Step= 730, Dmax= 3.6e-03 nm, Epot= -1.94703e+03 Fmax= 1.42455e+02, atom= 73\n", - "Step= 731, Dmax= 4.3e-03 nm, Epot= -1.94737e+03 Fmax= 1.32802e+02, atom= 73\n", - "Step= 733, Dmax= 2.6e-03 nm, Epot= -1.94792e+03 Fmax= 3.58905e+01, atom= 73\n", - "Step= 734, Dmax= 3.1e-03 nm, Epot= -1.94825e+03 Fmax= 1.57173e+02, atom= 73\n", - "Step= 735, Dmax= 3.7e-03 nm, Epot= -1.94886e+03 Fmax= 8.49004e+01, atom= 73\n", - "Step= 737, Dmax= 2.2e-03 nm, Epot= -1.94919e+03 Fmax= 5.61875e+01, atom= 73\n", - "Step= 738, Dmax= 2.7e-03 nm, Epot= -1.94941e+03 Fmax= 1.20476e+02, atom= 73\n", - "Step= 739, Dmax= 3.2e-03 nm, Epot= -1.94981e+03 Fmax= 8.45400e+01, atom= 73\n", - "Step= 740, Dmax= 3.8e-03 nm, Epot= -1.94982e+03 Fmax= 1.67385e+02, atom= 73\n", - "Step= 741, Dmax= 4.6e-03 nm, Epot= -1.95031e+03 Fmax= 1.28426e+02, atom= 73\n", - "Step= 743, Dmax= 2.8e-03 nm, Epot= -1.95082e+03 Fmax= 5.20341e+01, atom= 73\n", - "Step= 744, Dmax= 3.3e-03 nm, Epot= -1.95096e+03 Fmax= 1.57972e+02, atom= 73\n", - "Step= 745, Dmax= 4.0e-03 nm, Epot= -1.95152e+03 Fmax= 1.00780e+02, atom= 73\n", - "Step= 747, Dmax= 2.4e-03 nm, Epot= -1.95189e+03 Fmax= 5.08946e+01, atom= 73\n", - "Step= 748, Dmax= 2.9e-03 nm, Epot= -1.95208e+03 Fmax= 1.38563e+02, atom= 73\n", - "Step= 749, Dmax= 3.4e-03 nm, Epot= -1.95256e+03 Fmax= 8.17923e+01, atom= 73\n", - "Step= 751, Dmax= 2.1e-03 nm, Epot= -1.95289e+03 Fmax= 5.27576e+01, atom= 73\n", - "Step= 752, Dmax= 2.5e-03 nm, Epot= -1.95315e+03 Fmax= 1.03122e+02, atom= 73\n", - "Step= 753, Dmax= 3.0e-03 nm, Epot= -1.95348e+03 Fmax= 8.99841e+01, atom= 73\n", - "Step= 754, Dmax= 3.5e-03 nm, Epot= -1.95362e+03 Fmax= 1.36905e+02, atom= 73\n", - "Step= 755, Dmax= 4.3e-03 nm, Epot= -1.95390e+03 Fmax= 1.40274e+02, atom= 73\n", - "Step= 757, Dmax= 2.6e-03 nm, Epot= -1.95446e+03 Fmax= 3.14169e+01, atom= 50\n", - "Step= 758, Dmax= 3.1e-03 nm, Epot= -1.95502e+03 Fmax= 1.29954e+02, atom= 73\n", - "Step= 759, Dmax= 3.7e-03 nm, Epot= -1.95539e+03 Fmax= 1.07106e+02, atom= 73\n", - "Step= 761, Dmax= 2.2e-03 nm, Epot= -1.95579e+03 Fmax= 3.67246e+01, atom= 73\n", - "Step= 762, Dmax= 2.6e-03 nm, Epot= -1.95612e+03 Fmax= 1.29366e+02, atom= 73\n", - "Step= 763, Dmax= 3.2e-03 nm, Epot= -1.95658e+03 Fmax= 7.70396e+01, atom= 73\n", - "Step= 765, Dmax= 1.9e-03 nm, Epot= -1.95688e+03 Fmax= 4.35906e+01, atom= 73\n", - "Step= 766, Dmax= 2.3e-03 nm, Epot= -1.95715e+03 Fmax= 1.07219e+02, atom= 73\n", - "Step= 767, Dmax= 2.7e-03 nm, Epot= -1.95752e+03 Fmax= 6.77190e+01, atom= 73\n", - "Step= 768, Dmax= 3.3e-03 nm, Epot= -1.95759e+03 Fmax= 1.47101e+02, atom= 73\n", - "Step= 769, Dmax= 4.0e-03 nm, Epot= -1.95804e+03 Fmax= 1.05269e+02, atom= 73\n", - "Step= 771, Dmax= 2.4e-03 nm, Epot= -1.95844e+03 Fmax= 4.87556e+01, atom= 73\n", - "Step= 772, Dmax= 2.8e-03 nm, Epot= -1.95862e+03 Fmax= 1.30266e+02, atom= 73\n", - "Step= 773, Dmax= 3.4e-03 nm, Epot= -1.95905e+03 Fmax= 9.03279e+01, atom= 73\n", - "Step= 775, Dmax= 2.1e-03 nm, Epot= -1.95938e+03 Fmax= 3.89895e+01, atom= 73\n", - "Step= 776, Dmax= 2.5e-03 nm, Epot= -1.95962e+03 Fmax= 1.23243e+02, atom= 73\n", - "Step= 777, Dmax= 3.0e-03 nm, Epot= -1.96006e+03 Fmax= 6.43717e+01, atom= 73\n", - "Step= 779, Dmax= 1.8e-03 nm, Epot= -1.96034e+03 Fmax= 5.06886e+01, atom= 73\n", - "Step= 780, Dmax= 2.1e-03 nm, Epot= -1.96059e+03 Fmax= 8.24033e+01, atom= 73\n", - "Step= 781, Dmax= 2.6e-03 nm, Epot= -1.96086e+03 Fmax= 8.24685e+01, atom= 73\n", - "Step= 782, Dmax= 3.1e-03 nm, Epot= -1.96104e+03 Fmax= 1.10610e+02, atom= 73\n", - "Step= 783, Dmax= 3.7e-03 nm, Epot= -1.96124e+03 Fmax= 1.25870e+02, atom= 73\n", - "Step= 784, Dmax= 4.4e-03 nm, Epot= -1.96134e+03 Fmax= 1.53505e+02, atom= 73\n", - "Step= 785, Dmax= 5.3e-03 nm, Epot= -1.96137e+03 Fmax= 1.85916e+02, atom= 73\n", - "Step= 787, Dmax= 3.2e-03 nm, Epot= -1.96232e+03 Fmax= 2.88161e+01, atom= 50\n", - "Step= 788, Dmax= 3.8e-03 nm, Epot= -1.96301e+03 Fmax= 1.18516e+02, atom= 73\n", - "Step= 790, Dmax= 2.3e-03 nm, Epot= -1.96353e+03 Fmax= 3.09638e+01, atom= 45\n", - "Step= 791, Dmax= 2.7e-03 nm, Epot= -1.96377e+03 Fmax= 1.33223e+02, atom= 73\n", - "Step= 792, Dmax= 3.3e-03 nm, Epot= -1.96429e+03 Fmax= 7.14067e+01, atom= 73\n", - "Step= 794, Dmax= 2.0e-03 nm, Epot= -1.96458e+03 Fmax= 5.71279e+01, atom= 73\n", - "Step= 795, Dmax= 2.4e-03 nm, Epot= -1.96473e+03 Fmax= 9.03485e+01, atom= 73\n", - "Step= 796, Dmax= 2.8e-03 nm, Epot= -1.96497e+03 Fmax= 9.24984e+01, atom= 73\n", - "Step= 797, Dmax= 3.4e-03 nm, Epot= -1.96501e+03 Fmax= 1.21386e+02, atom= 73\n", - "Step= 798, Dmax= 4.1e-03 nm, Epot= -1.96507e+03 Fmax= 1.40550e+02, atom= 73\n", - "Step= 800, Dmax= 2.5e-03 nm, Epot= -1.96593e+03 Fmax= 2.79959e+01, atom= 50\n", - "Step= 801, Dmax= 2.9e-03 nm, Epot= -1.96636e+03 Fmax= 9.86573e+01, atom= 11\n", - "Step= 803, Dmax= 1.8e-03 nm, Epot= -1.96687e+03 Fmax= 2.85317e+01, atom= 50\n", - "Step= 804, Dmax= 2.1e-03 nm, Epot= -1.96729e+03 Fmax= 6.99878e+01, atom= 11\n", - "Step= 805, Dmax= 2.5e-03 nm, Epot= -1.96743e+03 Fmax= 8.90188e+01, atom= 23\n", - "Step= 806, Dmax= 3.1e-03 nm, Epot= -1.96753e+03 Fmax= 1.18734e+02, atom= 11\n", - "Step= 807, Dmax= 3.7e-03 nm, Epot= -1.96775e+03 Fmax= 1.14648e+02, atom= 11\n", - "Step= 809, Dmax= 2.2e-03 nm, Epot= -1.96829e+03 Fmax= 3.65236e+01, atom= 11\n", - "Step= 810, Dmax= 2.6e-03 nm, Epot= -1.96842e+03 Fmax= 1.19265e+02, atom= 23\n", - "Step= 811, Dmax= 3.2e-03 nm, Epot= -1.96878e+03 Fmax= 9.39507e+01, atom= 11\n", - "Step= 813, Dmax= 1.9e-03 nm, Epot= -1.96912e+03 Fmax= 3.04313e+01, atom= 23\n", - "Step= 814, Dmax= 2.3e-03 nm, Epot= -1.96931e+03 Fmax= 1.17416e+02, atom= 11\n", - "Step= 815, Dmax= 2.7e-03 nm, Epot= -1.96971e+03 Fmax= 5.97281e+01, atom= 23\n", - "Step= 817, Dmax= 1.6e-03 nm, Epot= -1.96993e+03 Fmax= 5.28330e+01, atom= 11\n", - "Step= 818, Dmax= 2.0e-03 nm, Epot= -1.97010e+03 Fmax= 7.03846e+01, atom= 23\n", - "Step= 819, Dmax= 2.4e-03 nm, Epot= -1.97026e+03 Fmax= 8.88194e+01, atom= 11\n", - "Step= 820, Dmax= 2.8e-03 nm, Epot= -1.97043e+03 Fmax= 9.20270e+01, atom= 23\n", - "Step= 821, Dmax= 3.4e-03 nm, Epot= -1.97044e+03 Fmax= 1.36377e+02, atom= 11\n", - "Step= 822, Dmax= 4.1e-03 nm, Epot= -1.97066e+03 Fmax= 1.25197e+02, atom= 23\n", - "Step= 824, Dmax= 2.5e-03 nm, Epot= -1.97116e+03 Fmax= 4.20069e+01, atom= 11\n", - "Step= 825, Dmax= 2.9e-03 nm, Epot= -1.97118e+03 Fmax= 1.36733e+02, atom= 23\n", - "Step= 826, Dmax= 3.5e-03 nm, Epot= -1.97156e+03 Fmax= 9.88405e+01, atom= 11\n", - "Step= 828, Dmax= 2.1e-03 nm, Epot= -1.97187e+03 Fmax= 3.90612e+01, atom= 23\n", - "Step= 829, Dmax= 2.5e-03 nm, Epot= -1.97192e+03 Fmax= 1.26153e+02, atom= 11\n", - "Step= 830, Dmax= 3.1e-03 nm, Epot= -1.97231e+03 Fmax= 7.11990e+01, atom= 23\n", - "Step= 832, Dmax= 1.8e-03 nm, Epot= -1.97252e+03 Fmax= 5.30064e+01, atom= 11\n", - "Step= 833, Dmax= 2.2e-03 nm, Epot= -1.97264e+03 Fmax= 8.47563e+01, atom= 23\n", - "Step= 834, Dmax= 2.6e-03 nm, Epot= -1.97280e+03 Fmax= 9.10007e+01, atom= 11\n", - "Step= 835, Dmax= 3.2e-03 nm, Epot= -1.97287e+03 Fmax= 1.11470e+02, atom= 23\n", - "Step= 836, Dmax= 3.8e-03 nm, Epot= -1.97290e+03 Fmax= 1.39098e+02, atom= 11\n", - "Step= 837, Dmax= 4.6e-03 nm, Epot= -1.97294e+03 Fmax= 1.54658e+02, atom= 23\n", - "Step= 839, Dmax= 2.7e-03 nm, Epot= -1.97361e+03 Fmax= 3.00050e+01, atom= 11\n", - "Step= 841, Dmax= 1.6e-03 nm, Epot= -1.97380e+03 Fmax= 6.97811e+01, atom= 23\n", - "Step= 842, Dmax= 2.0e-03 nm, Epot= -1.97398e+03 Fmax= 5.97237e+01, atom= 11\n", - "Step= 843, Dmax= 2.4e-03 nm, Epot= -1.97406e+03 Fmax= 9.08769e+01, atom= 23\n", - "Step= 844, Dmax= 2.8e-03 nm, Epot= -1.97420e+03 Fmax= 9.50209e+01, atom= 11\n", - "Step= 845, Dmax= 3.4e-03 nm, Epot= -1.97421e+03 Fmax= 1.24097e+02, atom= 23\n", - "Step= 846, Dmax= 4.1e-03 nm, Epot= -1.97425e+03 Fmax= 1.43640e+02, atom= 11\n", - "Step= 848, Dmax= 2.4e-03 nm, Epot= -1.97481e+03 Fmax= 2.14815e+01, atom= 50\n", - "Step= 849, Dmax= 2.9e-03 nm, Epot= -1.97512e+03 Fmax= 1.18182e+02, atom= 11\n", - "Step= 850, Dmax= 3.5e-03 nm, Epot= -1.97529e+03 Fmax= 1.09331e+02, atom= 23\n", - "Step= 852, Dmax= 2.1e-03 nm, Epot= -1.97566e+03 Fmax= 3.25021e+01, atom= 11\n", - "Step= 854, Dmax= 1.3e-03 nm, Epot= -1.97580e+03 Fmax= 4.87049e+01, atom= 23\n", - "Step= 855, Dmax= 1.5e-03 nm, Epot= -1.97593e+03 Fmax= 4.93154e+01, atom= 11\n", - "Step= 856, Dmax= 1.8e-03 nm, Epot= -1.97603e+03 Fmax= 6.87956e+01, atom= 23\n", - "Step= 857, Dmax= 2.2e-03 nm, Epot= -1.97615e+03 Fmax= 7.32493e+01, atom= 11\n", - "Step= 858, Dmax= 2.6e-03 nm, Epot= -1.97620e+03 Fmax= 9.72041e+01, atom= 23\n", - "Step= 859, Dmax= 3.2e-03 nm, Epot= -1.97627e+03 Fmax= 1.07860e+02, atom= 11\n", - "Step= 861, Dmax= 1.9e-03 nm, Epot= -1.97662e+03 Fmax= 1.91887e+01, atom= 50\n", - "Step= 862, Dmax= 2.3e-03 nm, Epot= -1.97687e+03 Fmax= 9.34073e+01, atom= 11\n", - "Step= 863, Dmax= 2.7e-03 nm, Epot= -1.97703e+03 Fmax= 8.54148e+01, atom= 23\n", - "Step= 865, Dmax= 1.6e-03 nm, Epot= -1.97727e+03 Fmax= 2.48764e+01, atom= 11\n", - "Step= 866, Dmax= 2.0e-03 nm, Epot= -1.97737e+03 Fmax= 9.27157e+01, atom= 23\n", - "Step= 867, Dmax= 2.4e-03 nm, Epot= -1.97758e+03 Fmax= 6.14610e+01, atom= 11\n", - "Step= 869, Dmax= 1.4e-03 nm, Epot= -1.97773e+03 Fmax= 3.21721e+01, atom= 23\n", - "Step= 870, Dmax= 1.7e-03 nm, Epot= -1.97781e+03 Fmax= 7.12656e+01, atom= 11\n", - "Step= 871, Dmax= 2.0e-03 nm, Epot= -1.97795e+03 Fmax= 6.19605e+01, atom= 23\n", - "Step= 872, Dmax= 2.4e-03 nm, Epot= -1.97796e+03 Fmax= 9.30125e+01, atom= 11\n", - "Step= 873, Dmax= 2.9e-03 nm, Epot= -1.97805e+03 Fmax= 9.77378e+01, atom= 23\n", - "Step= 875, Dmax= 1.8e-03 nm, Epot= -1.97834e+03 Fmax= 2.05468e+01, atom= 11\n", - "Step= 876, Dmax= 2.1e-03 nm, Epot= -1.97847e+03 Fmax= 1.01388e+02, atom= 23\n", - "Step= 877, Dmax= 2.5e-03 nm, Epot= -1.97869e+03 Fmax= 6.27675e+01, atom= 11\n", - "Step= 879, Dmax= 1.5e-03 nm, Epot= -1.97884e+03 Fmax= 3.76683e+01, atom= 23\n", - "Step= 880, Dmax= 1.8e-03 nm, Epot= -1.97889e+03 Fmax= 7.46273e+01, atom= 11\n", - "Step= 881, Dmax= 2.2e-03 nm, Epot= -1.97901e+03 Fmax= 6.83851e+01, atom= 23\n", - "Step= 883, Dmax= 1.3e-03 nm, Epot= -1.97918e+03 Fmax= 1.94359e+01, atom= 11\n", - "Step= 884, Dmax= 1.6e-03 nm, Epot= -1.97932e+03 Fmax= 7.35281e+01, atom= 23\n", - "Step= 885, Dmax= 1.9e-03 nm, Epot= -1.97948e+03 Fmax= 4.86883e+01, atom= 11\n", - "Step= 887, Dmax= 1.1e-03 nm, Epot= -1.97959e+03 Fmax= 2.74833e+01, atom= 23\n", - "Step= 888, Dmax= 1.4e-03 nm, Epot= -1.97969e+03 Fmax= 5.33395e+01, atom= 11\n", - "Step= 889, Dmax= 1.6e-03 nm, Epot= -1.97979e+03 Fmax= 5.36107e+01, atom= 23\n", - "Step= 890, Dmax= 2.0e-03 nm, Epot= -1.97985e+03 Fmax= 6.99175e+01, atom= 11\n", - "Step= 891, Dmax= 2.4e-03 nm, Epot= -1.97991e+03 Fmax= 8.32195e+01, atom= 23\n", - "Step= 892, Dmax= 2.8e-03 nm, Epot= -1.97994e+03 Fmax= 9.62321e+01, atom= 11\n", - "Step= 894, Dmax= 1.7e-03 nm, Epot= -1.98024e+03 Fmax= 1.70546e+01, atom= 23\n", - "Step= 895, Dmax= 2.0e-03 nm, Epot= -1.98042e+03 Fmax= 8.17866e+01, atom= 11\n", - "Step= 896, Dmax= 2.4e-03 nm, Epot= -1.98054e+03 Fmax= 7.87549e+01, atom= 23\n", - "Step= 898, Dmax= 1.5e-03 nm, Epot= -1.98074e+03 Fmax= 1.82801e+01, atom= 11\n", - "Step= 899, Dmax= 1.8e-03 nm, Epot= -1.98086e+03 Fmax= 8.60070e+01, atom= 23\n", - "Step= 900, Dmax= 2.1e-03 nm, Epot= -1.98105e+03 Fmax= 4.89054e+01, atom= 11\n", - "Step= 902, Dmax= 1.3e-03 nm, Epot= -1.98116e+03 Fmax= 3.55580e+01, atom= 23\n", - "Step= 903, Dmax= 1.5e-03 nm, Epot= -1.98123e+03 Fmax= 5.57065e+01, atom= 11\n", - "Step= 904, Dmax= 1.8e-03 nm, Epot= -1.98131e+03 Fmax= 6.39843e+01, atom= 23\n", - "Step= 905, Dmax= 2.2e-03 nm, Epot= -1.98136e+03 Fmax= 7.24722e+01, atom= 11\n", - "Step= 907, Dmax= 1.3e-03 nm, Epot= -1.98155e+03 Fmax= 1.69570e+01, atom= 23\n", - "Step= 908, Dmax= 1.6e-03 nm, Epot= -1.98174e+03 Fmax= 5.63275e+01, atom= 11\n", - "Step= 909, Dmax= 1.9e-03 nm, Epot= -1.98181e+03 Fmax= 6.83987e+01, atom= 23\n", - "Step= 910, Dmax= 2.3e-03 nm, Epot= -1.98187e+03 Fmax= 7.27648e+01, atom= 11\n", - "Step= 912, Dmax= 1.4e-03 nm, Epot= -1.98207e+03 Fmax= 1.95786e+01, atom= 23\n", - "Step= 913, Dmax= 1.6e-03 nm, Epot= -1.98221e+03 Fmax= 6.06944e+01, atom= 11\n", - "Step= 914, Dmax= 2.0e-03 nm, Epot= -1.98229e+03 Fmax= 6.88629e+01, atom= 23\n", - "Step= 915, Dmax= 2.4e-03 nm, Epot= -1.98233e+03 Fmax= 7.64097e+01, atom= 11\n", - "Step= 917, Dmax= 1.4e-03 nm, Epot= -1.98256e+03 Fmax= 1.92869e+01, atom= 23\n", - "Step= 918, Dmax= 1.7e-03 nm, Epot= -1.98270e+03 Fmax= 6.15076e+01, atom= 11\n", - "Step= 919, Dmax= 2.0e-03 nm, Epot= -1.98277e+03 Fmax= 7.30581e+01, atom= 23\n", - "Step= 920, Dmax= 2.4e-03 nm, Epot= -1.98283e+03 Fmax= 7.70883e+01, atom= 11\n", - "Step= 922, Dmax= 1.5e-03 nm, Epot= -1.98307e+03 Fmax= 2.17414e+01, atom= 23\n", - "Step= 923, Dmax= 1.8e-03 nm, Epot= -1.98318e+03 Fmax= 6.53928e+01, atom= 11\n", - "Step= 924, Dmax= 2.1e-03 nm, Epot= -1.98326e+03 Fmax= 7.44452e+01, atom= 23\n", - "Step= 925, Dmax= 2.5e-03 nm, Epot= -1.98330e+03 Fmax= 8.00918e+01, atom= 11\n", - "Step= 927, Dmax= 1.5e-03 nm, Epot= -1.98357e+03 Fmax= 2.23403e+01, atom= 23\n", - "Step= 928, Dmax= 1.8e-03 nm, Epot= -1.98366e+03 Fmax= 6.67667e+01, atom= 11\n", - "Step= 929, Dmax= 2.2e-03 nm, Epot= -1.98373e+03 Fmax= 7.85324e+01, atom= 23\n", - "Step= 930, Dmax= 2.6e-03 nm, Epot= -1.98378e+03 Fmax= 8.06128e+01, atom= 11\n", - "Step= 932, Dmax= 1.6e-03 nm, Epot= -1.98408e+03 Fmax= 2.40798e+01, atom= 23\n", - "Step= 933, Dmax= 1.9e-03 nm, Epot= -1.98412e+03 Fmax= 7.05713e+01, atom= 11\n", - "Step= 934, Dmax= 2.3e-03 nm, Epot= -1.98421e+03 Fmax= 7.84777e+01, atom= 23\n", - "Step= 935, Dmax= 2.7e-03 nm, Epot= -1.98421e+03 Fmax= 8.57801e+01, atom= 11\n", - "Step= 937, Dmax= 1.6e-03 nm, Epot= -1.98460e+03 Fmax= 2.50888e+01, atom= 23\n", - "Step= 938, Dmax= 2.0e-03 nm, Epot= -1.98463e+03 Fmax= 6.73701e+01, atom= 11\n", - "Step= 940, Dmax= 1.2e-03 nm, Epot= -1.98493e+03 Fmax= 1.87958e+01, atom= 34\n", - "Step= 941, Dmax= 1.4e-03 nm, Epot= -1.98514e+03 Fmax= 3.19280e+01, atom= 34\n", - "Step= 943, Dmax= 8.4e-04 nm, Epot= -1.98525e+03 Fmax= 2.54590e+01, atom= 23\n", - "Step= 944, Dmax= 1.0e-03 nm, Epot= -1.98536e+03 Fmax= 3.60196e+01, atom= 34\n", - "Step= 945, Dmax= 1.2e-03 nm, Epot= -1.98545e+03 Fmax= 3.79993e+01, atom= 23\n", - "Step= 946, Dmax= 1.5e-03 nm, Epot= -1.98550e+03 Fmax= 5.81890e+01, atom= 34\n", - "Step= 947, Dmax= 1.8e-03 nm, Epot= -1.98562e+03 Fmax= 5.25112e+01, atom= 34\n", - "Step= 949, Dmax= 1.1e-03 nm, Epot= -1.98582e+03 Fmax= 2.73786e+01, atom= 34\n", - "Step= 950, Dmax= 1.3e-03 nm, Epot= -1.98595e+03 Fmax= 3.64981e+01, atom= 34\n", - "Step= 951, Dmax= 1.5e-03 nm, Epot= -1.98601e+03 Fmax= 6.33636e+01, atom= 34\n", - "Step= 952, Dmax= 1.8e-03 nm, Epot= -1.98615e+03 Fmax= 5.25118e+01, atom= 34\n", - "Step= 954, Dmax= 1.1e-03 nm, Epot= -1.98631e+03 Fmax= 2.95759e+01, atom= 34\n", - "Step= 955, Dmax= 1.3e-03 nm, Epot= -1.98644e+03 Fmax= 3.90494e+01, atom= 34\n", - "Step= 956, Dmax= 1.6e-03 nm, Epot= -1.98652e+03 Fmax= 6.51853e+01, atom= 34\n", - "Step= 957, Dmax= 1.9e-03 nm, Epot= -1.98665e+03 Fmax= 5.48532e+01, atom= 34\n", - "Step= 959, Dmax= 1.1e-03 nm, Epot= -1.98681e+03 Fmax= 3.02958e+01, atom= 34\n", - "Step= 960, Dmax= 1.4e-03 nm, Epot= -1.98695e+03 Fmax= 4.04982e+01, atom= 34\n", - "Step= 961, Dmax= 1.6e-03 nm, Epot= -1.98704e+03 Fmax= 6.77057e+01, atom= 34\n", - "Step= 962, Dmax= 2.0e-03 nm, Epot= -1.98717e+03 Fmax= 5.70320e+01, atom= 34\n", - "Step= 963, Dmax= 2.3e-03 nm, Epot= -1.98718e+03 Fmax= 1.00063e+02, atom= 34\n", - "Step= 964, Dmax= 2.8e-03 nm, Epot= -1.98736e+03 Fmax= 8.14156e+01, atom= 34\n", - "Step= 966, Dmax= 1.7e-03 nm, Epot= -1.98758e+03 Fmax= 3.95078e+01, atom= 34\n", - "Step= 967, Dmax= 2.0e-03 nm, Epot= -1.98769e+03 Fmax= 7.13563e+01, atom= 34\n", - "Step= 968, Dmax= 2.4e-03 nm, Epot= -1.98777e+03 Fmax= 9.34324e+01, atom= 34\n", - "Step= 969, Dmax= 2.9e-03 nm, Epot= -1.98788e+03 Fmax= 9.26256e+01, atom= 34\n", - "Step= 971, Dmax= 1.7e-03 nm, Epot= -1.98814e+03 Fmax= 3.52017e+01, atom= 34\n", - "Step= 972, Dmax= 2.1e-03 nm, Epot= -1.98830e+03 Fmax= 6.84221e+01, atom= 34\n", - "Step= 973, Dmax= 2.5e-03 nm, Epot= -1.98835e+03 Fmax= 1.02324e+02, atom= 34\n", - "Step= 974, Dmax= 3.0e-03 nm, Epot= -1.98850e+03 Fmax= 9.14942e+01, atom= 34\n", - "Step= 976, Dmax= 1.8e-03 nm, Epot= -1.98875e+03 Fmax= 3.92685e+01, atom= 34\n", - "Step= 977, Dmax= 2.2e-03 nm, Epot= -1.98889e+03 Fmax= 7.54753e+01, atom= 34\n", - "Step= 978, Dmax= 2.6e-03 nm, Epot= -1.98896e+03 Fmax= 1.03195e+02, atom= 34\n", - "Step= 979, Dmax= 3.1e-03 nm, Epot= -1.98909e+03 Fmax= 9.77337e+01, atom= 34\n", - "Step= 981, Dmax= 1.9e-03 nm, Epot= -1.98936e+03 Fmax= 3.91313e+01, atom= 34\n", - "Step= 982, Dmax= 2.3e-03 nm, Epot= -1.98951e+03 Fmax= 7.66818e+01, atom= 34\n", - "Step= 983, Dmax= 2.7e-03 nm, Epot= -1.98958e+03 Fmax= 1.08347e+02, atom= 34\n", - "Step= 984, Dmax= 3.2e-03 nm, Epot= -1.98972e+03 Fmax= 9.96009e+01, atom= 34\n", - "Step= 986, Dmax= 1.9e-03 nm, Epot= -1.99000e+03 Fmax= 4.17852e+01, atom= 34\n", - "Step= 987, Dmax= 2.3e-03 nm, Epot= -1.99013e+03 Fmax= 8.13009e+01, atom= 34\n", - "Step= 988, Dmax= 2.8e-03 nm, Epot= -1.99020e+03 Fmax= 1.11223e+02, atom= 34\n", - "Step= 989, Dmax= 3.4e-03 nm, Epot= -1.99034e+03 Fmax= 1.04203e+02, atom= 34\n", - "Step= 991, Dmax= 2.0e-03 nm, Epot= -1.99063e+03 Fmax= 4.24564e+01, atom= 34\n", - "Step= 992, Dmax= 2.4e-03 nm, Epot= -1.99077e+03 Fmax= 8.35069e+01, atom= 34\n", - "Step= 993, Dmax= 2.9e-03 nm, Epot= -1.99083e+03 Fmax= 1.16341e+02, atom= 34\n", - "Step= 994, Dmax= 3.5e-03 nm, Epot= -1.99098e+03 Fmax= 1.07817e+02, atom= 34\n", - "Step= 996, Dmax= 2.1e-03 nm, Epot= -1.99128e+03 Fmax= 4.45800e+01, atom= 34\n", - "Step= 997, Dmax= 2.5e-03 nm, Epot= -1.99141e+03 Fmax= 8.71914e+01, atom= 34\n", - "Step= 998, Dmax= 3.0e-03 nm, Epot= -1.99147e+03 Fmax= 1.20368e+02, atom= 34\n", - "Step= 999, Dmax= 3.6e-03 nm, Epot= -1.99161e+03 Fmax= 1.11740e+02, atom= 34\n", - "Step= 1000, Dmax= 4.3e-03 nm, Epot= -1.99140e+03 Fmax= 1.84451e+02, atom= 34\n", + "Step= 0, Dmax= 1.0e-02 nm, Epot= 9.59019e+06 Fmax= 1.69656e+07, atom= 149\n", + "Step= 1, Dmax= 1.0e-02 nm, Epot= 6.21902e+06 Fmax= 6.01139e+06, atom= 478\n", + "Step= 2, Dmax= 1.2e-02 nm, Epot= 3.58839e+06 Fmax= 2.70774e+06, atom= 17\n", + "Step= 3, Dmax= 1.4e-02 nm, Epot= 2.18086e+06 Fmax= 1.08770e+06, atom= 1305\n", + "Step= 4, Dmax= 1.7e-02 nm, Epot= 1.25600e+06 Fmax= 5.29430e+05, atom= 1493\n", + "Step= 5, Dmax= 2.1e-02 nm, Epot= 7.79933e+05 Fmax= 2.60389e+05, atom= 1513\n", + "Step= 6, Dmax= 2.5e-02 nm, Epot= 4.76315e+05 Fmax= 1.79135e+05, atom= 1493\n", + "Step= 7, Dmax= 3.0e-02 nm, Epot= 3.20697e+05 Fmax= 2.25612e+05, atom= 544\n", + "Step= 8, Dmax= 3.6e-02 nm, Epot= 2.54493e+05 Fmax= 9.11997e+04, atom= 1513\n", + "Step= 9, Dmax= 4.3e-02 nm, Epot= 1.57693e+05 Fmax= 1.98551e+05, atom= 544\n", + "Step= 10, Dmax= 5.2e-02 nm, Epot= 1.29573e+05 Fmax= 6.97811e+04, atom= 1043\n", + "Step= 11, Dmax= 6.2e-02 nm, Epot= 8.43732e+04 Fmax= 2.96444e+05, atom= 200\n", + "Step= 12, Dmax= 7.4e-02 nm, Epot= 7.16053e+04 Fmax= 2.00454e+04, atom= 200\n", + "Step= 13, Dmax= 8.9e-02 nm, Epot= 1.52005e+04 Fmax= 5.75866e+04, atom= 200\n", + "Step= 14, Dmax= 1.1e-01 nm, Epot= 7.52938e+03 Fmax= 2.23148e+04, atom= 200\n", + "Step= 15, Dmax= 1.3e-01 nm, Epot= -2.26040e+03 Fmax= 3.65168e+04, atom= 1107\n", + "Step= 16, Dmax= 1.5e-01 nm, Epot= -7.31706e+03 Fmax= 3.22986e+04, atom= 1107\n", + "Step= 17, Dmax= 1.8e-01 nm, Epot= -8.75316e+03 Fmax= 1.04774e+05, atom= 898\n", + "Step= 18, Dmax= 2.2e-01 nm, Epot= -1.05843e+04 Fmax= 7.90213e+04, atom= 818\n", + "Step= 20, Dmax= 1.3e-01 nm, Epot= -1.44389e+04 Fmax= 1.77137e+04, atom= 1591\n", + "Step= 22, Dmax= 8.0e-02 nm, Epot= -1.69180e+04 Fmax= 2.36072e+04, atom= 1591\n", + "Step= 23, Dmax= 9.6e-02 nm, Epot= -1.85682e+04 Fmax= 1.69728e+04, atom= 1267\n", + "Step= 24, Dmax= 1.2e-01 nm, Epot= -2.05149e+04 Fmax= 1.35048e+04, atom= 1586\n", + "Step= 26, Dmax= 6.9e-02 nm, Epot= -2.22957e+04 Fmax= 7.78835e+03, atom= 1606\n", + "Step= 27, Dmax= 8.3e-02 nm, Epot= -2.46065e+04 Fmax= 8.23715e+03, atom= 1606\n", + "Step= 28, Dmax= 9.9e-02 nm, Epot= -2.60463e+04 Fmax= 2.03931e+04, atom= 1586\n", + "Step= 29, Dmax= 1.2e-01 nm, Epot= -2.71109e+04 Fmax= 8.51185e+03, atom= 1267\n", + "Step= 30, Dmax= 1.4e-01 nm, Epot= -2.77852e+04 Fmax= 5.10263e+04, atom= 1490\n", + "Step= 31, Dmax= 1.7e-01 nm, Epot= -2.89093e+04 Fmax= 8.58700e+03, atom= 1446\n", + "Step= 32, Dmax= 2.1e-01 nm, Epot= -3.02287e+04 Fmax= 2.27403e+04, atom= 1550\n", + "Step= 34, Dmax= 1.2e-01 nm, Epot= -3.08777e+04 Fmax= 1.66822e+04, atom= 1550\n", + "Step= 35, Dmax= 1.5e-01 nm, Epot= -3.15210e+04 Fmax= 7.84232e+03, atom= 468\n", + "Step= 36, Dmax= 1.8e-01 nm, Epot= -3.26742e+04 Fmax= 4.75751e+03, atom= 1596\n", + "Step= 37, Dmax= 2.1e-01 nm, Epot= -3.33775e+04 Fmax= 3.33247e+04, atom= 1461\n", + "Step= 38, Dmax= 2.6e-01 nm, Epot= -3.44663e+04 Fmax= 4.50562e+03, atom= 1596\n", + "Step= 40, Dmax= 1.5e-01 nm, Epot= -3.54502e+04 Fmax= 1.55012e+03, atom= 430\n", + "Step= 41, Dmax= 1.8e-01 nm, Epot= -3.68978e+04 Fmax= 1.01688e+04, atom= 430\n", + "Step= 43, Dmax= 1.1e-01 nm, Epot= -3.73994e+04 Fmax= 2.71564e+03, atom= 1090\n", + "Step= 44, Dmax= 1.3e-01 nm, Epot= -3.78345e+04 Fmax= 2.32950e+03, atom= 1200\n", + "Step= 45, Dmax= 1.6e-01 nm, Epot= -3.80154e+04 Fmax= 6.23586e+03, atom= 1363\n", + "Step= 47, Dmax= 9.6e-02 nm, Epot= -3.85621e+04 Fmax= 2.23179e+03, atom= 867\n", + "Step= 48, Dmax= 1.1e-01 nm, Epot= -3.89186e+04 Fmax= 1.51574e+03, atom= 666\n", + "Step= 50, Dmax= 6.9e-02 nm, Epot= -3.92438e+04 Fmax= 1.20399e+03, atom= 1190\n", + "Step= 52, Dmax= 4.1e-02 nm, Epot= -3.94257e+04 Fmax= 1.81706e+03, atom= 1190\n", + "Step= 53, Dmax= 5.0e-02 nm, Epot= -3.95622e+04 Fmax= 1.81324e+03, atom= 1190\n", + "Step= 54, Dmax= 6.0e-02 nm, Epot= -3.96129e+04 Fmax= 3.55332e+03, atom= 1190\n", + "Step= 55, Dmax= 7.1e-02 nm, Epot= -3.97856e+04 Fmax= 1.91005e+03, atom= 652\n", + "Step= 57, Dmax= 4.3e-02 nm, Epot= -3.99184e+04 Fmax= 1.12243e+03, atom= 1469\n", + "Step= 58, Dmax= 5.1e-02 nm, Epot= -4.00827e+04 Fmax= 1.67429e+03, atom= 652\n", + "Step= 59, Dmax= 6.2e-02 nm, Epot= -4.01536e+04 Fmax= 2.68805e+03, atom= 652\n", + "Step= 60, Dmax= 7.4e-02 nm, Epot= -4.02827e+04 Fmax= 2.17712e+03, atom= 1190\n", + "Step= 61, Dmax= 8.9e-02 nm, Epot= -4.03035e+04 Fmax= 2.90934e+03, atom= 1190\n", + "Step= 63, Dmax= 5.3e-02 nm, Epot= -4.05244e+04 Fmax= 7.06731e+02, atom= 5920\n", + "Step= 64, Dmax= 6.4e-02 nm, Epot= -4.07516e+04 Fmax= 1.27359e+03, atom= 620\n", + "Step= 66, Dmax= 3.8e-02 nm, Epot= -4.08794e+04 Fmax= 1.05973e+03, atom= 620\n", + "Step= 67, Dmax= 4.6e-02 nm, Epot= -4.09734e+04 Fmax= 1.25287e+03, atom= 1190\n", + "Step= 68, Dmax= 5.5e-02 nm, Epot= -4.10696e+04 Fmax= 1.23286e+03, atom= 652\n", + "Step= 69, Dmax= 6.6e-02 nm, Epot= -4.10934e+04 Fmax= 2.04140e+03, atom= 652\n", + "Step= 70, Dmax= 8.0e-02 nm, Epot= -4.11782e+04 Fmax= 2.16374e+03, atom= 652\n", + "Step= 72, Dmax= 4.8e-02 nm, Epot= -4.13409e+04 Fmax= 5.23621e+02, atom= 1469\n", + "Step= 73, Dmax= 5.7e-02 nm, Epot= -4.14399e+04 Fmax= 4.60012e+03, atom= 113\n", + "Step= 74, Dmax= 6.9e-02 nm, Epot= -4.15766e+04 Fmax= 1.02818e+03, atom= 170\n", + "Step= 75, Dmax= 8.3e-02 nm, Epot= -4.16145e+04 Fmax= 4.11463e+03, atom= 170\n", + "Step= 76, Dmax= 9.9e-02 nm, Epot= -4.17154e+04 Fmax= 1.43780e+03, atom= 113\n", + "Step= 77, Dmax= 1.2e-01 nm, Epot= -4.17179e+04 Fmax= 4.52138e+03, atom= 113\n", + "Step= 78, Dmax= 1.4e-01 nm, Epot= -4.17574e+04 Fmax= 5.42849e+03, atom= 170\n", + "Step= 80, Dmax= 8.6e-02 nm, Epot= -4.18853e+04 Fmax= 1.57744e+03, atom= 1281\n", + "Step= 81, Dmax= 1.0e-01 nm, Epot= -4.20080e+04 Fmax= 1.11946e+03, atom= 712\n", + "Step= 83, Dmax= 6.2e-02 nm, Epot= -4.21195e+04 Fmax= 4.11103e+02, atom= 1541\n", + "Step= 84, Dmax= 7.4e-02 nm, Epot= -4.21928e+04 Fmax= 1.94301e+03, atom= 712\n", + "Step= 85, Dmax= 8.9e-02 nm, Epot= -4.23274e+04 Fmax= 1.32241e+03, atom= 1589\n", + "Step= 87, Dmax= 5.3e-02 nm, Epot= -4.24331e+04 Fmax= 8.97786e+02, atom= 434\n", + "Step= 88, Dmax= 6.4e-02 nm, Epot= -4.24949e+04 Fmax= 1.14063e+03, atom= 434\n", + "Step= 90, Dmax= 3.8e-02 nm, Epot= -4.25673e+04 Fmax= 3.36942e+02, atom= 1589\n", + "Step= 91, Dmax= 4.6e-02 nm, Epot= -4.26762e+04 Fmax= 1.27605e+03, atom= 1589\n", + "Step= 92, Dmax= 5.5e-02 nm, Epot= -4.27289e+04 Fmax= 8.00429e+02, atom= 434\n", + "Step= 93, Dmax= 6.6e-02 nm, Epot= -4.27805e+04 Fmax= 1.06524e+03, atom= 434\n", + "Step= 95, Dmax= 4.0e-02 nm, Epot= -4.28472e+04 Fmax= 3.14248e+02, atom= 1589\n", + "Step= 96, Dmax= 4.8e-02 nm, Epot= -4.29489e+04 Fmax= 1.02626e+03, atom= 1589\n", + "Step= 97, Dmax= 5.7e-02 nm, Epot= -4.29942e+04 Fmax= 8.66540e+02, atom= 434\n", + "Step= 98, Dmax= 6.9e-02 nm, Epot= -4.30311e+04 Fmax= 9.53738e+02, atom= 434\n", + "Step= 100, Dmax= 4.1e-02 nm, Epot= -4.30996e+04 Fmax= 2.93202e+02, atom= 1589\n", + "Step= 101, Dmax= 4.9e-02 nm, Epot= -4.31753e+04 Fmax= 1.10153e+03, atom= 1589\n", + "Step= 102, Dmax= 5.9e-02 nm, Epot= -4.32252e+04 Fmax= 9.34391e+02, atom= 434\n", + "Step= 103, Dmax= 7.1e-02 nm, Epot= -4.32587e+04 Fmax= 9.34787e+02, atom= 317\n", + "Step= 104, Dmax= 8.5e-02 nm, Epot= -4.32610e+04 Fmax= 1.64631e+03, atom= 317\n", + "Step= 105, Dmax= 1.0e-01 nm, Epot= -4.33016e+04 Fmax= 1.28613e+03, atom= 317\n", + "Step= 107, Dmax= 6.2e-02 nm, Epot= -4.33906e+04 Fmax= 3.85737e+02, atom= 1589\n", + "Step= 108, Dmax= 7.4e-02 nm, Epot= -4.34217e+04 Fmax= 1.00007e+03, atom= 1310\n", + "Step= 110, Dmax= 4.4e-02 nm, Epot= -4.35166e+04 Fmax= 3.28319e+02, atom= 317\n", + "Step= 111, Dmax= 5.3e-02 nm, Epot= -4.35425e+04 Fmax= 6.75626e+02, atom= 317\n", + "Step= 113, Dmax= 3.2e-02 nm, Epot= -4.36161e+04 Fmax= 2.61455e+02, atom= 983\n", + "Step= 114, Dmax= 3.8e-02 nm, Epot= -4.36370e+04 Fmax= 1.02704e+03, atom= 983\n", + "Step= 115, Dmax= 4.6e-02 nm, Epot= -4.36909e+04 Fmax= 4.75666e+02, atom= 983\n", + "Step= 117, Dmax= 2.8e-02 nm, Epot= -4.37182e+04 Fmax= 3.08316e+02, atom= 292\n", + "Step= 118, Dmax= 3.3e-02 nm, Epot= -4.37412e+04 Fmax= 9.12164e+02, atom= 983\n", + "Step= 119, Dmax= 4.0e-02 nm, Epot= -4.37713e+04 Fmax= 4.20075e+02, atom= 983\n", + "Step= 120, Dmax= 4.8e-02 nm, Epot= -4.37839e+04 Fmax= 1.34372e+03, atom= 983\n", + "Step= 121, Dmax= 5.7e-02 nm, Epot= -4.38167e+04 Fmax= 5.46838e+02, atom= 983\n", + "Step= 123, Dmax= 3.4e-02 nm, Epot= -4.38482e+04 Fmax= 2.66963e+02, atom= 939\n", + "Step= 124, Dmax= 4.1e-02 nm, Epot= -4.38560e+04 Fmax= 1.05569e+03, atom= 983\n", + "Step= 125, Dmax= 4.9e-02 nm, Epot= -4.38997e+04 Fmax= 8.25245e+02, atom= 983\n", + "Step= 126, Dmax= 5.9e-02 nm, Epot= -4.39091e+04 Fmax= 8.54830e+02, atom= 983\n", + "Step= 128, Dmax= 3.6e-02 nm, Epot= -4.39503e+04 Fmax= 1.83632e+02, atom= 939\n", + "Step= 129, Dmax= 4.3e-02 nm, Epot= -4.39908e+04 Fmax= 6.90661e+02, atom= 1550\n", + "Step= 130, Dmax= 5.1e-02 nm, Epot= -4.39914e+04 Fmax= 1.60360e+03, atom= 983\n", + "Step= 131, Dmax= 6.1e-02 nm, Epot= -4.40363e+04 Fmax= 5.69990e+02, atom= 292\n", + "Step= 133, Dmax= 3.7e-02 nm, Epot= -4.40661e+04 Fmax= 2.55382e+02, atom= 939\n", + "Step= 134, Dmax= 4.4e-02 nm, Epot= -4.40729e+04 Fmax= 8.77303e+02, atom= 983\n", + "Step= 135, Dmax= 5.3e-02 nm, Epot= -4.40907e+04 Fmax= 1.33513e+03, atom= 983\n", + "Step= 136, Dmax= 6.4e-02 nm, Epot= -4.41246e+04 Fmax= 6.23039e+02, atom= 983\n", + "Step= 138, Dmax= 3.8e-02 nm, Epot= -4.41545e+04 Fmax= 2.58181e+02, atom= 1550\n", + "Step= 139, Dmax= 4.6e-02 nm, Epot= -4.41686e+04 Fmax= 8.33654e+02, atom= 983\n", + "Step= 140, Dmax= 5.5e-02 nm, Epot= -4.41853e+04 Fmax= 1.00435e+03, atom= 983\n", + "Step= 141, Dmax= 6.6e-02 nm, Epot= -4.42000e+04 Fmax= 7.38560e+02, atom= 292\n", + "Step= 143, Dmax= 4.0e-02 nm, Epot= -4.42394e+04 Fmax= 2.83898e+02, atom= 939\n", + "Step= 144, Dmax= 4.8e-02 nm, Epot= -4.42475e+04 Fmax= 6.70825e+02, atom= 939\n", + "Step= 146, Dmax= 2.9e-02 nm, Epot= -4.42901e+04 Fmax= 1.91053e+02, atom= 983\n", + "Step= 147, Dmax= 3.4e-02 nm, Epot= -4.43094e+04 Fmax= 6.79625e+02, atom= 983\n", + "Step= 148, Dmax= 4.1e-02 nm, Epot= -4.43327e+04 Fmax= 3.76758e+02, atom= 1550\n", + "Step= 150, Dmax= 2.5e-02 nm, Epot= -4.43506e+04 Fmax= 2.59805e+02, atom= 681\n", + "Step= 151, Dmax= 3.0e-02 nm, Epot= -4.43633e+04 Fmax= 5.66457e+02, atom= 681\n", + "Step= 152, Dmax= 3.5e-02 nm, Epot= -4.43787e+04 Fmax= 3.98318e+02, atom= 681\n", + "Step= 153, Dmax= 4.3e-02 nm, Epot= -4.43800e+04 Fmax= 8.90609e+02, atom= 681\n", + "Step= 154, Dmax= 5.1e-02 nm, Epot= -4.44011e+04 Fmax= 5.19996e+02, atom= 681\n", + "Step= 156, Dmax= 3.1e-02 nm, Epot= -4.44244e+04 Fmax= 1.34639e+02, atom= 1059\n", + "Step= 158, Dmax= 1.8e-02 nm, Epot= -4.44403e+04 Fmax= 3.69269e+02, atom= 681\n", + "Step= 159, Dmax= 2.2e-02 nm, Epot= -4.44568e+04 Fmax= 2.25993e+02, atom= 681\n", + "Step= 160, Dmax= 2.6e-02 nm, Epot= -4.44657e+04 Fmax= 4.53948e+02, atom= 681\n", + "Step= 161, Dmax= 3.2e-02 nm, Epot= -4.44808e+04 Fmax= 3.59969e+02, atom= 681\n", + "Step= 163, Dmax= 1.9e-02 nm, Epot= -4.44951e+04 Fmax= 1.48568e+02, atom= 681\n", + "Step= 164, Dmax= 2.3e-02 nm, Epot= -4.45087e+04 Fmax= 4.81990e+02, atom= 681\n", + "Step= 165, Dmax= 2.7e-02 nm, Epot= -4.45221e+04 Fmax= 2.76160e+02, atom= 681\n", + "Step= 166, Dmax= 3.3e-02 nm, Epot= -4.45262e+04 Fmax= 6.54042e+02, atom= 681\n", + "Step= 167, Dmax= 4.0e-02 nm, Epot= -4.45405e+04 Fmax= 3.98719e+02, atom= 681\n", + "Step= 169, Dmax= 2.4e-02 nm, Epot= -4.45557e+04 Fmax= 1.08335e+02, atom= 681\n", + "Step= 171, Dmax= 1.4e-02 nm, Epot= -4.45678e+04 Fmax= 2.85478e+02, atom= 681\n", + "Step= 172, Dmax= 1.7e-02 nm, Epot= -4.45791e+04 Fmax= 1.47014e+02, atom= 681\n", + "Step= 173, Dmax= 2.1e-02 nm, Epot= -4.45873e+04 Fmax= 3.79193e+02, atom= 681\n", + "Step= 174, Dmax= 2.5e-02 nm, Epot= -4.46000e+04 Fmax= 2.34392e+02, atom= 681\n", + "Step= 176, Dmax= 1.5e-02 nm, Epot= -4.46093e+04 Fmax= 1.49891e+02, atom= 681\n", + "Step= 177, Dmax= 1.8e-02 nm, Epot= -4.46186e+04 Fmax= 3.00452e+02, atom= 681\n", + "Step= 178, Dmax= 2.1e-02 nm, Epot= -4.46270e+04 Fmax= 2.48382e+02, atom= 681\n", + "Step= 179, Dmax= 2.6e-02 nm, Epot= -4.46328e+04 Fmax= 4.13687e+02, atom= 681\n", + "Step= 180, Dmax= 3.1e-02 nm, Epot= -4.46405e+04 Fmax= 3.58339e+02, atom= 681\n", + "Step= 181, Dmax= 3.7e-02 nm, Epot= -4.46421e+04 Fmax= 6.04580e+02, atom= 681\n", + "Step= 182, Dmax= 4.4e-02 nm, Epot= -4.46500e+04 Fmax= 4.85753e+02, atom= 681\n", + "Step= 184, Dmax= 2.6e-02 nm, Epot= -4.46687e+04 Fmax= 9.81433e+01, atom= 983\n", + "Step= 186, Dmax= 1.6e-02 nm, Epot= -4.46795e+04 Fmax= 2.40466e+02, atom= 681\n", + "Step= 187, Dmax= 1.9e-02 nm, Epot= -4.46874e+04 Fmax= 2.53126e+02, atom= 681\n", + "Step= 188, Dmax= 2.3e-02 nm, Epot= -4.46931e+04 Fmax= 3.08779e+02, atom= 681\n", + "Step= 189, Dmax= 2.7e-02 nm, Epot= -4.46993e+04 Fmax= 3.64428e+02, atom= 681\n", + "Step= 190, Dmax= 3.3e-02 nm, Epot= -4.47026e+04 Fmax= 4.24388e+02, atom= 681\n", + "Step= 191, Dmax= 3.9e-02 nm, Epot= -4.47059e+04 Fmax= 5.46354e+02, atom= 681\n", + "Step= 192, Dmax= 4.7e-02 nm, Epot= -4.47069e+04 Fmax= 5.62949e+02, atom= 681\n", + "Step= 194, Dmax= 2.8e-02 nm, Epot= -4.47327e+04 Fmax= 7.49773e+01, atom= 260\n", + "Step= 196, Dmax= 1.7e-02 nm, Epot= -4.47447e+04 Fmax= 2.33328e+02, atom= 983\n", + "Step= 197, Dmax= 2.0e-02 nm, Epot= -4.47513e+04 Fmax= 2.55777e+02, atom= 681\n", + "Step= 198, Dmax= 2.5e-02 nm, Epot= -4.47535e+04 Fmax= 3.28205e+02, atom= 681\n", + "Step= 199, Dmax= 2.9e-02 nm, Epot= -4.47564e+04 Fmax= 3.79900e+02, atom= 681\n", + "Step= 201, Dmax= 1.8e-02 nm, Epot= -4.47764e+04 Fmax= 7.24967e+01, atom= 681\n", + "Step= 202, Dmax= 2.1e-02 nm, Epot= -4.47823e+04 Fmax= 4.44399e+02, atom= 681\n", + "Step= 203, Dmax= 2.5e-02 nm, Epot= -4.47984e+04 Fmax= 2.05731e+02, atom= 681\n", + "Step= 205, Dmax= 1.5e-02 nm, Epot= -4.48056e+04 Fmax= 1.63623e+02, atom= 401\n", + "Step= 206, Dmax= 1.8e-02 nm, Epot= -4.48074e+04 Fmax= 3.37522e+02, atom= 401\n", + "Step= 207, Dmax= 2.2e-02 nm, Epot= -4.48169e+04 Fmax= 2.37977e+02, atom= 401\n", + "Step= 209, Dmax= 1.3e-02 nm, Epot= -4.48244e+04 Fmax= 1.01416e+02, atom= 401\n", + "Step= 210, Dmax= 1.6e-02 nm, Epot= -4.48304e+04 Fmax= 3.15960e+02, atom= 401\n", + "Step= 211, Dmax= 1.9e-02 nm, Epot= -4.48383e+04 Fmax= 1.91451e+02, atom= 401\n", + "Step= 212, Dmax= 2.3e-02 nm, Epot= -4.48402e+04 Fmax= 4.12632e+02, atom= 401\n", + "Step= 213, Dmax= 2.7e-02 nm, Epot= -4.48481e+04 Fmax= 3.09859e+02, atom= 401\n", + "Step= 215, Dmax= 1.6e-02 nm, Epot= -4.48559e+04 Fmax= 1.00911e+02, atom= 401\n", + "Step= 216, Dmax= 2.0e-02 nm, Epot= -4.48583e+04 Fmax= 5.16413e+02, atom= 401\n", + "Step= 217, Dmax= 2.4e-02 nm, Epot= -4.48718e+04 Fmax= 1.67997e+02, atom= 401\n", + "Step= 219, Dmax= 1.4e-02 nm, Epot= -4.48771e+04 Fmax= 1.91015e+02, atom= 401\n", + "Step= 220, Dmax= 1.7e-02 nm, Epot= -4.48818e+04 Fmax= 2.45644e+02, atom= 401\n", + "Step= 221, Dmax= 2.0e-02 nm, Epot= -4.48863e+04 Fmax= 2.90142e+02, atom= 401\n", + "Step= 222, Dmax= 2.5e-02 nm, Epot= -4.48898e+04 Fmax= 3.52635e+02, atom= 401\n", + "Step= 223, Dmax= 2.9e-02 nm, Epot= -4.48928e+04 Fmax= 4.25211e+02, atom= 401\n", + "Step= 224, Dmax= 3.5e-02 nm, Epot= -4.48938e+04 Fmax= 5.23681e+02, atom= 401\n", + "Step= 225, Dmax= 4.2e-02 nm, Epot= -4.48947e+04 Fmax= 6.04656e+02, atom= 401\n", + "Step= 227, Dmax= 2.5e-02 nm, Epot= -4.49131e+04 Fmax= 9.56179e+01, atom= 514\n", + "Step= 229, Dmax= 1.5e-02 nm, Epot= -4.49199e+04 Fmax= 2.78897e+02, atom= 401\n", + "Step= 230, Dmax= 1.8e-02 nm, Epot= -4.49260e+04 Fmax= 2.27570e+02, atom= 401\n", + "Step= 231, Dmax= 2.2e-02 nm, Epot= -4.49292e+04 Fmax= 3.37757e+02, atom= 401\n", + "Step= 232, Dmax= 2.6e-02 nm, Epot= -4.49334e+04 Fmax= 3.42104e+02, atom= 401\n", + "Step= 233, Dmax= 3.2e-02 nm, Epot= -4.49338e+04 Fmax= 4.95014e+02, atom= 401\n", + "Step= 234, Dmax= 3.8e-02 nm, Epot= -4.49364e+04 Fmax= 5.20282e+02, atom= 401\n", + "Step= 236, Dmax= 2.3e-02 nm, Epot= -4.49514e+04 Fmax= 8.81958e+01, atom= 1356\n", + "Step= 237, Dmax= 2.7e-02 nm, Epot= -4.49575e+04 Fmax= 6.14417e+02, atom= 401\n", + "Step= 238, Dmax= 3.3e-02 nm, Epot= -4.49684e+04 Fmax= 3.65380e+02, atom= 401\n", + "Step= 240, Dmax= 2.0e-02 nm, Epot= -4.49757e+04 Fmax= 1.09430e+02, atom= 401\n", + "Step= 242, Dmax= 1.2e-02 nm, Epot= -4.49804e+04 Fmax= 2.28978e+02, atom= 401\n", + "Step= 243, Dmax= 1.4e-02 nm, Epot= -4.49855e+04 Fmax= 1.39363e+02, atom= 401\n", + "Step= 244, Dmax= 1.7e-02 nm, Epot= -4.49892e+04 Fmax= 3.05832e+02, atom= 401\n", + "Step= 245, Dmax= 2.0e-02 nm, Epot= -4.49947e+04 Fmax= 2.18545e+02, atom= 401\n", + "Step= 246, Dmax= 2.4e-02 nm, Epot= -4.49951e+04 Fmax= 4.33387e+02, atom= 401\n", + "Step= 247, Dmax= 2.9e-02 nm, Epot= -4.50012e+04 Fmax= 3.37822e+02, atom= 401\n", + "Step= 249, Dmax= 1.8e-02 nm, Epot= -4.50092e+04 Fmax= 9.95405e+01, atom= 401\n", + "Step= 250, Dmax= 2.1e-02 nm, Epot= -4.50102e+04 Fmax= 5.24716e+02, atom= 401\n", + "Step= 251, Dmax= 2.5e-02 nm, Epot= -4.50224e+04 Fmax= 1.83671e+02, atom= 401\n", + "Step= 253, Dmax= 1.5e-02 nm, Epot= -4.50267e+04 Fmax= 1.70431e+02, atom= 401\n", + "Step= 254, Dmax= 1.8e-02 nm, Epot= -4.50293e+04 Fmax= 3.04775e+02, atom= 401\n", + "Step= 255, Dmax= 2.2e-02 nm, Epot= -4.50341e+04 Fmax= 2.57360e+02, atom= 401\n", + "Step= 257, Dmax= 1.3e-02 nm, Epot= -4.50399e+04 Fmax= 7.50503e+01, atom= 401\n", + "Step= 258, Dmax= 1.6e-02 nm, Epot= -4.50455e+04 Fmax= 3.44605e+02, atom= 401\n", + "Step= 259, Dmax= 1.9e-02 nm, Epot= -4.50525e+04 Fmax= 1.54818e+02, atom= 401\n", + "Step= 261, Dmax= 1.1e-02 nm, Epot= -4.50565e+04 Fmax= 1.20428e+02, atom= 401\n", + "Step= 262, Dmax= 1.4e-02 nm, Epot= -4.50600e+04 Fmax= 2.34153e+02, atom= 401\n", + "Step= 263, Dmax= 1.6e-02 nm, Epot= -4.50644e+04 Fmax= 1.85357e+02, atom= 401\n", + "Step= 264, Dmax= 2.0e-02 nm, Epot= -4.50660e+04 Fmax= 3.24057e+02, atom= 401\n", + "Step= 265, Dmax= 2.4e-02 nm, Epot= -4.50704e+04 Fmax= 2.87728e+02, atom= 401\n", + "Step= 267, Dmax= 1.4e-02 nm, Epot= -4.50769e+04 Fmax= 6.95540e+01, atom= 401\n", + "Step= 268, Dmax= 1.7e-02 nm, Epot= -4.50817e+04 Fmax= 3.94582e+02, atom= 401\n", + "Step= 269, Dmax= 2.0e-02 nm, Epot= -4.50899e+04 Fmax= 1.51428e+02, atom= 401\n", + "Step= 271, Dmax= 1.2e-02 nm, Epot= -4.50936e+04 Fmax= 1.39840e+02, atom= 401\n", + "Step= 272, Dmax= 1.5e-02 nm, Epot= -4.50964e+04 Fmax= 2.34467e+02, atom= 401\n", + "Step= 273, Dmax= 1.8e-02 nm, Epot= -4.51001e+04 Fmax= 2.12492e+02, atom= 401\n", + "Step= 274, Dmax= 2.1e-02 nm, Epot= -4.51013e+04 Fmax= 3.27600e+02, atom= 401\n", + "Step= 275, Dmax= 2.5e-02 nm, Epot= -4.51044e+04 Fmax= 3.28185e+02, atom= 401\n", + "Step= 277, Dmax= 1.5e-02 nm, Epot= -4.51122e+04 Fmax= 5.82710e+01, atom= 1356\n", + "Step= 278, Dmax= 1.8e-02 nm, Epot= -4.51176e+04 Fmax= 4.44603e+02, atom= 401\n", + "Step= 279, Dmax= 2.2e-02 nm, Epot= -4.51267e+04 Fmax= 1.55786e+02, atom= 401\n", + "Step= 281, Dmax= 1.3e-02 nm, Epot= -4.51300e+04 Fmax= 1.53556e+02, atom= 401\n", + "Step= 282, Dmax= 1.6e-02 nm, Epot= -4.51323e+04 Fmax= 2.41408e+02, atom= 401\n", + "Step= 283, Dmax= 1.9e-02 nm, Epot= -4.51355e+04 Fmax= 2.34651e+02, atom= 401\n", + "Step= 284, Dmax= 2.3e-02 nm, Epot= -4.51362e+04 Fmax= 3.36909e+02, atom= 401\n", + "Step= 285, Dmax= 2.7e-02 nm, Epot= -4.51382e+04 Fmax= 3.67313e+02, atom= 401\n", + "Step= 287, Dmax= 1.6e-02 nm, Epot= -4.51473e+04 Fmax= 5.07336e+01, atom= 1356\n", + "Step= 288, Dmax= 2.0e-02 nm, Epot= -4.51541e+04 Fmax= 4.70797e+02, atom= 401\n", + "Step= 289, Dmax= 2.4e-02 nm, Epot= -4.51630e+04 Fmax= 1.77990e+02, atom= 401\n", + "Step= 291, Dmax= 1.4e-02 nm, Epot= -4.51662e+04 Fmax= 1.55265e+02, atom= 401\n", + "Step= 292, Dmax= 1.7e-02 nm, Epot= -4.51677e+04 Fmax= 2.64924e+02, atom= 401\n", + "Step= 293, Dmax= 2.0e-02 nm, Epot= -4.51709e+04 Fmax= 2.44923e+02, atom= 401\n", + "Step= 295, Dmax= 1.2e-02 nm, Epot= -4.51761e+04 Fmax= 5.67225e+01, atom= 401\n", + "Step= 296, Dmax= 1.5e-02 nm, Epot= -4.51807e+04 Fmax= 3.18966e+02, atom= 401\n", + "Step= 297, Dmax= 1.8e-02 nm, Epot= -4.51868e+04 Fmax= 1.26951e+02, atom= 401\n", + "Step= 299, Dmax= 1.1e-02 nm, Epot= -4.51898e+04 Fmax= 1.21747e+02, atom= 401\n", + "Step= 300, Dmax= 1.3e-02 nm, Epot= -4.51922e+04 Fmax= 1.86619e+02, atom= 401\n", + "Step= 301, Dmax= 1.5e-02 nm, Epot= -4.51950e+04 Fmax= 1.89933e+02, atom= 401\n", + "Step= 302, Dmax= 1.8e-02 nm, Epot= -4.51966e+04 Fmax= 2.53997e+02, atom= 401\n", + "Step= 303, Dmax= 2.2e-02 nm, Epot= -4.51982e+04 Fmax= 2.99486e+02, atom= 401\n", + "Step= 304, Dmax= 2.6e-02 nm, Epot= -4.51993e+04 Fmax= 3.39627e+02, atom= 401\n", + "Step= 306, Dmax= 1.6e-02 nm, Epot= -4.52081e+04 Fmax= 6.44718e+01, atom= 732\n", + "Step= 307, Dmax= 1.9e-02 nm, Epot= -4.52102e+04 Fmax= 3.54375e+02, atom= 732\n", + "Step= 308, Dmax= 2.3e-02 nm, Epot= -4.52168e+04 Fmax= 2.67085e+02, atom= 401\n", + "Step= 310, Dmax= 1.4e-02 nm, Epot= -4.52223e+04 Fmax= 7.35888e+01, atom= 401\n", + "Step= 311, Dmax= 1.6e-02 nm, Epot= -4.52252e+04 Fmax= 3.17462e+02, atom= 401\n", + "Step= 312, Dmax= 2.0e-02 nm, Epot= -4.52308e+04 Fmax= 1.48920e+02, atom= 401\n", + "Step= 314, Dmax= 1.2e-02 nm, Epot= -4.52339e+04 Fmax= 1.24568e+02, atom= 401\n", + "Step= 315, Dmax= 1.4e-02 nm, Epot= -4.52356e+04 Fmax= 2.10116e+02, atom= 401\n", + "Step= 316, Dmax= 1.7e-02 nm, Epot= -4.52386e+04 Fmax= 2.07917e+02, atom= 401\n", + "Step= 317, Dmax= 2.0e-02 nm, Epot= -4.52395e+04 Fmax= 2.72514e+02, atom= 401\n", + "Step= 318, Dmax= 2.4e-02 nm, Epot= -4.52402e+04 Fmax= 3.42851e+02, atom= 401\n", + "Step= 319, Dmax= 2.9e-02 nm, Epot= -4.52420e+04 Fmax= 3.49525e+02, atom= 401\n", + "Step= 321, Dmax= 1.8e-02 nm, Epot= -4.52519e+04 Fmax= 9.30597e+01, atom= 732\n", + "Step= 323, Dmax= 1.1e-02 nm, Epot= -4.52552e+04 Fmax= 1.14687e+02, atom= 1356\n", + "Step= 324, Dmax= 1.3e-02 nm, Epot= -4.52573e+04 Fmax= 1.87465e+02, atom= 401\n", + "Step= 325, Dmax= 1.5e-02 nm, Epot= -4.52605e+04 Fmax= 1.65437e+02, atom= 401\n", + "Step= 326, Dmax= 1.8e-02 nm, Epot= -4.52609e+04 Fmax= 2.77895e+02, atom= 401\n", + "Step= 327, Dmax= 2.2e-02 nm, Epot= -4.52649e+04 Fmax= 2.27756e+02, atom= 401\n", + "Step= 329, Dmax= 1.3e-02 nm, Epot= -4.52703e+04 Fmax= 8.33427e+01, atom= 732\n", + "Step= 330, Dmax= 1.6e-02 nm, Epot= -4.52715e+04 Fmax= 2.74829e+02, atom= 732\n", + "Step= 331, Dmax= 1.9e-02 nm, Epot= -4.52768e+04 Fmax= 1.80904e+02, atom= 1356\n", + "Step= 333, Dmax= 1.1e-02 nm, Epot= -4.52807e+04 Fmax= 8.10176e+01, atom= 4016\n", + "Step= 334, Dmax= 1.4e-02 nm, Epot= -4.52828e+04 Fmax= 2.32433e+02, atom= 401\n", + "Step= 335, Dmax= 1.6e-02 nm, Epot= -4.52872e+04 Fmax= 1.43260e+02, atom= 1356\n", + "Step= 337, Dmax= 9.8e-03 nm, Epot= -4.52905e+04 Fmax= 7.93137e+01, atom= 732\n", + "Step= 338, Dmax= 1.2e-02 nm, Epot= -4.52927e+04 Fmax= 1.94381e+02, atom= 1356\n", + "Step= 339, Dmax= 1.4e-02 nm, Epot= -4.52964e+04 Fmax= 1.33096e+02, atom= 1356\n", + "Step= 340, Dmax= 1.7e-02 nm, Epot= -4.52966e+04 Fmax= 2.68275e+02, atom= 1356\n", + "Step= 341, Dmax= 2.0e-02 nm, Epot= -4.53009e+04 Fmax= 2.00702e+02, atom= 1356\n", + "Step= 343, Dmax= 1.2e-02 nm, Epot= -4.53055e+04 Fmax= 7.73948e+01, atom= 401\n", + "Step= 344, Dmax= 1.5e-02 nm, Epot= -4.53070e+04 Fmax= 2.50722e+02, atom= 401\n", + "Step= 345, Dmax= 1.8e-02 nm, Epot= -4.53119e+04 Fmax= 1.53401e+02, atom= 1356\n", + "Step= 347, Dmax= 1.1e-02 nm, Epot= -4.53153e+04 Fmax= 8.46940e+01, atom= 7326\n", + "Step= 348, Dmax= 1.3e-02 nm, Epot= -4.53172e+04 Fmax= 2.01191e+02, atom= 732\n", + "Step= 349, Dmax= 1.5e-02 nm, Epot= -4.53208e+04 Fmax= 1.40161e+02, atom= 1356\n", + "Step= 351, Dmax= 9.1e-03 nm, Epot= -4.53241e+04 Fmax= 5.95074e+01, atom= 401\n", + "Step= 352, Dmax= 1.1e-02 nm, Epot= -4.53266e+04 Fmax= 1.87251e+02, atom= 1356\n", + "Step= 353, Dmax= 1.3e-02 nm, Epot= -4.53306e+04 Fmax= 1.13401e+02, atom= 1356\n", + "Step= 354, Dmax= 1.6e-02 nm, Epot= -4.53308e+04 Fmax= 2.37663e+02, atom= 1356\n", + "Step= 355, Dmax= 1.9e-02 nm, Epot= -4.53347e+04 Fmax= 1.91627e+02, atom= 1356\n", + "Step= 357, Dmax= 1.1e-02 nm, Epot= -4.53392e+04 Fmax= 6.85218e+01, atom= 7326\n", + "Step= 358, Dmax= 1.4e-02 nm, Epot= -4.53414e+04 Fmax= 2.28151e+02, atom= 732\n", + "Step= 359, Dmax= 1.6e-02 nm, Epot= -4.53455e+04 Fmax= 1.32929e+02, atom= 732\n", + "Step= 361, Dmax= 9.8e-03 nm, Epot= -4.53484e+04 Fmax= 7.51858e+01, atom= 732\n", + "Step= 362, Dmax= 1.2e-02 nm, Epot= -4.53500e+04 Fmax= 1.84048e+02, atom= 732\n", + "Step= 363, Dmax= 1.4e-02 nm, Epot= -4.53536e+04 Fmax= 1.32221e+02, atom= 732\n", + "Step= 365, Dmax= 8.4e-03 nm, Epot= -4.53566e+04 Fmax= 5.64467e+01, atom= 732\n", + "Step= 366, Dmax= 1.0e-02 nm, Epot= -4.53593e+04 Fmax= 1.64438e+02, atom= 732\n", + "Step= 367, Dmax= 1.2e-02 nm, Epot= -4.53625e+04 Fmax= 1.01697e+02, atom= 732\n", + "Step= 368, Dmax= 1.5e-02 nm, Epot= -4.53629e+04 Fmax= 2.30214e+02, atom= 732\n", + "Step= 369, Dmax= 1.7e-02 nm, Epot= -4.53669e+04 Fmax= 1.52216e+02, atom= 732\n", + "Step= 371, Dmax= 1.0e-02 nm, Epot= -4.53701e+04 Fmax= 6.64692e+01, atom= 732\n", + "Step= 372, Dmax= 1.3e-02 nm, Epot= -4.53705e+04 Fmax= 2.16511e+02, atom= 732\n", + "Step= 373, Dmax= 1.5e-02 nm, Epot= -4.53755e+04 Fmax= 1.22384e+02, atom= 732\n", + "Step= 375, Dmax= 9.1e-03 nm, Epot= -4.53782e+04 Fmax= 7.43448e+01, atom= 732\n", + "Step= 376, Dmax= 1.1e-02 nm, Epot= -4.53798e+04 Fmax= 1.61537e+02, atom= 732\n", + "Step= 377, Dmax= 1.3e-02 nm, Epot= -4.53827e+04 Fmax= 1.20142e+02, atom= 732\n", + "Step= 379, Dmax= 7.8e-03 nm, Epot= -4.53855e+04 Fmax= 4.46628e+01, atom= 732\n", + "Step= 380, Dmax= 9.4e-03 nm, Epot= -4.53873e+04 Fmax= 1.63830e+02, atom= 732\n", + "Step= 381, Dmax= 1.1e-02 nm, Epot= -4.53914e+04 Fmax= 8.44229e+01, atom= 732\n", + "Step= 383, Dmax= 6.8e-03 nm, Epot= -4.53937e+04 Fmax= 6.03527e+01, atom= 732\n", + "Step= 384, Dmax= 8.1e-03 nm, Epot= -4.53953e+04 Fmax= 1.14338e+02, atom= 732\n", + "Step= 385, Dmax= 9.7e-03 nm, Epot= -4.53976e+04 Fmax= 9.84215e+01, atom= 1264\n", + "Step= 386, Dmax= 1.2e-02 nm, Epot= -4.53977e+04 Fmax= 1.64252e+02, atom= 1264\n", + "Step= 387, Dmax= 1.4e-02 nm, Epot= -4.54000e+04 Fmax= 1.49182e+02, atom= 787\n", + "Step= 389, Dmax= 8.4e-03 nm, Epot= -4.54049e+04 Fmax= 3.60901e+01, atom= 718\n", + "Step= 390, Dmax= 1.0e-02 nm, Epot= -4.54064e+04 Fmax= 1.66410e+02, atom= 718\n", + "Step= 391, Dmax= 1.2e-02 nm, Epot= -4.54110e+04 Fmax= 1.05040e+02, atom= 1264\n", + "Step= 393, Dmax= 7.3e-03 nm, Epot= -4.54139e+04 Fmax= 6.61495e+01, atom= 1156\n", + "Step= 394, Dmax= 8.7e-03 nm, Epot= -4.54148e+04 Fmax= 1.47879e+02, atom= 1156\n", + "Step= 395, Dmax= 1.0e-02 nm, Epot= -4.54178e+04 Fmax= 1.02769e+02, atom= 1156\n", + "Step= 396, Dmax= 1.3e-02 nm, Epot= -4.54180e+04 Fmax= 2.06505e+02, atom= 1156\n", + "Step= 397, Dmax= 1.5e-02 nm, Epot= -4.54212e+04 Fmax= 1.53777e+02, atom= 1156\n", + "Step= 399, Dmax= 9.0e-03 nm, Epot= -4.54244e+04 Fmax= 5.19430e+01, atom= 1156\n", + "Step= 400, Dmax= 1.1e-02 nm, Epot= -4.54263e+04 Fmax= 2.09038e+02, atom= 1156\n", + "Step= 401, Dmax= 1.3e-02 nm, Epot= -4.54300e+04 Fmax= 1.01438e+02, atom= 1156\n", + "Step= 402, Dmax= 1.6e-02 nm, Epot= -4.54301e+04 Fmax= 2.62119e+02, atom= 1156\n", + "Step= 403, Dmax= 1.9e-02 nm, Epot= -4.54338e+04 Fmax= 1.79294e+02, atom= 1156\n", + "Step= 405, Dmax= 1.1e-02 nm, Epot= -4.54364e+04 Fmax= 8.25895e+01, atom= 1156\n", + "Step= 406, Dmax= 1.4e-02 nm, Epot= -4.54373e+04 Fmax= 2.61566e+02, atom= 1156\n", + "Step= 407, Dmax= 1.6e-02 nm, Epot= -4.54407e+04 Fmax= 1.34431e+02, atom= 1156\n", + "Step= 409, Dmax= 9.7e-03 nm, Epot= -4.54428e+04 Fmax= 8.56312e+01, atom= 1156\n", + "Step= 410, Dmax= 1.2e-02 nm, Epot= -4.54443e+04 Fmax= 1.86190e+02, atom= 1156\n", + "Step= 411, Dmax= 1.4e-02 nm, Epot= -4.54467e+04 Fmax= 1.41469e+02, atom= 1156\n", + "Step= 412, Dmax= 1.7e-02 nm, Epot= -4.54473e+04 Fmax= 2.46066e+02, atom= 1156\n", + "Step= 413, Dmax= 2.0e-02 nm, Epot= -4.54496e+04 Fmax= 2.26702e+02, atom= 1156\n", + "Step= 415, Dmax= 1.2e-02 nm, Epot= -4.54528e+04 Fmax= 6.13745e+01, atom= 1066\n", + "Step= 416, Dmax= 1.5e-02 nm, Epot= -4.54545e+04 Fmax= 3.11539e+02, atom= 1156\n", + "Step= 417, Dmax= 1.7e-02 nm, Epot= -4.54584e+04 Fmax= 1.31022e+02, atom= 1156\n", + "Step= 419, Dmax= 1.0e-02 nm, Epot= -4.54604e+04 Fmax= 1.03603e+02, atom= 1156\n", + "Step= 420, Dmax= 1.3e-02 nm, Epot= -4.54619e+04 Fmax= 1.85451e+02, atom= 1156\n", + "Step= 421, Dmax= 1.5e-02 nm, Epot= -4.54640e+04 Fmax= 1.63973e+02, atom= 1156\n", + "Step= 422, Dmax= 1.8e-02 nm, Epot= -4.54647e+04 Fmax= 2.48883e+02, atom= 1156\n", + "Step= 423, Dmax= 2.2e-02 nm, Epot= -4.54666e+04 Fmax= 2.56839e+02, atom= 1156\n", + "Step= 425, Dmax= 1.3e-02 nm, Epot= -4.54703e+04 Fmax= 5.82463e+01, atom= 1066\n", + "Step= 426, Dmax= 1.6e-02 nm, Epot= -4.54726e+04 Fmax= 3.14469e+02, atom= 1156\n", + "Step= 427, Dmax= 1.9e-02 nm, Epot= -4.54763e+04 Fmax= 1.59195e+02, atom= 1156\n", + "Step= 429, Dmax= 1.1e-02 nm, Epot= -4.54786e+04 Fmax= 8.89682e+01, atom= 1156\n", + "Step= 430, Dmax= 1.3e-02 nm, Epot= -4.54799e+04 Fmax= 2.22102e+02, atom= 1156\n", + "Step= 431, Dmax= 1.6e-02 nm, Epot= -4.54828e+04 Fmax= 1.50545e+02, atom= 1156\n", + "Step= 433, Dmax= 9.7e-03 nm, Epot= -4.54849e+04 Fmax= 7.03927e+01, atom= 1156\n", + "Step= 434, Dmax= 1.2e-02 nm, Epot= -4.54869e+04 Fmax= 2.13873e+02, atom= 1156\n", + "Step= 435, Dmax= 1.4e-02 nm, Epot= -4.54895e+04 Fmax= 1.15643e+02, atom= 1156\n", + "Step= 436, Dmax= 1.7e-02 nm, Epot= -4.54900e+04 Fmax= 2.96026e+02, atom= 1156\n", + "Step= 437, Dmax= 2.0e-02 nm, Epot= -4.54933e+04 Fmax= 1.75966e+02, atom= 1156\n", + "Step= 439, Dmax= 1.2e-02 nm, Epot= -4.54960e+04 Fmax= 8.59731e+01, atom= 1156\n", + "Step= 440, Dmax= 1.4e-02 nm, Epot= -4.54972e+04 Fmax= 2.49303e+02, atom= 1156\n", + "Step= 441, Dmax= 1.7e-02 nm, Epot= -4.55007e+04 Fmax= 1.49656e+02, atom= 1156\n", + "Step= 443, Dmax= 1.0e-02 nm, Epot= -4.55029e+04 Fmax= 8.37383e+01, atom= 1156\n", + "Step= 444, Dmax= 1.3e-02 nm, Epot= -4.55046e+04 Fmax= 2.16624e+02, atom= 1156\n", + "Step= 445, Dmax= 1.5e-02 nm, Epot= -4.55072e+04 Fmax= 1.30897e+02, atom= 1156\n", + "Step= 446, Dmax= 1.8e-02 nm, Epot= -4.55076e+04 Fmax= 3.03976e+02, atom= 1156\n", + "Step= 447, Dmax= 2.2e-02 nm, Epot= -4.55108e+04 Fmax= 1.94901e+02, atom= 1156\n", + "Step= 449, Dmax= 1.3e-02 nm, Epot= -4.55139e+04 Fmax= 8.18339e+01, atom= 1156\n", + "Step= 450, Dmax= 1.6e-02 nm, Epot= -4.55150e+04 Fmax= 2.81635e+02, atom= 1156\n", + "Step= 451, Dmax= 1.9e-02 nm, Epot= -4.55191e+04 Fmax= 1.46740e+02, atom= 1156\n", + "Step= 453, Dmax= 1.1e-02 nm, Epot= -4.55213e+04 Fmax= 9.88467e+01, atom= 1156\n", + "Step= 454, Dmax= 1.3e-02 nm, Epot= -4.55229e+04 Fmax= 2.17986e+02, atom= 1156\n", + "Step= 455, Dmax= 1.6e-02 nm, Epot= -4.55255e+04 Fmax= 1.48312e+02, atom= 1156\n", + "Step= 456, Dmax= 1.9e-02 nm, Epot= -4.55257e+04 Fmax= 3.11856e+02, atom= 1156\n", + "Step= 457, Dmax= 2.3e-02 nm, Epot= -4.55288e+04 Fmax= 2.14631e+02, atom= 1156\n", + "Step= 459, Dmax= 1.4e-02 nm, Epot= -4.55323e+04 Fmax= 7.71938e+01, atom= 1156\n", + "Step= 460, Dmax= 1.7e-02 nm, Epot= -4.55330e+04 Fmax= 3.21334e+02, atom= 1156\n", + "Step= 461, Dmax= 2.0e-02 nm, Epot= -4.55381e+04 Fmax= 1.41615e+02, atom= 1156\n", + "Step= 463, Dmax= 1.2e-02 nm, Epot= -4.55403e+04 Fmax= 1.15698e+02, atom= 1156\n", + "Step= 464, Dmax= 1.4e-02 nm, Epot= -4.55418e+04 Fmax= 2.17832e+02, atom= 1156\n", + "Step= 465, Dmax= 1.7e-02 nm, Epot= -4.55442e+04 Fmax= 1.67154e+02, atom= 1156\n", + "Step= 466, Dmax= 2.1e-02 nm, Epot= -4.55444e+04 Fmax= 3.17514e+02, atom= 1156\n", + "Step= 467, Dmax= 2.5e-02 nm, Epot= -4.55473e+04 Fmax= 2.36436e+02, atom= 1156\n", + "Step= 469, Dmax= 1.5e-02 nm, Epot= -4.55513e+04 Fmax= 7.12272e+01, atom= 1156\n", + "Step= 470, Dmax= 1.8e-02 nm, Epot= -4.55515e+04 Fmax= 3.70785e+02, atom= 1156\n", + "Step= 471, Dmax= 2.2e-02 nm, Epot= -4.55580e+04 Fmax= 1.35358e+02, atom= 1156\n", + "Step= 473, Dmax= 1.3e-02 nm, Epot= -4.55602e+04 Fmax= 1.33076e+02, atom= 1156\n", + "Step= 474, Dmax= 1.6e-02 nm, Epot= -4.55617e+04 Fmax= 2.16578e+02, atom= 1156\n", + "Step= 475, Dmax= 1.9e-02 nm, Epot= -4.55639e+04 Fmax= 1.86607e+02, atom= 1156\n", + "Step= 476, Dmax= 2.2e-02 nm, Epot= -4.55641e+04 Fmax= 3.24494e+02, atom= 1156\n", + "Step= 477, Dmax= 2.7e-02 nm, Epot= -4.55667e+04 Fmax= 2.59519e+02, atom= 1156\n", + "Step= 479, Dmax= 1.6e-02 nm, Epot= -4.55715e+04 Fmax= 6.55095e+01, atom= 1156\n", + "Step= 481, Dmax= 9.7e-03 nm, Epot= -4.55741e+04 Fmax= 1.50405e+02, atom= 1156\n", + "Step= 482, Dmax= 1.2e-02 nm, Epot= -4.55766e+04 Fmax= 1.03609e+02, atom= 1156\n", + "Step= 483, Dmax= 1.4e-02 nm, Epot= -4.55781e+04 Fmax= 1.92464e+02, atom= 1156\n", + "Step= 484, Dmax= 1.7e-02 nm, Epot= -4.55806e+04 Fmax= 1.70362e+02, atom= 1156\n", + "Step= 485, Dmax= 2.0e-02 nm, Epot= -4.55808e+04 Fmax= 2.57242e+02, atom= 1156\n", + "Step= 486, Dmax= 2.4e-02 nm, Epot= -4.55825e+04 Fmax= 2.66114e+02, atom= 1156\n", + "Step= 488, Dmax= 1.4e-02 nm, Epot= -4.55879e+04 Fmax= 6.06032e+01, atom= 1066\n", + "Step= 489, Dmax= 1.7e-02 nm, Epot= -4.55881e+04 Fmax= 3.13496e+02, atom= 1156\n", + "Step= 490, Dmax= 2.1e-02 nm, Epot= -4.55935e+04 Fmax= 1.78824e+02, atom= 1156\n", + "Step= 492, Dmax= 1.2e-02 nm, Epot= -4.55970e+04 Fmax= 8.06860e+01, atom= 1129\n", + "Step= 494, Dmax= 7.5e-03 nm, Epot= -4.55990e+04 Fmax= 9.39491e+01, atom= 1129\n", + "Step= 495, Dmax= 9.0e-03 nm, Epot= -4.56008e+04 Fmax= 1.15327e+02, atom= 1129\n", + "Step= 496, Dmax= 1.1e-02 nm, Epot= -4.56026e+04 Fmax= 1.33503e+02, atom= 1129\n", + "Step= 497, Dmax= 1.3e-02 nm, Epot= -4.56041e+04 Fmax= 1.68267e+02, atom= 1129\n", + "Step= 498, Dmax= 1.6e-02 nm, Epot= -4.56056e+04 Fmax= 1.89476e+02, atom= 1129\n", + "Step= 499, Dmax= 1.9e-02 nm, Epot= -4.56064e+04 Fmax= 2.45543e+02, atom= 1129\n", + "Step= 500, Dmax= 2.2e-02 nm, Epot= -4.56076e+04 Fmax= 2.67980e+02, atom= 1129\n", + "Step= 502, Dmax= 1.3e-02 nm, Epot= -4.56126e+04 Fmax= 4.69913e+01, atom= 9499\n", + "Step= 503, Dmax= 1.6e-02 nm, Epot= -4.56147e+04 Fmax= 3.20608e+02, atom= 949\n", + "Step= 504, Dmax= 1.9e-02 nm, Epot= -4.56193e+04 Fmax= 1.80850e+02, atom= 1129\n", + "Step= 506, Dmax= 1.2e-02 nm, Epot= -4.56217e+04 Fmax= 7.40528e+01, atom= 1129\n", + "Step= 507, Dmax= 1.4e-02 nm, Epot= -4.56220e+04 Fmax= 2.82158e+02, atom= 1129\n", + "Step= 508, Dmax= 1.7e-02 nm, Epot= -4.56260e+04 Fmax= 1.16116e+02, atom= 1129\n", + "Step= 510, Dmax= 1.0e-02 nm, Epot= -4.56277e+04 Fmax= 1.03945e+02, atom= 1129\n", + "Step= 511, Dmax= 1.2e-02 nm, Epot= -4.56289e+04 Fmax= 1.71334e+02, atom= 1129\n", + "Step= 512, Dmax= 1.4e-02 nm, Epot= -4.56306e+04 Fmax= 1.61667e+02, atom= 1129\n", + "Step= 513, Dmax= 1.7e-02 nm, Epot= -4.56310e+04 Fmax= 2.34953e+02, atom= 1129\n", + "Step= 514, Dmax= 2.1e-02 nm, Epot= -4.56324e+04 Fmax= 2.43803e+02, atom= 1129\n", + "Step= 516, Dmax= 1.2e-02 nm, Epot= -4.56362e+04 Fmax= 4.91039e+01, atom= 1287\n", + "Step= 517, Dmax= 1.5e-02 nm, Epot= -4.56380e+04 Fmax= 3.06609e+02, atom= 1129\n", + "Step= 518, Dmax= 1.8e-02 nm, Epot= -4.56418e+04 Fmax= 1.35994e+02, atom= 1129\n", + "Step= 520, Dmax= 1.1e-02 nm, Epot= -4.56436e+04 Fmax= 9.97900e+01, atom= 1129\n", + "Step= 521, Dmax= 1.3e-02 nm, Epot= -4.56442e+04 Fmax= 1.97176e+02, atom= 1129\n", + "Step= 522, Dmax= 1.6e-02 nm, Epot= -4.56463e+04 Fmax= 1.58407e+02, atom= 1129\n", + "Step= 524, Dmax= 9.3e-03 nm, Epot= -4.56484e+04 Fmax= 5.35071e+01, atom= 1129\n", + "Step= 525, Dmax= 1.1e-02 nm, Epot= -4.56500e+04 Fmax= 2.12661e+02, atom= 1129\n", + "Step= 526, Dmax= 1.3e-02 nm, Epot= -4.56525e+04 Fmax= 9.93462e+01, atom= 1129\n", + "Step= 528, Dmax= 8.0e-03 nm, Epot= -4.56540e+04 Fmax= 7.90839e+01, atom= 1129\n", + "Step= 529, Dmax= 9.6e-03 nm, Epot= -4.56553e+04 Fmax= 1.39025e+02, atom= 1129\n", + "Step= 530, Dmax= 1.2e-02 nm, Epot= -4.56568e+04 Fmax= 1.25581e+02, atom= 1129\n", + "Step= 531, Dmax= 1.4e-02 nm, Epot= -4.56576e+04 Fmax= 1.88156e+02, atom= 1129\n", + "Step= 532, Dmax= 1.7e-02 nm, Epot= -4.56589e+04 Fmax= 1.92519e+02, atom= 1129\n", + "Step= 533, Dmax= 2.0e-02 nm, Epot= -4.56589e+04 Fmax= 2.58456e+02, atom= 1129\n", + "Step= 534, Dmax= 2.4e-02 nm, Epot= -4.56596e+04 Fmax= 2.89339e+02, atom= 1129\n", + "Step= 536, Dmax= 1.4e-02 nm, Epot= -4.56646e+04 Fmax= 5.21205e+01, atom= 1287\n", + "Step= 537, Dmax= 1.7e-02 nm, Epot= -4.56658e+04 Fmax= 3.31745e+02, atom= 1287\n", + "Step= 538, Dmax= 2.1e-02 nm, Epot= -4.56694e+04 Fmax= 1.70816e+02, atom= 1129\n", + "Step= 540, Dmax= 1.2e-02 nm, Epot= -4.56715e+04 Fmax= 9.49721e+01, atom= 1129\n", + "Step= 542, Dmax= 7.5e-03 nm, Epot= -4.56730e+04 Fmax= 7.46838e+01, atom= 1129\n", + "Step= 543, Dmax= 9.0e-03 nm, Epot= -4.56743e+04 Fmax= 1.26244e+02, atom= 1129\n", + "Step= 544, Dmax= 1.1e-02 nm, Epot= -4.56757e+04 Fmax= 1.13140e+02, atom= 1129\n", + "Step= 545, Dmax= 1.3e-02 nm, Epot= -4.56765e+04 Fmax= 1.79888e+02, atom= 1129\n", + "Step= 546, Dmax= 1.5e-02 nm, Epot= -4.56780e+04 Fmax= 1.64443e+02, atom= 1129\n", + "Step= 548, Dmax= 9.3e-03 nm, Epot= -4.56802e+04 Fmax= 3.81567e+01, atom= 1129\n", + "Step= 549, Dmax= 1.1e-02 nm, Epot= -4.56819e+04 Fmax= 2.28315e+02, atom= 1129\n", + "Step= 550, Dmax= 1.3e-02 nm, Epot= -4.56853e+04 Fmax= 8.72442e+01, atom= 1129\n", + "Step= 552, Dmax= 8.0e-03 nm, Epot= -4.56866e+04 Fmax= 8.59273e+01, atom= 1129\n", + "Step= 553, Dmax= 9.6e-03 nm, Epot= -4.56878e+04 Fmax= 1.30850e+02, atom= 1129\n", + "Step= 554, Dmax= 1.2e-02 nm, Epot= -4.56892e+04 Fmax= 1.23501e+02, atom= 1129\n", + "Step= 555, Dmax= 1.4e-02 nm, Epot= -4.56898e+04 Fmax= 1.89320e+02, atom= 1129\n", + "Step= 556, Dmax= 1.7e-02 nm, Epot= -4.56912e+04 Fmax= 1.77067e+02, atom= 1129\n", + "Step= 558, Dmax= 1.0e-02 nm, Epot= -4.56938e+04 Fmax= 3.85959e+01, atom= 1129\n", + "Step= 559, Dmax= 1.2e-02 nm, Epot= -4.56948e+04 Fmax= 2.50446e+02, atom= 1129\n", + "Step= 560, Dmax= 1.4e-02 nm, Epot= -4.56990e+04 Fmax= 8.93189e+01, atom= 1129\n", + "Step= 562, Dmax= 8.6e-03 nm, Epot= -4.57003e+04 Fmax= 9.35923e+01, atom= 1129\n", + "Step= 563, Dmax= 1.0e-02 nm, Epot= -4.57014e+04 Fmax= 1.36115e+02, atom= 1129\n", + "Step= 564, Dmax= 1.2e-02 nm, Epot= -4.57026e+04 Fmax= 1.34002e+02, atom= 1129\n", + "Step= 565, Dmax= 1.5e-02 nm, Epot= -4.57029e+04 Fmax= 1.97913e+02, atom= 1129\n", + "Step= 566, Dmax= 1.8e-02 nm, Epot= -4.57041e+04 Fmax= 1.91189e+02, atom= 1129\n", + "Step= 568, Dmax= 1.1e-02 nm, Epot= -4.57075e+04 Fmax= 3.80733e+01, atom= 9499\n", + "Step= 570, Dmax= 6.4e-03 nm, Epot= -4.57090e+04 Fmax= 1.05286e+02, atom= 1129\n", + "Step= 571, Dmax= 7.7e-03 nm, Epot= -4.57107e+04 Fmax= 6.82824e+01, atom= 1129\n", + "Step= 572, Dmax= 9.3e-03 nm, Epot= -4.57111e+04 Fmax= 1.30810e+02, atom= 1129\n", + "Step= 573, Dmax= 1.1e-02 nm, Epot= -4.57126e+04 Fmax= 1.24592e+02, atom= 626\n", + "Step= 575, Dmax= 6.7e-03 nm, Epot= -4.57151e+04 Fmax= 2.88645e+01, atom= 626\n", + "Step= 576, Dmax= 8.0e-03 nm, Epot= -4.57165e+04 Fmax= 1.74019e+02, atom= 626\n", + "Step= 577, Dmax= 9.6e-03 nm, Epot= -4.57198e+04 Fmax= 5.87299e+01, atom= 626\n", + "Step= 579, Dmax= 5.8e-03 nm, Epot= -4.57210e+04 Fmax= 7.44324e+01, atom= 626\n", + "Step= 580, Dmax= 6.9e-03 nm, Epot= -4.57222e+04 Fmax= 8.57592e+01, atom= 626\n", + "Step= 581, Dmax= 8.3e-03 nm, Epot= -4.57233e+04 Fmax= 1.07498e+02, atom= 626\n", + "Step= 582, Dmax= 1.0e-02 nm, Epot= -4.57243e+04 Fmax= 1.24789e+02, atom= 626\n", + "Step= 583, Dmax= 1.2e-02 nm, Epot= -4.57251e+04 Fmax= 1.53355e+02, atom= 626\n", + "Step= 584, Dmax= 1.4e-02 nm, Epot= -4.57257e+04 Fmax= 1.83535e+02, atom= 626\n", + "Step= 585, Dmax= 1.7e-02 nm, Epot= -4.57261e+04 Fmax= 2.16522e+02, atom= 626\n", + "Step= 587, Dmax= 1.0e-02 nm, Epot= -4.57302e+04 Fmax= 3.34683e+01, atom= 111\n", + "Step= 588, Dmax= 1.2e-02 nm, Epot= -4.57319e+04 Fmax= 2.23706e+02, atom= 626\n", + "Step= 589, Dmax= 1.5e-02 nm, Epot= -4.57349e+04 Fmax= 1.57227e+02, atom= 626\n", + "Step= 591, Dmax= 8.9e-03 nm, Epot= -4.57371e+04 Fmax= 4.69325e+01, atom= 339\n", + "Step= 592, Dmax= 1.1e-02 nm, Epot= -4.57375e+04 Fmax= 2.13229e+02, atom= 626\n", + "Step= 593, Dmax= 1.3e-02 nm, Epot= -4.57408e+04 Fmax= 9.23533e+01, atom= 626\n", + "Step= 595, Dmax= 7.7e-03 nm, Epot= -4.57420e+04 Fmax= 7.89265e+01, atom= 626\n", + "Step= 596, Dmax= 9.3e-03 nm, Epot= -4.57428e+04 Fmax= 1.38552e+02, atom= 626\n", + "Step= 597, Dmax= 1.1e-02 nm, Epot= -4.57442e+04 Fmax= 1.20676e+02, atom= 626\n", + "Step= 598, Dmax= 1.3e-02 nm, Epot= -4.57443e+04 Fmax= 1.90618e+02, atom= 626\n", + "Step= 599, Dmax= 1.6e-02 nm, Epot= -4.57455e+04 Fmax= 1.85581e+02, atom= 626\n", + "Step= 601, Dmax= 9.6e-03 nm, Epot= -4.57485e+04 Fmax= 3.84797e+01, atom= 339\n", + "Step= 602, Dmax= 1.2e-02 nm, Epot= -4.57498e+04 Fmax= 2.27593e+02, atom= 626\n", + "Step= 603, Dmax= 1.4e-02 nm, Epot= -4.57530e+04 Fmax= 1.00841e+02, atom= 626\n", + "Step= 605, Dmax= 8.3e-03 nm, Epot= -4.57542e+04 Fmax= 8.62654e+01, atom= 626\n", + "Step= 606, Dmax= 1.0e-02 nm, Epot= -4.57549e+04 Fmax= 1.46401e+02, atom= 626\n", + "Step= 607, Dmax= 1.2e-02 nm, Epot= -4.57562e+04 Fmax= 1.32638e+02, atom= 626\n", + "Step= 608, Dmax= 1.4e-02 nm, Epot= -4.57563e+04 Fmax= 2.01107e+02, atom= 626\n", + "Step= 609, Dmax= 1.7e-02 nm, Epot= -4.57573e+04 Fmax= 2.04194e+02, atom= 626\n", + "Step= 611, Dmax= 1.0e-02 nm, Epot= -4.57607e+04 Fmax= 3.78875e+01, atom= 339\n", + "Step= 612, Dmax= 1.2e-02 nm, Epot= -4.57621e+04 Fmax= 2.42805e+02, atom= 626\n", + "Step= 613, Dmax= 1.5e-02 nm, Epot= -4.57653e+04 Fmax= 1.11611e+02, atom= 626\n", + "Step= 615, Dmax= 8.9e-03 nm, Epot= -4.57666e+04 Fmax= 8.98677e+01, atom= 626\n", + "Step= 616, Dmax= 1.1e-02 nm, Epot= -4.57671e+04 Fmax= 1.60285e+02, atom= 626\n", + "Step= 617, Dmax= 1.3e-02 nm, Epot= -4.57685e+04 Fmax= 1.40252e+02, atom= 626\n", + "Step= 619, Dmax= 7.7e-03 nm, Epot= -4.57705e+04 Fmax= 3.85007e+01, atom= 626\n", + "Step= 620, Dmax= 9.2e-03 nm, Epot= -4.57720e+04 Fmax= 1.75561e+02, atom= 626\n", + "Step= 621, Dmax= 1.1e-02 nm, Epot= -4.57742e+04 Fmax= 8.31898e+01, atom= 626\n", + "Step= 623, Dmax= 6.7e-03 nm, Epot= -4.57754e+04 Fmax= 6.76687e+01, atom= 626\n", + "Step= 624, Dmax= 8.0e-03 nm, Epot= -4.57764e+04 Fmax= 1.18686e+02, atom= 626\n", + "Step= 625, Dmax= 9.6e-03 nm, Epot= -4.57776e+04 Fmax= 1.04747e+02, atom= 626\n", + "Step= 626, Dmax= 1.2e-02 nm, Epot= -4.57781e+04 Fmax= 1.62329e+02, atom= 626\n", + "Step= 627, Dmax= 1.4e-02 nm, Epot= -4.57792e+04 Fmax= 1.61684e+02, atom= 626\n", + "Step= 629, Dmax= 8.3e-03 nm, Epot= -4.57815e+04 Fmax= 3.11100e+01, atom= 626\n", + "Step= 630, Dmax= 9.9e-03 nm, Epot= -4.57835e+04 Fmax= 2.00061e+02, atom= 626\n", + "Step= 631, Dmax= 1.2e-02 nm, Epot= -4.57861e+04 Fmax= 8.06966e+01, atom= 626\n", + "Step= 633, Dmax= 7.2e-03 nm, Epot= -4.57872e+04 Fmax= 8.20879e+01, atom= 626\n", + "Step= 634, Dmax= 8.6e-03 nm, Epot= -4.57881e+04 Fmax= 1.16511e+02, atom= 626\n", + "Step= 635, Dmax= 1.0e-02 nm, Epot= -4.57891e+04 Fmax= 1.23377e+02, atom= 626\n", + "Step= 636, Dmax= 1.2e-02 nm, Epot= -4.57897e+04 Fmax= 1.62122e+02, atom= 626\n", + "Step= 637, Dmax= 1.5e-02 nm, Epot= -4.57903e+04 Fmax= 1.86355e+02, atom= 626\n", + "Step= 638, Dmax= 1.8e-02 nm, Epot= -4.57905e+04 Fmax= 2.24158e+02, atom= 626\n", + "Step= 640, Dmax= 1.1e-02 nm, Epot= -4.57942e+04 Fmax= 3.34035e+01, atom= 111\n", + "Step= 641, Dmax= 1.3e-02 nm, Epot= -4.57957e+04 Fmax= 2.23691e+02, atom= 626\n", + "Step= 642, Dmax= 1.5e-02 nm, Epot= -4.57982e+04 Fmax= 1.73777e+02, atom= 626\n", + "Step= 644, Dmax= 9.2e-03 nm, Epot= -4.58004e+04 Fmax= 4.01915e+01, atom= 339\n", + "Step= 645, Dmax= 1.1e-02 nm, Epot= -4.58010e+04 Fmax= 2.16701e+02, atom= 626\n", + "Step= 646, Dmax= 1.3e-02 nm, Epot= -4.58039e+04 Fmax= 9.80511e+01, atom= 626\n", + "Step= 648, Dmax= 8.0e-03 nm, Epot= -4.58050e+04 Fmax= 7.75466e+01, atom= 626\n", + "Step= 649, Dmax= 9.6e-03 nm, Epot= -4.58056e+04 Fmax= 1.45271e+02, atom= 626\n", + "Step= 650, Dmax= 1.1e-02 nm, Epot= -4.58069e+04 Fmax= 1.21950e+02, atom= 626\n", + "Step= 652, Dmax= 6.9e-03 nm, Epot= -4.58084e+04 Fmax= 3.68743e+01, atom= 626\n", + "Step= 653, Dmax= 8.3e-03 nm, Epot= -4.58097e+04 Fmax= 1.53413e+02, atom= 626\n", + "Step= 654, Dmax= 9.9e-03 nm, Epot= -4.58115e+04 Fmax= 7.53789e+01, atom= 626\n", + "Step= 656, Dmax= 6.0e-03 nm, Epot= -4.58125e+04 Fmax= 5.92159e+01, atom= 626\n", + "Step= 657, Dmax= 7.1e-03 nm, Epot= -4.58134e+04 Fmax= 1.05945e+02, atom= 626\n", + "Step= 658, Dmax= 8.6e-03 nm, Epot= -4.58144e+04 Fmax= 9.28509e+01, atom= 626\n", + "Step= 659, Dmax= 1.0e-02 nm, Epot= -4.58149e+04 Fmax= 1.43778e+02, atom= 626\n", + "Step= 660, Dmax= 1.2e-02 nm, Epot= -4.58158e+04 Fmax= 1.44076e+02, atom= 626\n", + "Step= 661, Dmax= 1.5e-02 nm, Epot= -4.58159e+04 Fmax= 1.96017e+02, atom= 626\n", + "Step= 662, Dmax= 1.8e-02 nm, Epot= -4.58162e+04 Fmax= 2.21198e+02, atom= 626\n", + "Step= 664, Dmax= 1.1e-02 nm, Epot= -4.58197e+04 Fmax= 2.86682e+01, atom= 339\n", + "Step= 665, Dmax= 1.3e-02 nm, Epot= -4.58216e+04 Fmax= 2.46250e+02, atom= 339\n", + "Step= 666, Dmax= 1.5e-02 nm, Epot= -4.58244e+04 Fmax= 1.17483e+02, atom= 626\n", + "Step= 668, Dmax= 9.2e-03 nm, Epot= -4.58255e+04 Fmax= 9.35294e+01, atom= 626\n", + "Step= 669, Dmax= 1.1e-02 nm, Epot= -4.58257e+04 Fmax= 1.60133e+02, atom= 626\n", + "Step= 670, Dmax= 1.3e-02 nm, Epot= -4.58268e+04 Fmax= 1.47075e+02, atom= 626\n", + "Step= 672, Dmax= 8.0e-03 nm, Epot= -4.58286e+04 Fmax= 3.48702e+01, atom= 626\n", + "Step= 673, Dmax= 9.6e-03 nm, Epot= -4.58296e+04 Fmax= 1.84975e+02, atom= 626\n", + "Step= 674, Dmax= 1.1e-02 nm, Epot= -4.58317e+04 Fmax= 7.91715e+01, atom= 626\n", + "Step= 676, Dmax= 6.9e-03 nm, Epot= -4.58326e+04 Fmax= 7.54126e+01, atom= 626\n", + "Step= 677, Dmax= 8.3e-03 nm, Epot= -4.58332e+04 Fmax= 1.13053e+02, atom= 626\n", + "Step= 678, Dmax= 9.9e-03 nm, Epot= -4.58341e+04 Fmax= 1.13923e+02, atom= 626\n", + "Step= 679, Dmax= 1.2e-02 nm, Epot= -4.58344e+04 Fmax= 1.56866e+02, atom= 626\n", + "Step= 680, Dmax= 1.4e-02 nm, Epot= -4.58349e+04 Fmax= 1.73781e+02, atom= 626\n", + "Step= 682, Dmax= 8.6e-03 nm, Epot= -4.58373e+04 Fmax= 2.43104e+01, atom= 339\n", + "Step= 683, Dmax= 1.0e-02 nm, Epot= -4.58392e+04 Fmax= 1.98552e+02, atom= 626\n", + "Step= 684, Dmax= 1.2e-02 nm, Epot= -4.58414e+04 Fmax= 8.76776e+01, atom= 626\n", + "Step= 686, Dmax= 7.4e-03 nm, Epot= -4.58423e+04 Fmax= 7.96636e+01, atom= 626\n", + "Step= 687, Dmax= 8.9e-03 nm, Epot= -4.58428e+04 Fmax= 1.22100e+02, atom= 626\n", + "Step= 688, Dmax= 1.1e-02 nm, Epot= -4.58436e+04 Fmax= 1.22873e+02, atom= 626\n", + "Step= 689, Dmax= 1.3e-02 nm, Epot= -4.58437e+04 Fmax= 1.67119e+02, atom= 626\n", + "Step= 690, Dmax= 1.5e-02 nm, Epot= -4.58441e+04 Fmax= 1.88465e+02, atom= 626\n", + "Step= 692, Dmax= 9.2e-03 nm, Epot= -4.58468e+04 Fmax= 2.43464e+01, atom= 339\n", + "Step= 693, Dmax= 1.1e-02 nm, Epot= -4.58485e+04 Fmax= 2.13060e+02, atom= 626\n", + "Step= 694, Dmax= 1.3e-02 nm, Epot= -4.58508e+04 Fmax= 9.51410e+01, atom= 626\n", + "Step= 696, Dmax= 7.9e-03 nm, Epot= -4.58517e+04 Fmax= 8.46092e+01, atom= 626\n", + "Step= 697, Dmax= 9.5e-03 nm, Epot= -4.58520e+04 Fmax= 1.31069e+02, atom= 626\n", + "Step= 698, Dmax= 1.1e-02 nm, Epot= -4.58527e+04 Fmax= 1.31274e+02, atom= 626\n", + "Step= 700, Dmax= 6.9e-03 nm, Epot= -4.58543e+04 Fmax= 2.45783e+01, atom= 626\n", + "Step= 701, Dmax= 8.2e-03 nm, Epot= -4.58556e+04 Fmax= 1.62084e+02, atom= 626\n", + "Step= 702, Dmax= 9.9e-03 nm, Epot= -4.58574e+04 Fmax= 6.35204e+01, atom= 626\n", + "Step= 704, Dmax= 5.9e-03 nm, Epot= -4.58581e+04 Fmax= 6.93124e+01, atom= 626\n", + "Step= 705, Dmax= 7.1e-03 nm, Epot= -4.58587e+04 Fmax= 9.09135e+01, atom= 626\n", + "Step= 706, Dmax= 8.5e-03 nm, Epot= -4.58593e+04 Fmax= 1.03836e+02, atom= 626\n", + "Step= 707, Dmax= 1.0e-02 nm, Epot= -4.58597e+04 Fmax= 1.26700e+02, atom= 626\n", + "Step= 708, Dmax= 1.2e-02 nm, Epot= -4.58600e+04 Fmax= 1.55535e+02, atom= 626\n", + "Step= 709, Dmax= 1.5e-02 nm, Epot= -4.58602e+04 Fmax= 1.76519e+02, atom= 626\n", + "Step= 711, Dmax= 8.9e-03 nm, Epot= -4.58627e+04 Fmax= 2.80137e+01, atom= 111\n", + "Step= 713, Dmax= 5.3e-03 nm, Epot= -4.58637e+04 Fmax= 8.28236e+01, atom= 626\n", + "Step= 714, Dmax= 6.4e-03 nm, Epot= -4.58646e+04 Fmax= 6.59385e+01, atom= 626\n", + "Step= 715, Dmax= 7.7e-03 nm, Epot= -4.58648e+04 Fmax= 1.04491e+02, atom= 626\n", + "Step= 716, Dmax= 9.2e-03 nm, Epot= -4.58654e+04 Fmax= 1.04483e+02, atom= 626\n", + "Step= 718, Dmax= 5.5e-03 nm, Epot= -4.58669e+04 Fmax= 2.96837e+01, atom= 696\n", + "Step= 719, Dmax= 6.6e-03 nm, Epot= -4.58676e+04 Fmax= 1.36893e+02, atom= 696\n", + "Step= 720, Dmax= 7.9e-03 nm, Epot= -4.58690e+04 Fmax= 5.98559e+01, atom= 696\n", + "Step= 722, Dmax= 4.8e-03 nm, Epot= -4.58696e+04 Fmax= 5.55559e+01, atom= 696\n", + "Step= 723, Dmax= 5.7e-03 nm, Epot= -4.58703e+04 Fmax= 8.28382e+01, atom= 696\n", + "Step= 724, Dmax= 6.9e-03 nm, Epot= -4.58709e+04 Fmax= 8.51594e+01, atom= 696\n", + "Step= 725, Dmax= 8.2e-03 nm, Epot= -4.58714e+04 Fmax= 1.14127e+02, atom= 696\n", + "Step= 726, Dmax= 9.9e-03 nm, Epot= -4.58719e+04 Fmax= 1.27865e+02, atom= 696\n", + "Step= 727, Dmax= 1.2e-02 nm, Epot= -4.58722e+04 Fmax= 1.58770e+02, atom= 696\n", + "Step= 728, Dmax= 1.4e-02 nm, Epot= -4.58725e+04 Fmax= 1.91316e+02, atom= 696\n", + "Step= 730, Dmax= 8.5e-03 nm, Epot= -4.58743e+04 Fmax= 2.53731e+01, atom= 191\n", + "Step= 731, Dmax= 1.0e-02 nm, Epot= -4.58754e+04 Fmax= 2.27614e+02, atom= 696\n", + "Step= 732, Dmax= 1.2e-02 nm, Epot= -4.58774e+04 Fmax= 9.43082e+01, atom= 696\n", + "Step= 734, Dmax= 7.4e-03 nm, Epot= -4.58781e+04 Fmax= 8.37465e+01, atom= 696\n", + "Step= 735, Dmax= 8.8e-03 nm, Epot= -4.58784e+04 Fmax= 1.30938e+02, atom= 696\n", + "Step= 736, Dmax= 1.1e-02 nm, Epot= -4.58791e+04 Fmax= 1.29128e+02, atom= 696\n", + "Step= 737, Dmax= 1.3e-02 nm, Epot= -4.58791e+04 Fmax= 1.79510e+02, atom= 696\n", + "Step= 738, Dmax= 1.5e-02 nm, Epot= -4.58796e+04 Fmax= 1.96587e+02, atom= 696\n", + "Step= 740, Dmax= 9.2e-03 nm, Epot= -4.58815e+04 Fmax= 3.34952e+01, atom= 696\n", + "Step= 741, Dmax= 1.1e-02 nm, Epot= -4.58815e+04 Fmax= 2.61026e+02, atom= 696\n", + "Step= 742, Dmax= 1.3e-02 nm, Epot= -4.58840e+04 Fmax= 8.84561e+01, atom= 696\n", + "Step= 744, Dmax= 7.9e-03 nm, Epot= -4.58846e+04 Fmax= 1.03517e+02, atom= 696\n", + "Step= 745, Dmax= 9.5e-03 nm, Epot= -4.58850e+04 Fmax= 1.27714e+02, atom= 696\n", + "Step= 746, Dmax= 1.1e-02 nm, Epot= -4.58855e+04 Fmax= 1.53982e+02, atom= 696\n", + "Step= 747, Dmax= 1.4e-02 nm, Epot= -4.58857e+04 Fmax= 1.79021e+02, atom= 696\n", + "Step= 749, Dmax= 8.2e-03 nm, Epot= -4.58875e+04 Fmax= 1.68681e+01, atom= 696\n", + "Step= 750, Dmax= 9.9e-03 nm, Epot= -4.58890e+04 Fmax= 2.55762e+02, atom= 696\n", + "Step= 751, Dmax= 1.2e-02 nm, Epot= -4.58921e+04 Fmax= 6.30489e+01, atom= 696\n", + "Step= 753, Dmax= 7.1e-03 nm, Epot= -4.58928e+04 Fmax= 9.88373e+01, atom= 696\n", + "Step= 754, Dmax= 8.5e-03 nm, Epot= -4.58934e+04 Fmax= 1.09249e+02, atom= 696\n", + "Step= 755, Dmax= 1.0e-02 nm, Epot= -4.58937e+04 Fmax= 1.39228e+02, atom= 696\n", + "Step= 756, Dmax= 1.2e-02 nm, Epot= -4.58941e+04 Fmax= 1.64990e+02, atom= 696\n", + "Step= 757, Dmax= 1.5e-02 nm, Epot= -4.58942e+04 Fmax= 1.93183e+02, atom= 696\n", + "Step= 759, Dmax= 8.8e-03 nm, Epot= -4.58963e+04 Fmax= 1.79444e+01, atom= 1511\n", + "Step= 760, Dmax= 1.1e-02 nm, Epot= -4.58975e+04 Fmax= 2.75260e+02, atom= 696\n", + "Step= 761, Dmax= 1.3e-02 nm, Epot= -4.59011e+04 Fmax= 7.16349e+01, atom= 696\n", + "Step= 763, Dmax= 7.6e-03 nm, Epot= -4.59017e+04 Fmax= 1.01123e+02, atom= 696\n", + "Step= 764, Dmax= 9.2e-03 nm, Epot= -4.59022e+04 Fmax= 1.24428e+02, atom= 696\n", + "Step= 765, Dmax= 1.1e-02 nm, Epot= -4.59026e+04 Fmax= 1.42586e+02, atom= 696\n", + "Step= 766, Dmax= 1.3e-02 nm, Epot= -4.59029e+04 Fmax= 1.86544e+02, atom= 696\n", + "Step= 767, Dmax= 1.6e-02 nm, Epot= -4.59032e+04 Fmax= 1.98758e+02, atom= 696\n", + "Step= 769, Dmax= 9.5e-03 nm, Epot= -4.59053e+04 Fmax= 2.60362e+01, atom= 696\n", + "Step= 771, Dmax= 5.7e-03 nm, Epot= -4.59065e+04 Fmax= 1.21331e+02, atom= 696\n", + "Step= 772, Dmax= 6.8e-03 nm, Epot= -4.59075e+04 Fmax= 5.12257e+01, atom= 696\n", + "Step= 773, Dmax= 8.2e-03 nm, Epot= -4.59081e+04 Fmax= 1.43502e+02, atom= 696\n", + "Step= 774, Dmax= 9.8e-03 nm, Epot= -4.59091e+04 Fmax= 9.64388e+01, atom= 696\n", + "Step= 776, Dmax= 5.9e-03 nm, Epot= -4.59100e+04 Fmax= 4.93222e+01, atom= 696\n", + "Step= 777, Dmax= 7.1e-03 nm, Epot= -4.59106e+04 Fmax= 1.27857e+02, atom= 696\n", + "Step= 778, Dmax= 8.5e-03 nm, Epot= -4.59115e+04 Fmax= 8.28113e+01, atom= 696\n", + "Step= 779, Dmax= 1.0e-02 nm, Epot= -4.59117e+04 Fmax= 1.74407e+02, atom= 696\n", + "Step= 780, Dmax= 1.2e-02 nm, Epot= -4.59127e+04 Fmax= 1.28255e+02, atom= 696\n", + "Step= 782, Dmax= 7.3e-03 nm, Epot= -4.59139e+04 Fmax= 4.71149e+01, atom= 696\n", + "Step= 783, Dmax= 8.8e-03 nm, Epot= -4.59143e+04 Fmax= 1.70745e+02, atom= 696\n", + "Step= 784, Dmax= 1.1e-02 nm, Epot= -4.59159e+04 Fmax= 9.03932e+01, atom= 696\n", + "Step= 786, Dmax= 6.3e-03 nm, Epot= -4.59167e+04 Fmax= 6.52017e+01, atom= 696\n", + "Step= 787, Dmax= 7.6e-03 nm, Epot= -4.59173e+04 Fmax= 1.24195e+02, atom= 696\n", + "Step= 788, Dmax= 9.1e-03 nm, Epot= -4.59182e+04 Fmax= 1.00740e+02, atom= 696\n", + "Step= 789, Dmax= 1.1e-02 nm, Epot= -4.59184e+04 Fmax= 1.73851e+02, atom= 696\n", + "Step= 790, Dmax= 1.3e-02 nm, Epot= -4.59193e+04 Fmax= 1.49320e+02, atom= 696\n", + "Step= 792, Dmax= 7.9e-03 nm, Epot= -4.59208e+04 Fmax= 3.80837e+01, atom= 696\n", + "Step= 793, Dmax= 9.5e-03 nm, Epot= -4.59213e+04 Fmax= 2.01673e+02, atom= 696\n", + "Step= 794, Dmax= 1.1e-02 nm, Epot= -4.59235e+04 Fmax= 8.16628e+01, atom= 696\n", + "Step= 796, Dmax= 6.8e-03 nm, Epot= -4.59242e+04 Fmax= 8.32237e+01, atom= 696\n", + "Step= 797, Dmax= 8.2e-03 nm, Epot= -4.59249e+04 Fmax= 1.18894e+02, atom= 696\n", + "Step= 798, Dmax= 9.8e-03 nm, Epot= -4.59257e+04 Fmax= 1.20546e+02, atom= 696\n", + "Step= 799, Dmax= 1.2e-02 nm, Epot= -4.59261e+04 Fmax= 1.73150e+02, atom= 696\n", + "Step= 800, Dmax= 1.4e-02 nm, Epot= -4.59267e+04 Fmax= 1.71757e+02, atom= 696\n", + "Step= 802, Dmax= 8.5e-03 nm, Epot= -4.59286e+04 Fmax= 2.88038e+01, atom= 696\n", + "Step= 803, Dmax= 1.0e-02 nm, Epot= -4.59295e+04 Fmax= 2.37911e+02, atom= 696\n", + "Step= 804, Dmax= 1.2e-02 nm, Epot= -4.59325e+04 Fmax= 7.37178e+01, atom= 696\n", + "Step= 806, Dmax= 7.3e-03 nm, Epot= -4.59333e+04 Fmax= 9.95469e+01, atom= 696\n", + "Step= 807, Dmax= 8.8e-03 nm, Epot= -4.59341e+04 Fmax= 1.16390e+02, atom= 696\n", + "Step= 808, Dmax= 1.1e-02 nm, Epot= -4.59347e+04 Fmax= 1.39321e+02, atom= 696\n", + "Step= 809, Dmax= 1.3e-02 nm, Epot= -4.59353e+04 Fmax= 1.74346e+02, atom= 696\n", + "Step= 810, Dmax= 1.5e-02 nm, Epot= -4.59357e+04 Fmax= 1.93123e+02, atom= 696\n", + "Step= 812, Dmax= 9.1e-03 nm, Epot= -4.59379e+04 Fmax= 2.10786e+01, atom= 696\n", + "Step= 813, Dmax= 1.1e-02 nm, Epot= -4.59394e+04 Fmax= 2.86557e+02, atom= 696\n", + "Step= 814, Dmax= 1.3e-02 nm, Epot= -4.59437e+04 Fmax= 6.38750e+01, atom= 696\n", + "Step= 816, Dmax= 7.9e-03 nm, Epot= -4.59446e+04 Fmax= 1.11839e+02, atom= 696\n", + "Step= 817, Dmax= 9.5e-03 nm, Epot= -4.59454e+04 Fmax= 1.15613e+02, atom= 696\n", + "Step= 818, Dmax= 1.1e-02 nm, Epot= -4.59458e+04 Fmax= 1.56136e+02, atom= 696\n", + "Step= 819, Dmax= 1.4e-02 nm, Epot= -4.59465e+04 Fmax= 1.78894e+02, atom= 696\n", + "Step= 820, Dmax= 1.6e-02 nm, Epot= -4.59465e+04 Fmax= 2.12800e+02, atom= 696\n", + "Step= 822, Dmax= 9.8e-03 nm, Epot= -4.59492e+04 Fmax= 2.06677e+01, atom= 1511\n", + "Step= 823, Dmax= 1.2e-02 nm, Epot= -4.59516e+04 Fmax= 2.51790e+02, atom= 696\n", + "Step= 824, Dmax= 1.4e-02 nm, Epot= -4.59549e+04 Fmax= 1.31246e+02, atom= 696\n", + "Step= 826, Dmax= 8.5e-03 nm, Epot= -4.59559e+04 Fmax= 6.92900e+01, atom= 696\n", + "Step= 827, Dmax= 1.0e-02 nm, Epot= -4.59560e+04 Fmax= 1.96379e+02, atom= 696\n", + "Step= 828, Dmax= 1.2e-02 nm, Epot= -4.59576e+04 Fmax= 1.05095e+02, atom= 696\n", + "Step= 830, Dmax= 7.3e-03 nm, Epot= -4.59586e+04 Fmax= 6.67046e+01, atom= 696\n", + "Step= 831, Dmax= 8.8e-03 nm, Epot= -4.59591e+04 Fmax= 1.44450e+02, atom= 696\n", + "Step= 832, Dmax= 1.1e-02 nm, Epot= -4.59603e+04 Fmax= 1.10789e+02, atom= 696\n", + "Step= 834, Dmax= 6.3e-03 nm, Epot= -4.59613e+04 Fmax= 4.47419e+01, atom= 696\n", + "Step= 835, Dmax= 7.6e-03 nm, Epot= -4.59622e+04 Fmax= 1.41817e+02, atom= 696\n", + "Step= 836, Dmax= 9.1e-03 nm, Epot= -4.59633e+04 Fmax= 7.99906e+01, atom= 696\n", + "Step= 837, Dmax= 1.1e-02 nm, Epot= -4.59634e+04 Fmax= 1.94667e+02, atom= 696\n", + "Step= 838, Dmax= 1.3e-02 nm, Epot= -4.59648e+04 Fmax= 1.25324e+02, atom= 696\n", + "Step= 840, Dmax= 7.9e-03 nm, Epot= -4.59660e+04 Fmax= 5.69470e+01, atom= 696\n", + "Step= 841, Dmax= 9.4e-03 nm, Epot= -4.59663e+04 Fmax= 1.70257e+02, atom= 696\n", + "Step= 842, Dmax= 1.1e-02 nm, Epot= -4.59679e+04 Fmax= 1.02786e+02, atom= 696\n", + "Step= 844, Dmax= 6.8e-03 nm, Epot= -4.59688e+04 Fmax= 6.11445e+01, atom= 696\n", + "Step= 845, Dmax= 8.2e-03 nm, Epot= -4.59694e+04 Fmax= 1.37869e+02, atom= 696\n", + "Step= 846, Dmax= 9.8e-03 nm, Epot= -4.59704e+04 Fmax= 9.83886e+01, atom= 696\n", + "Step= 848, Dmax= 5.9e-03 nm, Epot= -4.59714e+04 Fmax= 3.85417e+01, atom= 696\n", + "Step= 849, Dmax= 7.1e-03 nm, Epot= -4.59723e+04 Fmax= 1.29147e+02, atom= 696\n", + "Step= 850, Dmax= 8.5e-03 nm, Epot= -4.59735e+04 Fmax= 7.34971e+01, atom= 696\n", + "Step= 851, Dmax= 1.0e-02 nm, Epot= -4.59736e+04 Fmax= 1.64444e+02, atom= 696\n", + "Step= 852, Dmax= 1.2e-02 nm, Epot= -4.59749e+04 Fmax= 1.26935e+02, atom= 696\n", + "Step= 854, Dmax= 7.3e-03 nm, Epot= -4.59761e+04 Fmax= 5.01021e+01, atom= 696\n", + "Step= 855, Dmax= 8.8e-03 nm, Epot= -4.59766e+04 Fmax= 1.64919e+02, atom= 696\n", + "Step= 856, Dmax= 1.1e-02 nm, Epot= -4.59779e+04 Fmax= 8.98120e+01, atom= 696\n", + "Step= 858, Dmax= 6.3e-03 nm, Epot= -4.59788e+04 Fmax= 5.65161e+01, atom= 696\n", + "Step= 859, Dmax= 7.6e-03 nm, Epot= -4.59794e+04 Fmax= 1.22357e+02, atom= 696\n", + "Step= 860, Dmax= 9.1e-03 nm, Epot= -4.59804e+04 Fmax= 9.39430e+01, atom= 696\n", + "Step= 861, Dmax= 1.1e-02 nm, Epot= -4.59805e+04 Fmax= 1.61725e+02, atom= 696\n", + "Step= 862, Dmax= 1.3e-02 nm, Epot= -4.59814e+04 Fmax= 1.51142e+02, atom= 696\n", + "Step= 864, Dmax= 7.9e-03 nm, Epot= -4.59829e+04 Fmax= 3.98937e+01, atom= 696\n", + "Step= 865, Dmax= 9.4e-03 nm, Epot= -4.59835e+04 Fmax= 1.92098e+02, atom= 696\n", + "Step= 866, Dmax= 1.1e-02 nm, Epot= -4.59852e+04 Fmax= 8.41308e+01, atom= 696\n", + "Step= 868, Dmax= 6.8e-03 nm, Epot= -4.59860e+04 Fmax= 7.31203e+01, atom= 696\n", + "Step= 869, Dmax= 8.1e-03 nm, Epot= -4.59865e+04 Fmax= 1.17310e+02, atom= 696\n", + "Step= 870, Dmax= 9.8e-03 nm, Epot= -4.59873e+04 Fmax= 1.13644e+02, atom= 696\n", + "Step= 871, Dmax= 1.2e-02 nm, Epot= -4.59874e+04 Fmax= 1.59660e+02, atom= 696\n", + "Step= 872, Dmax= 1.4e-02 nm, Epot= -4.59880e+04 Fmax= 1.75921e+02, atom= 696\n", + "Step= 874, Dmax= 8.4e-03 nm, Epot= -4.59899e+04 Fmax= 2.95566e+01, atom= 191\n", + "Step= 875, Dmax= 1.0e-02 nm, Epot= -4.59908e+04 Fmax= 2.21059e+02, atom= 696\n", + "Step= 876, Dmax= 1.2e-02 nm, Epot= -4.59930e+04 Fmax= 8.19043e+01, atom= 696\n", + "Step= 878, Dmax= 7.3e-03 nm, Epot= -4.59937e+04 Fmax= 8.62007e+01, atom= 696\n", + "Step= 879, Dmax= 8.8e-03 nm, Epot= -4.59942e+04 Fmax= 1.16754e+02, atom= 696\n", + "Step= 880, Dmax= 1.1e-02 nm, Epot= -4.59948e+04 Fmax= 1.30602e+02, atom= 696\n", + "Step= 881, Dmax= 1.3e-02 nm, Epot= -4.59950e+04 Fmax= 1.60549e+02, atom= 696\n", + "Step= 882, Dmax= 1.5e-02 nm, Epot= -4.59953e+04 Fmax= 1.99084e+02, atom= 696\n", + "Step= 883, Dmax= 1.8e-02 nm, Epot= -4.59953e+04 Fmax= 2.19377e+02, atom= 696\n", + "Step= 885, Dmax= 1.1e-02 nm, Epot= -4.59983e+04 Fmax= 2.72405e+01, atom= 1511\n", + "Step= 887, Dmax= 6.5e-03 nm, Epot= -4.59995e+04 Fmax= 1.16456e+02, atom= 696\n", + "Step= 888, Dmax= 7.8e-03 nm, Epot= -4.60006e+04 Fmax= 7.52595e+01, atom= 696\n", + "Step= 889, Dmax= 9.4e-03 nm, Epot= -4.60009e+04 Fmax= 1.36825e+02, atom= 696\n", + "Step= 890, Dmax= 1.1e-02 nm, Epot= -4.60018e+04 Fmax= 1.23755e+02, atom= 696\n", + "Step= 892, Dmax= 6.8e-03 nm, Epot= -4.60029e+04 Fmax= 3.58911e+01, atom= 696\n", + "Step= 893, Dmax= 8.1e-03 nm, Epot= -4.60037e+04 Fmax= 1.59753e+02, atom= 696\n", + "Step= 894, Dmax= 9.8e-03 nm, Epot= -4.60051e+04 Fmax= 7.26474e+01, atom= 696\n", + "Step= 896, Dmax= 5.9e-03 nm, Epot= -4.60058e+04 Fmax= 6.05773e+01, atom= 696\n", + "Step= 897, Dmax= 7.0e-03 nm, Epot= -4.60064e+04 Fmax= 9.97408e+01, atom= 696\n", + "Step= 898, Dmax= 8.4e-03 nm, Epot= -4.60071e+04 Fmax= 9.56890e+01, atom= 696\n", + "Step= 899, Dmax= 1.0e-02 nm, Epot= -4.60074e+04 Fmax= 1.34885e+02, atom= 696\n", + "Step= 900, Dmax= 1.2e-02 nm, Epot= -4.60080e+04 Fmax= 1.47724e+02, atom= 696\n", + "Step= 902, Dmax= 7.3e-03 nm, Epot= -4.60095e+04 Fmax= 2.60782e+01, atom= 696\n", + "Step= 903, Dmax= 8.7e-03 nm, Epot= -4.60107e+04 Fmax= 1.81071e+02, atom= 696\n", + "Step= 904, Dmax= 1.0e-02 nm, Epot= -4.60123e+04 Fmax= 6.99609e+01, atom= 696\n", + "Step= 906, Dmax= 6.3e-03 nm, Epot= -4.60130e+04 Fmax= 7.39022e+01, atom= 696\n", + "Step= 907, Dmax= 7.6e-03 nm, Epot= -4.60136e+04 Fmax= 9.79917e+01, atom= 696\n", + "Step= 908, Dmax= 9.1e-03 nm, Epot= -4.60142e+04 Fmax= 1.10863e+02, atom= 696\n", + "Step= 909, Dmax= 1.1e-02 nm, Epot= -4.60145e+04 Fmax= 1.35643e+02, atom= 696\n", + "Step= 910, Dmax= 1.3e-02 nm, Epot= -4.60149e+04 Fmax= 1.66970e+02, atom= 696\n", + "Step= 911, Dmax= 1.6e-02 nm, Epot= -4.60150e+04 Fmax= 1.86074e+02, atom= 696\n", + "Step= 913, Dmax= 9.4e-03 nm, Epot= -4.60173e+04 Fmax= 2.15397e+01, atom= 1511\n", + "Step= 914, Dmax= 1.1e-02 nm, Epot= -4.60175e+04 Fmax= 2.43080e+02, atom= 696\n", + "Step= 915, Dmax= 1.4e-02 nm, Epot= -4.60212e+04 Fmax= 9.64143e+01, atom= 696\n", + "Step= 917, Dmax= 8.1e-03 nm, Epot= -4.60219e+04 Fmax= 8.13839e+01, atom= 696\n", + "Step= 918, Dmax= 9.7e-03 nm, Epot= -4.60221e+04 Fmax= 1.46521e+02, atom= 696\n", + "Step= 919, Dmax= 1.2e-02 nm, Epot= -4.60229e+04 Fmax= 1.17913e+02, atom= 696\n", + "Step= 921, Dmax= 7.0e-03 nm, Epot= -4.60241e+04 Fmax= 3.54228e+01, atom= 696\n", + "Step= 922, Dmax= 8.4e-03 nm, Epot= -4.60244e+04 Fmax= 1.56269e+02, atom= 696\n", + "Step= 923, Dmax= 1.0e-02 nm, Epot= -4.60260e+04 Fmax= 7.40305e+01, atom= 696\n", + "Step= 925, Dmax= 6.1e-03 nm, Epot= -4.60267e+04 Fmax= 6.27464e+01, atom= 696\n", + "Step= 926, Dmax= 7.3e-03 nm, Epot= -4.60271e+04 Fmax= 1.02365e+02, atom= 696\n", + "Step= 927, Dmax= 8.7e-03 nm, Epot= -4.60278e+04 Fmax= 9.37348e+01, atom= 696\n", + "Step= 928, Dmax= 1.0e-02 nm, Epot= -4.60279e+04 Fmax= 1.46106e+02, atom= 696\n", + "Step= 929, Dmax= 1.3e-02 nm, Epot= -4.60286e+04 Fmax= 1.35090e+02, atom= 696\n", + "Step= 931, Dmax= 7.5e-03 nm, Epot= -4.60300e+04 Fmax= 2.75206e+01, atom= 696\n", + "Step= 932, Dmax= 9.1e-03 nm, Epot= -4.60302e+04 Fmax= 1.83359e+02, atom= 696\n", + "Step= 933, Dmax= 1.1e-02 nm, Epot= -4.60325e+04 Fmax= 6.64250e+01, atom= 696\n", + "Step= 935, Dmax= 6.5e-03 nm, Epot= -4.60331e+04 Fmax= 7.74249e+01, atom= 696\n", + "Step= 936, Dmax= 7.8e-03 nm, Epot= -4.60336e+04 Fmax= 9.81062e+01, atom= 696\n", + "Step= 937, Dmax= 9.4e-03 nm, Epot= -4.60340e+04 Fmax= 1.09572e+02, atom= 696\n", + "Step= 938, Dmax= 1.1e-02 nm, Epot= -4.60343e+04 Fmax= 1.45081e+02, atom= 696\n", + "Step= 939, Dmax= 1.4e-02 nm, Epot= -4.60347e+04 Fmax= 1.52938e+02, atom= 696\n", + "Step= 941, Dmax= 8.1e-03 nm, Epot= -4.60364e+04 Fmax= 2.02457e+01, atom= 696\n", + "Step= 942, Dmax= 9.7e-03 nm, Epot= -4.60365e+04 Fmax= 2.16684e+02, atom= 696\n", + "Step= 943, Dmax= 1.2e-02 nm, Epot= -4.60399e+04 Fmax= 5.84330e+01, atom= 696\n", + "Step= 945, Dmax= 7.0e-03 nm, Epot= -4.60404e+04 Fmax= 9.02180e+01, atom= 696\n", + "Step= 946, Dmax= 8.4e-03 nm, Epot= -4.60410e+04 Fmax= 9.50576e+01, atom= 696\n", + "Step= 947, Dmax= 1.0e-02 nm, Epot= -4.60413e+04 Fmax= 1.24530e+02, atom= 696\n", + "Step= 948, Dmax= 1.2e-02 nm, Epot= -4.60417e+04 Fmax= 1.44572e+02, atom= 696\n", + "Step= 950, Dmax= 7.3e-03 nm, Epot= -4.60432e+04 Fmax= 2.13276e+01, atom= 696\n", + "Step= 951, Dmax= 8.7e-03 nm, Epot= -4.60445e+04 Fmax= 1.70152e+02, atom= 191\n", + "Step= 952, Dmax= 1.0e-02 nm, Epot= -4.60461e+04 Fmax= 6.71149e+01, atom= 696\n", + "Step= 954, Dmax= 6.3e-03 nm, Epot= -4.60467e+04 Fmax= 6.99240e+01, atom= 696\n", + "Step= 955, Dmax= 7.5e-03 nm, Epot= -4.60472e+04 Fmax= 9.29654e+01, atom= 696\n", + "Step= 956, Dmax= 9.0e-03 nm, Epot= -4.60477e+04 Fmax= 1.06140e+02, atom= 696\n", + "Step= 957, Dmax= 1.1e-02 nm, Epot= -4.60480e+04 Fmax= 1.27478e+02, atom= 696\n", + "Step= 958, Dmax= 1.3e-02 nm, Epot= -4.60482e+04 Fmax= 1.60675e+02, atom= 696\n", + "Step= 959, Dmax= 1.6e-02 nm, Epot= -4.60483e+04 Fmax= 1.74802e+02, atom= 696\n", + "Step= 961, Dmax= 9.4e-03 nm, Epot= -4.60506e+04 Fmax= 2.13263e+01, atom= 1511\n", + "Step= 963, Dmax= 5.6e-03 nm, Epot= -4.60515e+04 Fmax= 1.06058e+02, atom= 696\n", + "Step= 964, Dmax= 6.7e-03 nm, Epot= -4.60527e+04 Fmax= 4.72374e+01, atom= 696\n", + "Step= 965, Dmax= 8.1e-03 nm, Epot= -4.60529e+04 Fmax= 1.22496e+02, atom= 696\n", + "Step= 966, Dmax= 9.7e-03 nm, Epot= -4.60540e+04 Fmax= 8.66934e+01, atom= 696\n", + "Step= 968, Dmax= 5.8e-03 nm, Epot= -4.60548e+04 Fmax= 4.15966e+01, atom= 696\n", + "Step= 969, Dmax= 7.0e-03 nm, Epot= -4.60552e+04 Fmax= 1.09255e+02, atom= 696\n", + "Step= 970, Dmax= 8.4e-03 nm, Epot= -4.60561e+04 Fmax= 7.27999e+01, atom= 696\n", + "Step= 972, Dmax= 5.0e-03 nm, Epot= -4.60568e+04 Fmax= 3.34387e+01, atom= 696\n", + "Step= 973, Dmax= 6.0e-03 nm, Epot= -4.60574e+04 Fmax= 9.65631e+01, atom= 696\n", + "Step= 974, Dmax= 7.3e-03 nm, Epot= -4.60583e+04 Fmax= 5.99155e+01, atom= 696\n", + "Step= 975, Dmax= 8.7e-03 nm, Epot= -4.60583e+04 Fmax= 1.24573e+02, atom= 696\n", + "Step= 976, Dmax= 1.0e-02 nm, Epot= -4.60592e+04 Fmax= 1.00296e+02, atom= 696\n", + "Step= 978, Dmax= 6.3e-03 nm, Epot= -4.60602e+04 Fmax= 3.68558e+01, atom= 696\n", + "Step= 979, Dmax= 7.5e-03 nm, Epot= -4.60606e+04 Fmax= 1.24790e+02, atom= 696\n", + "Step= 980, Dmax= 9.0e-03 nm, Epot= -4.60617e+04 Fmax= 6.99728e+01, atom= 696\n", + "Step= 982, Dmax= 5.4e-03 nm, Epot= -4.60624e+04 Fmax= 4.32977e+01, atom= 696\n", + "Step= 983, Dmax= 6.5e-03 nm, Epot= -4.60627e+04 Fmax= 9.44745e+01, atom= 696\n", + "Step= 984, Dmax= 7.8e-03 nm, Epot= -4.60635e+04 Fmax= 7.23624e+01, atom= 191\n", + "Step= 986, Dmax= 4.7e-03 nm, Epot= -4.60642e+04 Fmax= 2.87493e+01, atom= 696\n", + "Step= 987, Dmax= 5.6e-03 nm, Epot= -4.60649e+04 Fmax= 9.08944e+01, atom= 191\n", + "Step= 988, Dmax= 6.7e-03 nm, Epot= -4.60657e+04 Fmax= 5.25537e+01, atom= 696\n", + "Step= 989, Dmax= 8.1e-03 nm, Epot= -4.60658e+04 Fmax= 1.24282e+02, atom= 191\n", + "Step= 990, Dmax= 9.7e-03 nm, Epot= -4.60667e+04 Fmax= 8.18549e+01, atom= 696\n", + "Step= 992, Dmax= 5.8e-03 nm, Epot= -4.60675e+04 Fmax= 3.90673e+01, atom= 191\n", + "Step= 993, Dmax= 7.0e-03 nm, Epot= -4.60678e+04 Fmax= 1.05917e+02, atom= 191\n", + "Step= 994, Dmax= 8.4e-03 nm, Epot= -4.60687e+04 Fmax= 7.41061e+01, atom= 191\n", + "Step= 996, Dmax= 5.0e-03 nm, Epot= -4.60694e+04 Fmax= 3.27753e+01, atom= 696\n", + "Step= 997, Dmax= 6.0e-03 nm, Epot= -4.60699e+04 Fmax= 9.71702e+01, atom= 191\n", + "Step= 998, Dmax= 7.2e-03 nm, Epot= -4.60707e+04 Fmax= 5.52218e+01, atom= 191\n", + "Step= 1000, Dmax= 4.3e-03 nm, Epot= -4.60713e+04 Fmax= 3.61445e+01, atom= 191\n", + "\n", "Energy minimization reached the maximum number of steps before the forces\n", "reached the requested precision Fmax < 10.\n", "\n", "writing lowest energy coordinates.\n", "\n", - "Back Off! I just backed up em.pdb to ./#em.pdb.3#\n", + "Back Off! I just backed up em.pdb to ./#em.pdb.11#\n", "\n", "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n", - "Potential Energy = -1.9916112e+03\n", - "Maximum force = 1.1173969e+02 on atom 34\n", - "Norm of force = 1.9757371e+01\n", + "Potential Energy = -4.6071258e+04\n", + "Maximum force = 3.6144512e+01 on atom 191\n", + "Norm of force = 2.4094036e+00\n", "\n", - "GROMACS reminds you: \"Have a Nice Day\" (R. McDonald)\n", + "GROMACS reminds you: \"You see it through a charmed medium: you can not discern that the gilding is slime and the silk draperies cobwebs; that the marble is sordid slate, and the polished woods mere refuse chips and scale bark.\" (Mr. Rochester in Jane Eyre by Charlotte Bronte)\n", "\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] Setting up MD...\n", @@ -1531,12 +1526,12 @@ " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top\n", "\n", "\n", - "Back Off! I just backed up processed.top to ./#processed.top.2#\n", - "Number of degrees of freedom in T-Coupling group System is 291.00\n", + "Back Off! I just backed up processed.top to ./#processed.top.11#\n", + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.2#\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.11#\n", "\n", - "GROMACS reminds you: \"I have a hunch that the unknown sequences of DNA will decode into copyright notices and patent protections.\" (Donald Knuth)\n", + "GROMACS reminds you: \"You see it through a charmed medium: you can not discern that the gilding is slime and the silk draperies cobwebs; that the marble is sordid slate, and the polished woods mere refuse chips and scale bark.\" (Mr. Rochester in Jane Eyre by Charlotte Bronte)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -1545,14 +1540,14 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] All files set up for a run time of 5000 ps (dt=0.0001, nsteps=5e+07)\n" + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] All files set up for a run time of 1000 ps (dt=0.01, nsteps=100000)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1873764311\n", + "Setting the LD random seed to -1881604097\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -1562,13 +1557,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.100 nm, buffer size 0.000 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.132 nm, buffer size 0.032 nm\n", "\n", - "Set rlist, assuming 4x4 atom pair-list, to 1.100 nm, buffer size 0.000 nm\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.108 nm, buffer size 0.008 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 224 Mb of data\n" + "This run will generate roughly 1 Mb of data\n" ] }, { @@ -1584,7 +1579,7 @@ " '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top']}" ] }, - "execution_count": 30, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -1598,55 +1593,78 @@ " mdp={\n", " \"energy_minimize\": str(EM_FILE.absolute()),\n", " \"MD_relaxed\": str(EQ_FILE.absolute()),\n", - " \"MD_NPT\": str(RUN_FILE.absolute()),\n", + " \"MD_NPT\": str(EQ_FILE.absolute()),\n", " \"MD_restrained\": str(RUN_FILE.absolute()),\n", " },\n", + " distance=3.0,\n", ")\n", "sim.topology(str(BENZENE_ITP))\n", "sim.solvate(struct=MARTINI_BENZENE, maxwarn=1)\n", "sim.energy_minimize(maxwarn=1)\n", - "sim.MD_relaxed(runtime=5e3) # should be at least 1e3 ps for production not just 5 ps" + "sim.MD_relaxed(runtime=1e3, dt=0.01)" ] }, { "cell_type": "code", - "execution_count": 41, - "metadata": { - "vscode": { - "languageId": "shellscript" - } - }, + "execution_count": 6, + "metadata": {}, "outputs": [ { - "ename": "CalledProcessError", - "evalue": "Command 'b'MD_PATH=./Equilibrium/water/MD_relaxed\\nchmod +x $MD_PATH/local.sh\\n$MD_PATH/local.sh >> mdrun.log\\n'' returned non-zero exit status 66.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[41], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m get_ipython()\u001b[39m.\u001b[39;49mrun_cell_magic(\u001b[39m'\u001b[39;49m\u001b[39mscript\u001b[39;49m\u001b[39m'\u001b[39;49m, \u001b[39m'\u001b[39;49m\u001b[39mbash\u001b[39;49m\u001b[39m'\u001b[39;49m, \u001b[39m'\u001b[39;49m\u001b[39mMD_PATH=./Equilibrium/water/MD_relaxed\u001b[39;49m\u001b[39m\\n\u001b[39;49;00m\u001b[39mchmod +x $MD_PATH/local.sh\u001b[39;49m\u001b[39m\\n\u001b[39;49;00m\u001b[39m$MD_PATH/local.sh >> mdrun.log\u001b[39;49m\u001b[39m\\n\u001b[39;49;00m\u001b[39m'\u001b[39;49m)\n", - "File \u001b[0;32m~/mambaforge/envs/mdpow/lib/python3.11/site-packages/IPython/core/interactiveshell.py:2478\u001b[0m, in \u001b[0;36mInteractiveShell.run_cell_magic\u001b[0;34m(self, magic_name, line, cell)\u001b[0m\n\u001b[1;32m 2476\u001b[0m \u001b[39mwith\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mbuiltin_trap:\n\u001b[1;32m 2477\u001b[0m args \u001b[39m=\u001b[39m (magic_arg_s, cell)\n\u001b[0;32m-> 2478\u001b[0m result \u001b[39m=\u001b[39m fn(\u001b[39m*\u001b[39;49margs, \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mkwargs)\n\u001b[1;32m 2480\u001b[0m \u001b[39m# The code below prevents the output from being displayed\u001b[39;00m\n\u001b[1;32m 2481\u001b[0m \u001b[39m# when using magics with decodator @output_can_be_silenced\u001b[39;00m\n\u001b[1;32m 2482\u001b[0m \u001b[39m# when the last Python token in the expression is a ';'.\u001b[39;00m\n\u001b[1;32m 2483\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mgetattr\u001b[39m(fn, magic\u001b[39m.\u001b[39mMAGIC_OUTPUT_CAN_BE_SILENCED, \u001b[39mFalse\u001b[39;00m):\n", - "File \u001b[0;32m~/mambaforge/envs/mdpow/lib/python3.11/site-packages/IPython/core/magics/script.py:314\u001b[0m, in \u001b[0;36mScriptMagics.shebang\u001b[0;34m(self, line, cell)\u001b[0m\n\u001b[1;32m 309\u001b[0m \u001b[39mif\u001b[39;00m args\u001b[39m.\u001b[39mraise_error \u001b[39mand\u001b[39;00m p\u001b[39m.\u001b[39mreturncode \u001b[39m!=\u001b[39m \u001b[39m0\u001b[39m:\n\u001b[1;32m 310\u001b[0m \u001b[39m# If we get here and p.returncode is still None, we must have\u001b[39;00m\n\u001b[1;32m 311\u001b[0m \u001b[39m# killed it but not yet seen its return code. We don't wait for it,\u001b[39;00m\n\u001b[1;32m 312\u001b[0m \u001b[39m# in case it's stuck in uninterruptible sleep. -9 = SIGKILL\u001b[39;00m\n\u001b[1;32m 313\u001b[0m rc \u001b[39m=\u001b[39m p\u001b[39m.\u001b[39mreturncode \u001b[39mor\u001b[39;00m \u001b[39m-\u001b[39m\u001b[39m9\u001b[39m\n\u001b[0;32m--> 314\u001b[0m \u001b[39mraise\u001b[39;00m CalledProcessError(rc, cell)\n", - "\u001b[0;31mCalledProcessError\u001b[0m: Command 'b'MD_PATH=./Equilibrium/water/MD_relaxed\\nchmod +x $MD_PATH/local.sh\\n$MD_PATH/local.sh >> mdrun.log\\n'' returned non-zero exit status 66." + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 10 to 50, rlist from 1.107 to 1.268\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the GPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "100000 steps, 1000.0 ps (continuing from step 100000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.11#\n", + "step 100000, remaining wall clock time: 0 s \n", + "NOTE: 42 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.100 0.025 398.4\n", + " (ns/day) (hour/ns)\n", + "Performance: 34.436 0.697\n", + "\n", + "GROMACS reminds you: \"I originally implemented PME to prove that you didn't need it...\" (Erik Lindahl)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" ] + }, + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "%%script bash\n", - "MD_PATH=./Equilibrium/water/MD_relaxed\n", - "chmod +x $MD_PATH/local.sh\n", - "$MD_PATH/local.sh >> mdrun.log" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "# run simulation externally or use MDrunner\n", - "# (see docs for using mpi etc)\n", "import gromacs\n", "\n", "r = gromacs.run.MDrunner(\n", @@ -1654,35 +1672,7352 @@ " deffnm=\"md\",\n", " c=\"md.pdb\",\n", " cpi=True,\n", - " append=True,\n", " v=True,\n", ")\n", - "r.run() # runs mdrun in the python shell\n", - "\n", - "\n", + "r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.equil : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.gro').\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 't']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -t /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.10#\n", + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "Last frame -1 time 1000.000 \n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.9#\n", + "\n", + "GROMACS reminds you: \"I originally implemented PME to prove that you didn't need it...\" (Erik Lindahl)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] All files set up for a run time of 10000 ps (dt=0.02, nsteps=500000)\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -269549605\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.175 nm, buffer size 0.075 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.133 nm, buffer size 0.033 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "Reading Coordinates, Velocities and Box size from old trajectory\n", + "\n", + "Will read whole trajectory\n", + "\n", + "Using frame at t = 1000 ps\n", + "\n", + "Starting time for run is 0 ps\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 10 to 25, rlist from 1.133 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the GPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "500000 steps, 10000.0 ps (continuing from step 500000, 10000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.9#\n", + "step 500000, remaining wall clock time: 0 s \n", + "NOTE: 11 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.054 0.014 397.1\n", + " (ns/day) (hour/ns)\n", + "Performance: 126.362 0.190\n", + "\n", + "GROMACS reminds you: \"Philosophy of science is about as useful to scientists as ornithology is to birds.\" (Richard Feynman)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + }, + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ "sim.MD(\n", - " runtime=10, qscript=[\"local.sh\"]\n", - ") # should be at least 10e3 ps for production, not just 10 ps\n", - "# run simulation\n", - "r = gromacs.run.MDrunner(\n", - " dirname=sim.dirs[\"MD_NPT\"], deffnm=\"md\", c=\"md.pdb\", cpi=True, append=True, v=True\n", + " runtime=10e3, qscript=[\"local.sh\"], dt=0.02\n", ")\n", - "r.run() # runs mdrun in the python shell\n", - "\n", - "\n", - "import mdpow.fep\n", - "\n", - "gwat = mdpow.fep.Ghyd(simulation=sim, runtime=10)\n", - "gwat.setup()\n", - "\n", - "# run multiple simulations on cluster\n", "\n", - "\n", - "O = mdpow.equil.OctanolSimulation(molecule=\"BNZ\")\n", - "O.topology(\"benzene.itp\")\n", - "O.solvate(struct=\"benzene.pdb\")\n", - "O.energy_minimize()\n", - "O.MD_relaxed(runtime=0.5)" + "r = gromacs.run.MDrunner(\n", + " dirname=sim.dirs[\"MD_NPT\"], deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True\n", + ")\n", + "r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning on use of the timeseries module: If the inherent timescales of the system are long compared to those being analyzed, this statistical inefficiency may be an underestimate. The estimate presumes the use of many statistically independent samples. Tests should be performed to assess whether this condition is satisfied. Be cautious in the interpretation of the data.\n", + "\n", + "****** PyMBAR will use 64-bit JAX! *******\n", + "* JAX is currently set to 32-bit bitsize *\n", + "* which is its default. *\n", + "* *\n", + "* PyMBAR requires 64-bit mode and WILL *\n", + "* enable JAX's 64-bit mode when called. *\n", + "* *\n", + "* This MAY cause problems with other *\n", + "* Uses of JAX in the same code. *\n", + "******************************************\n", + "\n", + "mdpow.fep : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.gro').\n", + "/home/awsm/MDPOW/mdpow/fep.py:596: UserWarning: Directory 'FEP/water' already exists --- will overwrite existing files.\n", + " warnings.warn(wmsg)\n", + "mdpow.fep : WARNING Directory 'FEP/water' already exists --- will overwrite existing files.\n", + "mdpow.fep : INFO Solvation free energy calculation for molecule BENZ in solvent water.\n", + "mdpow.fep : INFO Base directory is '/home/awsm/MDPOW/doc/examples/martini'\n", + "mdpow.fep : INFO Using setup directories under 'FEP/water': {'coulomb': 'FEP/water/Coulomb', 'vdw': 'FEP/water/VDW'}\n", + "mdpow.fep : INFO Default checkpoint file is '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep'\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Pain is inevitable. Suffering is optional.\" (Haruki Murakami)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.25\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -30909756\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 15 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Pain is inevitable. Suffering is optional.\" (Haruki Murakami)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.5\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -154140945\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 15 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Wait a Minute, aren't You.... ? (gunshots) Yeah.\" (Bodycount)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.75\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1612087323\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 15 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Wait a Minute, aren't You.... ? (gunshots) Yeah.\" (Bodycount)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=1\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -20971547\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 15 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I Quit My Job Blowing Leaves\" (Beck)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", + "mdpow.fep : INFO [coulomb] Wrote array job scripts [None]\n", + "mdpow.fep : INFO Preparing vdw for lambda=0\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -71374085\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 15 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I Quit My Job Blowing Leaves\" (Beck)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.05\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1173802941\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Welcome to the Power Age\" (2 Unlimited)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.1\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1411402275\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Welcome to the Power Age\" (2 Unlimited)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.2\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1678026753\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Like other defaulters, I like to lay half the blame on ill-fortune and adverse circumstances\" (Mr. Rochester in Jane Eyre by Charlotte Bronte)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.3\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -963675284\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"GROMACS First : Making MD Great Again\" (Vedran Miletic)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.4\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -375586905\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"GROMACS First : Making MD Great Again\" (Vedran Miletic)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.5\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1658150910\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"C has the power of assembly language and the convenience of... assembly language.\" (Dennis Ritchie)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.6\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -102768749\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"C has the power of assembly language and the convenience of... assembly language.\" (Dennis Ritchie)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.65\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1126270785\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I Have a Bad Case Of Purple Diarrhea\" (Urban Dance Squad)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.7\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -265217\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I Have a Bad Case Of Purple Diarrhea\" (Urban Dance Squad)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.75\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 2077204442\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Erwin with his psi can do / Calculations quite a few. / But one thing has not been seen / Just what psi really mean.\" (Felix Bloch)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.8\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -170917891\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Erwin with his psi can do / Calculations quite a few. / But one thing has not been seen / Just what psi really mean.\" (Felix Bloch)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.85\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1128333313\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Not everyone is capable of madness; and of those lucky enough to be capable, not many have the courage for it.\" (August Strindberg)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.9\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -143274449\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it.\" (Max Planck)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.95\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1994323699\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it.\" (Max Planck)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=1\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1484915985\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 4902.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"It always takes longer than you think even when you take Hofstadter's Law into account.\" (Hofstadter's Law)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", + "mdpow.fep : INFO [vdw] Wrote array job scripts [None]\n", + "mdpow.fep : INFO Saved state information to '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep'; reload later with G = Ghyd(filename='/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep').\n", + "mdpow.fep : INFO Finished setting up all individual simulations. Now run them...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -170164757\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'W'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 17 Mb of data\n" + ] + }, + { + "data": { + "text/plain": [ + "{'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top',\n", + " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx',\n", + " 'qscript': ['./local.sh'],\n", + " 'mainselection': None,\n", + " 'deffnm': 'md',\n", + " 'includes': ['/home/awsm/MDPOW/mdpow/top'],\n", + " 'maxwarn': 1,\n", + " 'couple-intramol': 'no',\n", + " 'couple_lambda0': 'vdw',\n", + " 'couple_lambda1': 'none',\n", + " 'sc_alpha': 0.5,\n", + " 'sc_power': 1,\n", + " 'sc_sigma': 0.3,\n", + " 'separate-dhdl-file': 'yes',\n", + " 'ref_t': 300.0,\n", + " 'gen_temp': 300.0,\n", + " 'free_energy': 'yes',\n", + " 'couple_moltype': 'BENZ',\n", + " 'init_lambda_state': 15,\n", + " 'fep_lambdas': array([0. , 0.05, 0.1 , 0.2 , 0.3 , 0.4 , 0.5 , 0.6 , 0.65, 0.7 , 0.75,\n", + " 0.8 , 0.85, 0.9 , 0.95, 1. ]),\n", + " 'calc_lambda_neighbors': -1}" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import mdpow.fep\n", + "\n", + "gwat = mdpow.fep.Ghyd(simulation=sim, runtime=1e+3, mdp=str(RUN_FILE.absolute()))\n", + "gwat.setup(dt=0.02, edr=False)\n", + "\n", + "# run multiple simulations on cluster" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "\n", + "Back Off! I just backed up md.log to ./#md.log.1#\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "\n", + "Back Off! I just backed up md.xtc to ./#md.xtc.1#\n", + "\n", + "Back Off! I just backed up md.trr to ./#md.trr.1#\n", + "\n", + "Back Off! I just backed up md.edr to ./#md.edr.1#\n", + "\n", + "Back Off! I just backed up md.xvg to ./#md.xvg.1#\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 705.172 176.293 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2450.475 0.010\n", + "\n", + "GROMACS reminds you: \"You always pass failure on the way to success.\" (Mickey Rooney)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 638.689 159.672 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2705.554 0.009\n", + "\n", + "GROMACS reminds you: \"The first 90% of the code accounts for the first 90% of the development time. The remaining 10% of the code accounts for the other 90% of the development time.\" (Tom Cargill)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 661.083 165.271 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2613.900 0.009\n", + "\n", + "GROMACS reminds you: \"In science it often happens that scientists say, 'You know that's a really good argument; my position is mistaken,' and then they would actually change their minds and you never hear that old view from them again. They really do it. It doesn't happen as often as it should, because scientists are human and change is sometimes painful. But it happens every day. I cannot recall the last time something like that happened in politics or religion.\" (Carl Sagan)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 637.299 159.325 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2711.452 0.009\n", + "\n", + "GROMACS reminds you: \"With a Little Penknife\" (Nick Cave)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s 6400, remaining wall clock time: 126 s , remaining wall clock time: 71 s 168000, remaining wall clock time: 54 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 662.486 165.622 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2608.366 0.009\n", + "\n", + "GROMACS reminds you: \"Computer system analysis is like child-rearing; you can do grievous damage, but you cannot ensure success.\" (Tom DeMarcho)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 1004.487 251.122 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1720.288 0.014\n", + "\n", + "GROMACS reminds you: \"Torture numbers, and they'll confess to anything.\" (Greg Easterbrook)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 723.325 180.831 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2388.977 0.010\n", + "\n", + "GROMACS reminds you: \"UNIX is basically a simple operating system. It just takes a genius to understand its simplicity.\" (Dennis Ritchie)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s 9800, remaining wall clock time: 105 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 844.038 211.009 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2047.310 0.012\n", + "\n", + "GROMACS reminds you: \"By denying scientific principles, one may maintain any paradox.\" (Galileo Galilei)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s 140200, remaining wall clock time: 105 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 1036.599 259.150 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1666.996 0.014\n", + "\n", + "GROMACS reminds you: \"What's the point, yo, what's the spread?\" (Red Hot Chili Peppers)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 992.378 248.095 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1741.278 0.014\n", + "\n", + "GROMACS reminds you: \"Being Great is Not So Good\" (Red Hot Chili Peppers)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 946.990 236.748 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1824.735 0.013\n", + "\n", + "GROMACS reminds you: \"We must be clear that when it comes to atoms, language can be used only as in poetry. \" (Niels Bohr)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 1081.532 270.383 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1597.740 0.015\n", + "\n", + "GROMACS reminds you: \"Occams Razor is the scientific principle that, all things being equal, the simplest explanation is always the dog ate my homework.\" (Greg Tamblyn)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s 139100, remaining wall clock time: 276 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 1634.983 408.746 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1056.896 0.023\n", + "\n", + "GROMACS reminds you: \"Facts are stubborn things, but statistics are more pliable.\" (Laurence Peter)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s remaining wall clock time: 199 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 801.529 200.382 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2155.887 0.011\n", + "\n", + "GROMACS reminds you: \"I'm Looking for a New Simulation\" (Stone Temple Pilots)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 675.882 168.971 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2556.668 0.009\n", + "\n", + "GROMACS reminds you: \"It's Because Of the Metric System\" (Pulp Fiction)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 664.554 166.139 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2600.249 0.009\n", + "\n", + "GROMACS reminds you: \"Research ! A mere excuse for idleness; it has never achieved, and will never achieve any results of the slightest value.\" (Benjamin Jowett, British theologian, 1817-93)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 675.300 168.825 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2558.871 0.009\n", + "\n", + "GROMACS reminds you: \"There was no preconception on what to do\" (Daft Punk)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s 4500, remaining wall clock time: 101 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 683.395 170.849 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2528.560 0.009\n", + "\n", + "GROMACS reminds you: \"The easiest way to scale well is to have bad single-core performance\" (Blind Freddie)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s 5000, remaining wall clock time: 126 s , remaining wall clock time: 136 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 683.647 170.912 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2527.629 0.009\n", + "\n", + "GROMACS reminds you: \"Mathematics is like love; a simple idea, but it can get complicated.\" (Anonymous)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 658.028 164.507 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2626.036 0.009\n", + "\n", + "GROMACS reminds you: \"The most exciting phrase to hear in science, the one that heralds new discoveries, is not \"Eureka\" but \"That's funny...\".\" (Isaac Asimov)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in water'\n", + "250000 steps, 5000.0 ps.\n", + "step 249900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 250000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 657.966 164.492 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2626.283 0.009\n", + "\n", + "GROMACS reminds you: \"I see they found out the universe is 80 million years older than we thought. It's also been lying about its weight.\" (Bill Maher)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + } + ], + "source": [ + "for dir_ in gwat.fep_dirs():\n", + " r = gromacs.run.MDrunner(\n", + " dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=\"md.xvg\"\n", + " )\n", + " r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Finding dgdl xvg files, reading with stride=1 permissive=False.\n", + "mdpow.fep : INFO Analysis stride is 1.\n", + "mdpow.fep : INFO Analyzing stored data.\n", + "mdpow.fep : INFO [BENZ coulomb] Computing averages and errors for 5 lambda values.\n", + "numkit.integration: WARNING Approximating Simpson integration statistical error with the average spacing.\n", + "mdpow.fep : INFO [BENZ vdw] Computing averages and errors for 16 lambda values.\n", + "numkit.integration: WARNING Approximating Simpson integration statistical error with the average spacing.\n", + "mdpow.fep : INFO DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (coulomb) -34014.8 (4.01) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (vdw) -34012 (2.23) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (Gibbs) 68026.8 (4.59) kJ/mol\n" + ] + }, + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "gwat.collect_alchemlyb()\n", + "gwat.analyze_alchemlyb()\n", + "gwat.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/octanol.gro'...\n", + " :-) GROMACS - gmx editconf, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 4.0\n", + "\n", + "\n", + "GROMACS reminds you: \"C is not a high-level language.\" (Brian Kernighan, C author)\n", + "\n", + " :-) GROMACS - gmx solvate, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx solvate -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -cp boxed.gro -cs /home/awsm/MDPOW/doc/examples/martini/octanol.gro -o solvated.gro\n", + "\n", + "Reading solute configuration\n", + "Reading solvent configuration\n", + "\n", + "Initialising inter-atomic distances...\n", + "Generating solvent configuration\n", + "Will generate new solvent configuration of 2x2x2 boxes\n", + "Solvent box contains 5943 atoms in 1981 residues\n", + "Removed 828 solvent atoms due to solvent-solvent overlap\n", + "Removed 3 solvent atoms due to solute-solvent overlap\n", + "Sorting configuration\n", + "Found 1 molecule type:\n", + " OCO ( 3 atoms): 1704 residues\n", + "Generated solvent containing 5112 atoms in 1704 residues\n", + "Writing generated configuration to solvated.gro\n", + "\n", + "Output configuration contains 5115 atoms in 1705 residues\n", + "Volume : 399.981 (nm^3)\n", + "Density : 389.199 (g/l)\n", + "Number of solvent molecules: 1704 \n", + "\n", + "Processing topology\n", + "\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/#system.top.1#\n", + "\n", + "GROMACS reminds you: \"C is not a high-level language.\" (Brian Kernighan, C author)\n", + "\n", + "gromacs.setup: INFO Solvated system with /home/awsm/MDPOW/doc/examples/martini/octanol.gro\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Note that major changes are planned in future for editconf, to improve usability and utility.\n", + "Read 3 atoms\n", + "Volume: 4050 nm^3, corresponds to roughly 1822500 electrons\n", + "No velocities found\n", + " system size : 0.210 0.160 0.248 (nm)\n", + " diameter : 0.270 (nm)\n", + " center : 2.987 0.606 2.315 (nm)\n", + " box vectors : 15.000 15.000 18.000 (nm)\n", + " box angles : 90.00 90.00 90.00 (degrees)\n", + " box volume :4050.00 (nm^3)\n", + " shift : 3.216 5.597 0.609 (nm)\n", + "new center : 6.203 6.203 2.924 (nm)\n", + "new box vectors : 8.270 8.270 8.270 (nm)\n", + "new box angles : 60.00 60.00 90.00 (degrees)\n", + "new box volume : 399.98 (nm^3)\n", + "\n", + "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n", + " based on residue and atom names, since they could not be\n", + " definitively assigned from the information in your input\n", + " files. These guessed numbers might deviate from the mass\n", + " and radius of the atom type. Please check the output\n", + " files if necessary. Note, that this functionality may\n", + " be removed in a future GROMACS version. Please, consider\n", + " using another file format for your input.\n", + "\n", + "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n", + "from the source below. This means the results may be different\n", + "compared to previous GROMACS versions.\n", + "\n", + "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n", + "A. Bondi\n", + "van der Waals Volumes and Radii\n", + "J. Phys. Chem. 68 (1964) pp. 441-451\n", + "-------- -------- --- Thank You --- -------- --------\n", + "\n", + "Adding line for 1704 solvent molecules with resname (OCO) to topology file (/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.cbook: INFO system total charge qtot = 0\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] After solvation: total charge qtot = 0 = 0\n", + "gromacs.cbook: INFO system total charge qtot = 0\n", + "gromacs.setup: INFO Building the main index file 'main.ndx'...\n", + " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx make_ndx -f ionized.tpr -o main.ndx\n", + "\n", + "\n", + "Reading structure file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "GROMACS reminds you: \"You Leave Me Dry\" (P.J. Harvey)\n", + "\n", + " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx make_ndx -f ionized.tpr -n main.ndx -o main.ndx\n", + "\n", + "\n", + "Reading structure file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.1#\n", + "\n", + "GROMACS reminds you: \"You Leave Me Dry\" (P.J. Harvey)\n", + "\n", + " :-) GROMACS - gmx trjconv, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx trjconv -ur compact -center -boxcenter tric -pbc mol -f ionized.gro -s ionized.tpr -o compact.pdb -n main.ndx\n", + "\n", + "Will write pdb: Protein data bank file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Group 0 ( System) has 5115 elements\n", + "Group 1 ( Other) has 5115 elements\n", + "Group 2 ( BENZ) has 3 elements\n", + "Group 3 ( OCO) has 5112 elements\n", + "Group 4 ( __main__) has 3 elements\n", + "Group 5 (__environment__) has 5112 elements\n", + "Select a group: Group 0 ( System) has 5115 elements\n", + "Group 1 ( Other) has 5115 elements\n", + "Group 2 ( BENZ) has 3 elements\n", + "Group 3 ( OCO) has 5112 elements\n", + "Group 4 ( __main__) has 3 elements\n", + "Group 5 (__environment__) has 5112 elements\n", + "Select a group: Reading frames from gro file 'This is an auto generated system', 5115 atoms.\n", + "Reading frame 0 time 0.000 \n", + "Precision of ionized.gro is 0.001 (nm)\n", + "Last frame 0 time 0.000 \n", + " -> frame 0 time 0.000 \n", + "Last written: frame 0 time 0.000\n", + "\n", + "\n", + "GROMACS reminds you: \"You Leave Me Dry\" (P.J. Harvey)\n", + "\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -f /tmp/tmpwoe68rau.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -nov\n", + "\n", + "\n", + "NOTE 1 [file /tmp/tmpwoe68rau.mdp]:\n", + " For a correct single-point energy evaluation with nsteps = 0, use\n", + " continuation = yes to avoid constraining the input coordinates.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Note that major changes are planned in future for trjconv, to improve usability and utility.\n", + "Select group for centering\n", + "Selected 4: '__main__'\n", + "Select group for output\n", + "Selected 0: 'System'\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n", + "NOTE 2 [file system.top, line 28]:\n", + " For energy conservation with LINCS, lincs_iter should be 2 or larger.\n", + "\n", + "\n", + "Number of degrees of freedom in T-Coupling group rest is 15339.00\n", + "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "\n", + "NOTE 3 [file /tmp/tmpwoe68rau.mdp]:\n", + " NVE simulation with an initial temperature of zero: will use a Verlet\n", + " buffer of 10%. Check your energy drift!\n", + "\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "GROMACS reminds you: \"Research ! A mere excuse for idleness; it has never achieved, and will never achieve any results of the slightest value.\" (Benjamin Jowett, British theologian, 1817-93)\n", + "\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top', mdp='em.mdp' ...\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'em.mdp': ['maxwarn', 'pp']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'maxwarn': 1, 'pp': 'processed.top'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'maxwarn': 1, 'pp': 'processed.top'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em\n", + "Command line:\n", + " gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -maxwarn 1 -pp processed.top\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -394305602\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "Analysing residue names:\n", + "There are: 1705 Other residues\n", + "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", + "\n", + "This run will generate roughly 0 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group rest is 15339.00\n", + "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "\n", + "GROMACS reminds you: \"Research ! A mere excuse for idleness; it has never achieved, and will never achieve any results of the slightest value.\" (Benjamin Jowett, British theologian, 1817-93)\n", + "\n", + "gromacs.run : WARNING No 'mdrun_d' binary found so trying 'mdrun' instead.\n", + "(Note that energy minimization runs better with mdrun_d.)\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/run.py:423: AutoCorrectionWarning: No 'mdrun_d' binary found so trying 'mdrun' instead.\n", + "(Note that energy minimization runs better with mdrun_d.)\n", + " warnings.warn(wmsg, category=AutoCorrectionWarning)\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em\n", + "Command line:\n", + " gmx mdrun -v -stepout 10 -deffnm em -c em.pdb\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1843264573\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "Analysing residue names:\n", + "There are: 1705 Other residues\n", + "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", + "\n", + "This run will generate roughly 1 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Reading file em.tpr, VERSION 2023.2 (single precision)\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "\n", + "Steepest Descents:\n", + " Tolerance (Fmax) = 1.00000e+01\n", + " Number of steps = 1000\n", + "Step= 0, Dmax= 1.0e-02 nm, Epot= 1.02801e+07 Fmax= 2.05315e+07, atom= 5083\n", + "Step= 1, Dmax= 1.0e-02 nm, Epot= 7.41994e+06 Fmax= 5.74654e+06, atom= 3110\n", + "Step= 2, Dmax= 1.2e-02 nm, Epot= 4.40326e+06 Fmax= 2.44532e+06, atom= 4997\n", + "Step= 3, Dmax= 1.4e-02 nm, Epot= 2.73794e+06 Fmax= 9.51879e+05, atom= 1685\n", + "Step= 4, Dmax= 1.7e-02 nm, Epot= 1.53428e+06 Fmax= 4.51665e+05, atom= 1684\n", + "Step= 5, Dmax= 2.1e-02 nm, Epot= 8.87445e+05 Fmax= 1.90248e+05, atom= 1990\n", + "Step= 6, Dmax= 2.5e-02 nm, Epot= 4.61156e+05 Fmax= 1.05731e+05, atom= 3691\n", + "Step= 7, Dmax= 3.0e-02 nm, Epot= 2.59013e+05 Fmax= 7.39295e+04, atom= 3626\n", + "Step= 8, Dmax= 3.6e-02 nm, Epot= 1.57144e+05 Fmax= 4.51091e+04, atom= 3691\n", + "Step= 9, Dmax= 4.3e-02 nm, Epot= 8.70638e+04 Fmax= 3.11807e+04, atom= 3047\n", + "Step= 10, Dmax= 5.2e-02 nm, Epot= 4.74060e+04 Fmax= 1.09883e+05, atom= 3020\n", + "Step= 11, Dmax= 6.2e-02 nm, Epot= 3.89493e+04 Fmax= 1.54250e+04, atom= 1088\n", + "Step= 12, Dmax= 7.4e-02 nm, Epot= 6.83724e+03 Fmax= 1.68745e+04, atom= 1088\n", + "Step= 13, Dmax= 8.9e-02 nm, Epot= -4.12860e+03 Fmax= 1.03436e+04, atom= 1088\n", + "Step= 14, Dmax= 1.1e-01 nm, Epot= -1.13032e+04 Fmax= 1.60196e+05, atom= 4\n", + "Step= 15, Dmax= 1.3e-01 nm, Epot= -1.48685e+04 Fmax= 1.22377e+04, atom= 4\n", + "Step= 16, Dmax= 1.5e-01 nm, Epot= -2.01121e+04 Fmax= 3.01369e+04, atom= 4\n", + "Step= 17, Dmax= 1.8e-01 nm, Epot= -2.17950e+04 Fmax= 4.10930e+04, atom= 2520\n", + "Step= 18, Dmax= 2.2e-01 nm, Epot= -2.41455e+04 Fmax= 2.58498e+04, atom= 4\n", + "Step= 19, Dmax= 2.7e-01 nm, Epot= -2.66240e+04 Fmax= 2.69402e+04, atom= 835\n", + "Step= 23, Dmax= 4.0e-02 nm, Epot= -2.72905e+04 Fmax= 1.12462e+04, atom= 5360\n", + "Step= 24, Dmax= 4.8e-02 nm, Epot= -2.82618e+04 Fmax= 8.89258e+03, atom= 3110\n", + "Step= 25, Dmax= 5.8e-02 nm, Epot= -2.94485e+04 Fmax= 7.02500e+03, atom= 835\n", + "Step= 26, Dmax= 6.9e-02 nm, Epot= -3.10718e+04 Fmax= 4.20735e+03, atom= 835\n", + "Step= 27, Dmax= 8.3e-02 nm, Epot= -3.33640e+04 Fmax= 1.18144e+04, atom= 835\n", + "Step= 28, Dmax= 9.9e-02 nm, Epot= -3.46020e+04 Fmax= 2.13260e+03, atom= 3110\n", + "Step= 29, Dmax= 1.2e-01 nm, Epot= -3.82089e+04 Fmax= 4.27695e+04, atom= 3110\n", + "Step= 30, Dmax= 1.4e-01 nm, Epot= -3.94408e+04 Fmax= 2.82754e+03, atom= 536\n", + "Step= 31, Dmax= 1.7e-01 nm, Epot= -3.97104e+04 Fmax= 1.20557e+05, atom= 413\n", + "Step= 33, Dmax= 1.0e-01 nm, Epot= -4.13529e+04 Fmax= 3.83121e+04, atom= 413\n", + "Step= 34, Dmax= 1.2e-01 nm, Epot= -4.20900e+04 Fmax= 3.46040e+03, atom= 5051\n", + "Step= 35, Dmax= 1.5e-01 nm, Epot= -4.35923e+04 Fmax= 8.93873e+03, atom= 5051\n", + "Step= 36, Dmax= 1.8e-01 nm, Epot= -4.39487e+04 Fmax= 3.05296e+03, atom= 413\n", + "Step= 37, Dmax= 2.1e-01 nm, Epot= -4.53159e+04 Fmax= 8.39938e+03, atom= 5051\n", + "Step= 39, Dmax= 1.3e-01 nm, Epot= -4.58889e+04 Fmax= 6.37810e+03, atom= 4135\n", + "Step= 40, Dmax= 1.5e-01 nm, Epot= -4.66503e+04 Fmax= 2.17876e+03, atom= 413\n", + "Step= 42, Dmax= 9.2e-02 nm, Epot= -4.73329e+04 Fmax= 3.49740e+03, atom= 4130\n", + "Step= 43, Dmax= 1.1e-01 nm, Epot= -4.76411e+04 Fmax= 5.47566e+03, atom= 5050\n", + "Step= 44, Dmax= 1.3e-01 nm, Epot= -4.79772e+04 Fmax= 6.20737e+03, atom= 1883\n", + "Step= 45, Dmax= 1.6e-01 nm, Epot= -4.80615e+04 Fmax= 1.18165e+04, atom= 1883\n", + "Step= 47, Dmax= 9.6e-02 nm, Epot= -4.85170e+04 Fmax= 1.25836e+03, atom= 2244\n", + "Step= 48, Dmax= 1.1e-01 nm, Epot= -4.93841e+04 Fmax= 4.12020e+03, atom= 1883\n", + "Step= 49, Dmax= 1.4e-01 nm, Epot= -4.98325e+04 Fmax= 6.95321e+02, atom= 1883\n", + "Step= 51, Dmax= 8.3e-02 nm, Epot= -5.06075e+04 Fmax= 4.29779e+03, atom= 5062\n", + "Step= 52, Dmax= 9.9e-02 nm, Epot= -5.08344e+04 Fmax= 1.55311e+03, atom= 1684\n", + "Step= 54, Dmax= 6.0e-02 nm, Epot= -5.10811e+04 Fmax= 2.58606e+03, atom= 1684\n", + "Step= 55, Dmax= 7.1e-02 nm, Epot= -5.12316e+04 Fmax= 1.94541e+03, atom= 1684\n", + "Step= 56, Dmax= 8.6e-02 nm, Epot= -5.14540e+04 Fmax= 3.79274e+03, atom= 1684\n", + "Step= 57, Dmax= 1.0e-01 nm, Epot= -5.15757e+04 Fmax= 2.28648e+03, atom= 1684\n", + "Step= 58, Dmax= 1.2e-01 nm, Epot= -5.17068e+04 Fmax= 5.86852e+03, atom= 1684\n", + "Step= 59, Dmax= 1.5e-01 nm, Epot= -5.17809e+04 Fmax= 4.05461e+03, atom= 1684\n", + "Step= 61, Dmax= 8.9e-02 nm, Epot= -5.21152e+04 Fmax= 1.19647e+03, atom= 5089\n", + "Step= 62, Dmax= 1.1e-01 nm, Epot= -5.24892e+04 Fmax= 1.98810e+03, atom= 1685\n", + "Step= 63, Dmax= 1.3e-01 nm, Epot= -5.25173e+04 Fmax= 3.38293e+03, atom= 1685\n", + "Step= 65, Dmax= 7.7e-02 nm, Epot= -5.28031e+04 Fmax= 1.59406e+03, atom= 15\n", + "Step= 66, Dmax= 9.2e-02 nm, Epot= -5.30527e+04 Fmax= 1.02223e+03, atom= 2171\n", + "Step= 67, Dmax= 1.1e-01 nm, Epot= -5.30732e+04 Fmax= 7.81743e+03, atom= 2171\n", + "Step= 68, Dmax= 1.3e-01 nm, Epot= -5.34332e+04 Fmax= 6.62480e+02, atom= 1684\n", + "Step= 70, Dmax= 8.0e-02 nm, Epot= -5.35749e+04 Fmax= 5.88957e+03, atom= 3179\n", + "Step= 71, Dmax= 9.6e-02 nm, Epot= -5.37497e+04 Fmax= 2.39396e+03, atom= 2567\n", + "Step= 72, Dmax= 1.1e-01 nm, Epot= -5.38901e+04 Fmax= 1.90550e+03, atom= 1079\n", + "Step= 73, Dmax= 1.4e-01 nm, Epot= -5.39738e+04 Fmax= 2.74704e+03, atom= 2366\n", + "Step= 75, Dmax= 8.3e-02 nm, Epot= -5.41336e+04 Fmax= 2.65971e+03, atom= 4446\n", + "Step= 77, Dmax= 5.0e-02 nm, Epot= -5.42250e+04 Fmax= 1.30975e+03, atom= 3046\n", + "Step= 78, Dmax= 5.9e-02 nm, Epot= -5.43393e+04 Fmax= 8.65460e+02, atom= 3046\n", + "Step= 79, Dmax= 7.1e-02 nm, Epot= -5.44704e+04 Fmax= 1.58444e+03, atom= 3046\n", + "Step= 80, Dmax= 8.6e-02 nm, Epot= -5.45726e+04 Fmax= 1.36866e+03, atom= 3046\n", + "Step= 81, Dmax= 1.0e-01 nm, Epot= -5.46030e+04 Fmax= 5.03876e+03, atom= 444\n", + "Step= 82, Dmax= 1.2e-01 nm, Epot= -5.47013e+04 Fmax= 2.52246e+03, atom= 2366\n", + "Step= 83, Dmax= 1.5e-01 nm, Epot= -5.47871e+04 Fmax= 3.43336e+03, atom= 1079\n", + "Step= 84, Dmax= 1.8e-01 nm, Epot= -5.49199e+04 Fmax= 1.89007e+03, atom= 2559\n", + "Step= 85, Dmax= 2.1e-01 nm, Epot= -5.49722e+04 Fmax= 3.24062e+03, atom= 2559\n", + "Step= 87, Dmax= 1.3e-01 nm, Epot= -5.50446e+04 Fmax= 4.58713e+03, atom= 2760\n", + "Step= 89, Dmax= 7.7e-02 nm, Epot= -5.51553e+04 Fmax= 1.82867e+03, atom= 4360\n", + "Step= 90, Dmax= 9.2e-02 nm, Epot= -5.52639e+04 Fmax= 5.26539e+02, atom= 2261\n", + "Step= 91, Dmax= 1.1e-01 nm, Epot= -5.53684e+04 Fmax= 5.66826e+03, atom= 4360\n", + "Step= 92, Dmax= 1.3e-01 nm, Epot= -5.55561e+04 Fmax= 4.54173e+02, atom= 4360\n", + "Step= 93, Dmax= 1.6e-01 nm, Epot= -5.55593e+04 Fmax= 4.81414e+03, atom= 4360\n", + "Step= 95, Dmax= 9.5e-02 nm, Epot= -5.57775e+04 Fmax= 5.16815e+03, atom= 4360\n", + "Step= 96, Dmax= 1.1e-01 nm, Epot= -5.59213e+04 Fmax= 8.86091e+02, atom= 2568\n", + "Step= 97, Dmax= 1.4e-01 nm, Epot= -5.59392e+04 Fmax= 4.13422e+03, atom= 2568\n", + "Step= 99, Dmax= 8.2e-02 nm, Epot= -5.60849e+04 Fmax= 5.59378e+02, atom= 2760\n", + "Step= 100, Dmax= 9.9e-02 nm, Epot= -5.61778e+04 Fmax= 7.36354e+02, atom= 2261\n", + "Step= 102, Dmax= 5.9e-02 nm, Epot= -5.63295e+04 Fmax= 3.84610e+02, atom= 2567\n", + "Step= 103, Dmax= 7.1e-02 nm, Epot= -5.63583e+04 Fmax= 1.33306e+03, atom= 2567\n", + "Step= 104, Dmax= 8.5e-02 nm, Epot= -5.64837e+04 Fmax= 6.59975e+02, atom= 2567\n", + "Step= 106, Dmax= 5.1e-02 nm, Epot= -5.65690e+04 Fmax= 2.71290e+02, atom= 2567\n", + "Step= 107, Dmax= 6.2e-02 nm, Epot= -5.65777e+04 Fmax= 1.65116e+03, atom= 3180\n", + "Step= 108, Dmax= 7.4e-02 nm, Epot= -5.67310e+04 Fmax= 4.94173e+02, atom= 2567\n", + "Step= 109, Dmax= 8.9e-02 nm, Epot= -5.67486e+04 Fmax= 1.94536e+03, atom= 2567\n", + "Step= 110, Dmax= 1.1e-01 nm, Epot= -5.68570e+04 Fmax= 4.43982e+02, atom= 3179\n", + "Step= 112, Dmax= 6.4e-02 nm, Epot= -5.69402e+04 Fmax= 4.47751e+02, atom= 3179\n", + "Step= 113, Dmax= 7.7e-02 nm, Epot= -5.69597e+04 Fmax= 9.20285e+02, atom= 2139\n", + "Step= 114, Dmax= 9.2e-02 nm, Epot= -5.70078e+04 Fmax= 9.37800e+02, atom= 2139\n", + "Step= 116, Dmax= 5.5e-02 nm, Epot= -5.71175e+04 Fmax= 2.86563e+02, atom= 1078\n", + "Step= 117, Dmax= 6.6e-02 nm, Epot= -5.71881e+04 Fmax= 4.72104e+02, atom= 2567\n", + "Step= 119, Dmax= 4.0e-02 nm, Epot= -5.72505e+04 Fmax= 3.34971e+02, atom= 3179\n", + "Step= 120, Dmax= 4.8e-02 nm, Epot= -5.72684e+04 Fmax= 6.68821e+02, atom= 1088\n", + "Step= 121, Dmax= 5.7e-02 nm, Epot= -5.73208e+04 Fmax= 5.89958e+02, atom= 1088\n", + "Step= 122, Dmax= 6.9e-02 nm, Epot= -5.73273e+04 Fmax= 1.00541e+03, atom= 1088\n", + "Step= 123, Dmax= 8.2e-02 nm, Epot= -5.73823e+04 Fmax= 9.18556e+02, atom= 1088\n", + "Step= 125, Dmax= 4.9e-02 nm, Epot= -5.74540e+04 Fmax= 3.33559e+02, atom= 1088\n", + "Step= 126, Dmax= 5.9e-02 nm, Epot= -5.75094e+04 Fmax= 7.16891e+02, atom= 1088\n", + "Step= 127, Dmax= 7.1e-02 nm, Epot= -5.75464e+04 Fmax= 5.50998e+02, atom= 1088\n", + "Step= 128, Dmax= 8.5e-02 nm, Epot= -5.75679e+04 Fmax= 1.20153e+03, atom= 1088\n", + "Step= 129, Dmax= 1.0e-01 nm, Epot= -5.76115e+04 Fmax= 6.52398e+02, atom= 1088\n", + "Step= 131, Dmax= 6.1e-02 nm, Epot= -5.76713e+04 Fmax= 2.53581e+02, atom= 1088\n", + "Step= 133, Dmax= 3.7e-02 nm, Epot= -5.77124e+04 Fmax= 3.86314e+02, atom= 1088\n", + "Step= 134, Dmax= 4.4e-02 nm, Epot= -5.77482e+04 Fmax= 3.73108e+02, atom= 1088\n", + "Step= 135, Dmax= 5.3e-02 nm, Epot= -5.77629e+04 Fmax= 5.31183e+02, atom= 1088\n", + "Step= 136, Dmax= 6.4e-02 nm, Epot= -5.77879e+04 Fmax= 6.43519e+02, atom= 2750\n", + "Step= 138, Dmax= 3.8e-02 nm, Epot= -5.78558e+04 Fmax= 1.85832e+02, atom= 2750\n", + "Step= 139, Dmax= 4.6e-02 nm, Epot= -5.78925e+04 Fmax= 1.09288e+03, atom= 2750\n", + "Step= 140, Dmax= 5.5e-02 nm, Epot= -5.79367e+04 Fmax= 2.69548e+02, atom= 2750\n", + "Step= 141, Dmax= 6.6e-02 nm, Epot= -5.79484e+04 Fmax= 1.95160e+03, atom= 2750\n", + "Step= 142, Dmax= 7.9e-02 nm, Epot= -5.80068e+04 Fmax= 2.88227e+02, atom= 2750\n", + "Step= 144, Dmax= 4.8e-02 nm, Epot= -5.80458e+04 Fmax= 3.98323e+02, atom= 2750\n", + "Step= 145, Dmax= 5.7e-02 nm, Epot= -5.80633e+04 Fmax= 5.81518e+02, atom= 2750\n", + "Step= 146, Dmax= 6.8e-02 nm, Epot= -5.80932e+04 Fmax= 6.58553e+02, atom= 2750\n", + "Step= 147, Dmax= 8.2e-02 nm, Epot= -5.80940e+04 Fmax= 7.38113e+02, atom= 2750\n", + "Step= 148, Dmax= 9.9e-02 nm, Epot= -5.80943e+04 Fmax= 1.21411e+03, atom= 2750\n", + "Step= 149, Dmax= 1.2e-01 nm, Epot= -5.81100e+04 Fmax= 9.10252e+02, atom= 2750\n", + "Step= 151, Dmax= 7.1e-02 nm, Epot= -5.82095e+04 Fmax= 2.71693e+02, atom= 1416\n", + "Step= 153, Dmax= 4.3e-02 nm, Epot= -5.82354e+04 Fmax= 3.70157e+02, atom= 1037\n", + "Step= 154, Dmax= 5.1e-02 nm, Epot= -5.82509e+04 Fmax= 5.47522e+02, atom= 1037\n", + "Step= 155, Dmax= 6.1e-02 nm, Epot= -5.82635e+04 Fmax= 5.14065e+02, atom= 1037\n", + "Step= 157, Dmax= 3.7e-02 nm, Epot= -5.83180e+04 Fmax= 1.92017e+02, atom= 5043\n", + "Step= 158, Dmax= 4.4e-02 nm, Epot= -5.83328e+04 Fmax= 9.64419e+02, atom= 4635\n", + "Step= 159, Dmax= 5.3e-02 nm, Epot= -5.83731e+04 Fmax= 3.20299e+02, atom= 4635\n", + "Step= 160, Dmax= 6.4e-02 nm, Epot= -5.83903e+04 Fmax= 9.33434e+02, atom= 4635\n", + "Step= 161, Dmax= 7.6e-02 nm, Epot= -5.84114e+04 Fmax= 4.89153e+02, atom= 4635\n", + "Step= 163, Dmax= 4.6e-02 nm, Epot= -5.84404e+04 Fmax= 3.90576e+02, atom= 2855\n", + "Step= 164, Dmax= 5.5e-02 nm, Epot= -5.84639e+04 Fmax= 3.89971e+02, atom= 285\n", + "Step= 166, Dmax= 3.3e-02 nm, Epot= -5.84896e+04 Fmax= 1.85394e+02, atom= 285\n", + "Step= 167, Dmax= 4.0e-02 nm, Epot= -5.85081e+04 Fmax= 6.35285e+02, atom= 285\n", + "Step= 168, Dmax= 4.7e-02 nm, Epot= -5.85385e+04 Fmax= 2.95014e+02, atom= 285\n", + "Step= 169, Dmax= 5.7e-02 nm, Epot= -5.85451e+04 Fmax= 9.77754e+02, atom= 285\n", + "Step= 170, Dmax= 6.8e-02 nm, Epot= -5.85778e+04 Fmax= 3.63391e+02, atom= 285\n", + "Step= 172, Dmax= 4.1e-02 nm, Epot= -5.86024e+04 Fmax= 2.02615e+02, atom= 5043\n", + "Step= 174, Dmax= 2.5e-02 nm, Epot= -5.86247e+04 Fmax= 2.03310e+02, atom= 2855\n", + "Step= 175, Dmax= 3.0e-02 nm, Epot= -5.86436e+04 Fmax= 2.96942e+02, atom= 285\n", + "Step= 176, Dmax= 3.5e-02 nm, Epot= -5.86611e+04 Fmax= 3.10824e+02, atom= 285\n", + "Step= 177, Dmax= 4.3e-02 nm, Epot= -5.86736e+04 Fmax= 4.93776e+02, atom= 285\n", + "Step= 178, Dmax= 5.1e-02 nm, Epot= -5.86940e+04 Fmax= 3.89987e+02, atom= 285\n", + "Step= 180, Dmax= 3.1e-02 nm, Epot= -5.87218e+04 Fmax= 1.06833e+02, atom= 5043\n", + "Step= 181, Dmax= 3.7e-02 nm, Epot= -5.87361e+04 Fmax= 6.44166e+02, atom= 4635\n", + "Step= 182, Dmax= 4.4e-02 nm, Epot= -5.87811e+04 Fmax= 3.19544e+02, atom= 4635\n", + "Step= 183, Dmax= 5.3e-02 nm, Epot= -5.87921e+04 Fmax= 4.90715e+02, atom= 4635\n", + "Step= 184, Dmax= 6.3e-02 nm, Epot= -5.87959e+04 Fmax= 7.74901e+02, atom= 285\n", + "Step= 185, Dmax= 7.6e-02 nm, Epot= -5.88137e+04 Fmax= 5.99807e+02, atom= 285\n", + "Step= 187, Dmax= 4.6e-02 nm, Epot= -5.88498e+04 Fmax= 1.62855e+02, atom= 1551\n", + "Step= 188, Dmax= 5.5e-02 nm, Epot= -5.88566e+04 Fmax= 5.94842e+02, atom= 1550\n", + "Step= 189, Dmax= 6.6e-02 nm, Epot= -5.88797e+04 Fmax= 7.11423e+02, atom= 285\n", + "Step= 190, Dmax= 7.9e-02 nm, Epot= -5.88856e+04 Fmax= 6.80859e+02, atom= 4635\n", + "Step= 192, Dmax= 4.7e-02 nm, Epot= -5.89348e+04 Fmax= 2.08451e+02, atom= 5043\n", + "Step= 193, Dmax= 5.7e-02 nm, Epot= -5.89433e+04 Fmax= 6.04278e+02, atom= 4635\n", + "Step= 194, Dmax= 6.8e-02 nm, Epot= -5.89509e+04 Fmax= 9.42196e+02, atom= 4635\n", + "Step= 195, Dmax= 8.2e-02 nm, Epot= -5.89724e+04 Fmax= 7.30556e+02, atom= 285\n", + "Step= 196, Dmax= 9.8e-02 nm, Epot= -5.89776e+04 Fmax= 5.60661e+02, atom= 285\n", + "Step= 198, Dmax= 5.9e-02 nm, Epot= -5.90097e+04 Fmax= 3.13266e+02, atom= 284\n", + "Step= 200, Dmax= 3.5e-02 nm, Epot= -5.90345e+04 Fmax= 2.61433e+02, atom= 284\n", + "Step= 201, Dmax= 4.2e-02 nm, Epot= -5.90393e+04 Fmax= 3.44039e+02, atom= 284\n", + "Step= 203, Dmax= 2.5e-02 nm, Epot= -5.90742e+04 Fmax= 6.14359e+01, atom= 4625\n", + "Step= 204, Dmax= 3.1e-02 nm, Epot= -5.90799e+04 Fmax= 4.51359e+02, atom= 4625\n", + "Step= 205, Dmax= 3.7e-02 nm, Epot= -5.91354e+04 Fmax= 1.74673e+02, atom= 2162\n", + "Step= 207, Dmax= 2.2e-02 nm, Epot= -5.91481e+04 Fmax= 1.95328e+02, atom= 2162\n", + "Step= 208, Dmax= 2.6e-02 nm, Epot= -5.91559e+04 Fmax= 2.55103e+02, atom= 2162\n", + "Step= 209, Dmax= 3.2e-02 nm, Epot= -5.91669e+04 Fmax= 2.86077e+02, atom= 2750\n", + "Step= 210, Dmax= 3.8e-02 nm, Epot= -5.91675e+04 Fmax= 3.50601e+02, atom= 2162\n", + "Step= 211, Dmax= 4.6e-02 nm, Epot= -5.91689e+04 Fmax= 4.72392e+02, atom= 2750\n", + "Step= 212, Dmax= 5.5e-02 nm, Epot= -5.91789e+04 Fmax= 4.46180e+02, atom= 2750\n", + "Step= 214, Dmax= 3.3e-02 nm, Epot= -5.92348e+04 Fmax= 9.62019e+01, atom= 1037\n", + "Step= 216, Dmax= 2.0e-02 nm, Epot= -5.92468e+04 Fmax= 2.07440e+02, atom= 1037\n", + "Step= 217, Dmax= 2.4e-02 nm, Epot= -5.92606e+04 Fmax= 2.08207e+02, atom= 1037\n", + "Step= 218, Dmax= 2.8e-02 nm, Epot= -5.92666e+04 Fmax= 2.65871e+02, atom= 1037\n", + "Step= 219, Dmax= 3.4e-02 nm, Epot= -5.92731e+04 Fmax= 3.31445e+02, atom= 1037\n", + "Step= 220, Dmax= 4.1e-02 nm, Epot= -5.92789e+04 Fmax= 3.56153e+02, atom= 1037\n", + "Step= 222, Dmax= 2.5e-02 nm, Epot= -5.93179e+04 Fmax= 5.21486e+01, atom= 1037\n", + "Step= 223, Dmax= 2.9e-02 nm, Epot= -5.93196e+04 Fmax= 4.67079e+02, atom= 5050\n", + "Step= 224, Dmax= 3.5e-02 nm, Epot= -5.93757e+04 Fmax= 1.66102e+02, atom= 5050\n", + "Step= 226, Dmax= 2.1e-02 nm, Epot= -5.93867e+04 Fmax= 1.66684e+02, atom= 5051\n", + "Step= 227, Dmax= 2.5e-02 nm, Epot= -5.93889e+04 Fmax= 2.47359e+02, atom= 1037\n", + "Step= 228, Dmax= 3.1e-02 nm, Epot= -5.93961e+04 Fmax= 2.66854e+02, atom= 1037\n", + "Step= 230, Dmax= 1.8e-02 nm, Epot= -5.94274e+04 Fmax= 5.09855e+01, atom= 5050\n", + "Step= 231, Dmax= 2.2e-02 nm, Epot= -5.94429e+04 Fmax= 3.58031e+02, atom= 5050\n", + "Step= 232, Dmax= 2.6e-02 nm, Epot= -5.94728e+04 Fmax= 1.08357e+02, atom= 5050\n", + "Step= 234, Dmax= 1.6e-02 nm, Epot= -5.94838e+04 Fmax= 1.43123e+02, atom= 5051\n", + "Step= 235, Dmax= 1.9e-02 nm, Epot= -5.94932e+04 Fmax= 1.72068e+02, atom= 5051\n", + "Step= 236, Dmax= 2.3e-02 nm, Epot= -5.95016e+04 Fmax= 2.04237e+02, atom= 5051\n", + "Step= 237, Dmax= 2.7e-02 nm, Epot= -5.95070e+04 Fmax= 2.48763e+02, atom= 5051\n", + "Step= 238, Dmax= 3.3e-02 nm, Epot= -5.95103e+04 Fmax= 2.89528e+02, atom= 5051\n", + "Step= 240, Dmax= 2.0e-02 nm, Epot= -5.95414e+04 Fmax= 5.12312e+01, atom= 5050\n", + "Step= 241, Dmax= 2.4e-02 nm, Epot= -5.95550e+04 Fmax= 3.89078e+02, atom= 5050\n", + "Step= 242, Dmax= 2.8e-02 nm, Epot= -5.95861e+04 Fmax= 1.10845e+02, atom= 5050\n", + "Step= 244, Dmax= 1.7e-02 nm, Epot= -5.95961e+04 Fmax= 1.58399e+02, atom= 5051\n", + "Step= 245, Dmax= 2.0e-02 nm, Epot= -5.96051e+04 Fmax= 1.78986e+02, atom= 5051\n", + "Step= 246, Dmax= 2.4e-02 nm, Epot= -5.96118e+04 Fmax= 2.22749e+02, atom= 5051\n", + "Step= 247, Dmax= 2.9e-02 nm, Epot= -5.96166e+04 Fmax= 2.61684e+02, atom= 5051\n", + "Step= 248, Dmax= 3.5e-02 nm, Epot= -5.96172e+04 Fmax= 3.13383e+02, atom= 5051\n", + "Step= 250, Dmax= 2.1e-02 nm, Epot= -5.96506e+04 Fmax= 4.86983e+01, atom= 5050\n", + "Step= 251, Dmax= 2.5e-02 nm, Epot= -5.96578e+04 Fmax= 4.31252e+02, atom= 5050\n", + "Step= 252, Dmax= 3.0e-02 nm, Epot= -5.96961e+04 Fmax= 1.11653e+02, atom= 5050\n", + "Step= 254, Dmax= 1.8e-02 nm, Epot= -5.97045e+04 Fmax= 1.70830e+02, atom= 5051\n", + "Step= 255, Dmax= 2.2e-02 nm, Epot= -5.97121e+04 Fmax= 1.91495e+02, atom= 5051\n", + "Step= 256, Dmax= 2.6e-02 nm, Epot= -5.97167e+04 Fmax= 2.38105e+02, atom= 5051\n", + "Step= 257, Dmax= 3.2e-02 nm, Epot= -5.97191e+04 Fmax= 2.79075e+02, atom= 5051\n", + "Step= 259, Dmax= 1.9e-02 nm, Epot= -5.97454e+04 Fmax= 4.23782e+01, atom= 1319\n", + "Step= 260, Dmax= 2.3e-02 nm, Epot= -5.97519e+04 Fmax= 3.81711e+02, atom= 1319\n", + "Step= 261, Dmax= 2.7e-02 nm, Epot= -5.97869e+04 Fmax= 1.28726e+02, atom= 1319\n", + "Step= 263, Dmax= 1.6e-02 nm, Epot= -5.97949e+04 Fmax= 1.65876e+02, atom= 1319\n", + "Step= 264, Dmax= 2.0e-02 nm, Epot= -5.98026e+04 Fmax= 1.75747e+02, atom= 1319\n", + "Step= 265, Dmax= 2.4e-02 nm, Epot= -5.98091e+04 Fmax= 2.40416e+02, atom= 1319\n", + "Step= 266, Dmax= 2.8e-02 nm, Epot= -5.98163e+04 Fmax= 2.55718e+02, atom= 1319\n", + "Step= 267, Dmax= 3.4e-02 nm, Epot= -5.98209e+04 Fmax= 3.39142e+02, atom= 1319\n", + "Step= 268, Dmax= 4.1e-02 nm, Epot= -5.98261e+04 Fmax= 3.75544e+02, atom= 1319\n", + "Step= 269, Dmax= 4.9e-02 nm, Epot= -5.98282e+04 Fmax= 4.73619e+02, atom= 1319\n", + "Step= 271, Dmax= 2.9e-02 nm, Epot= -5.98530e+04 Fmax= 6.18993e+01, atom= 1318\n", + "Step= 272, Dmax= 3.5e-02 nm, Epot= -5.98663e+04 Fmax= 6.46697e+02, atom= 1318\n", + "Step= 273, Dmax= 4.2e-02 nm, Epot= -5.98917e+04 Fmax= 1.65695e+02, atom= 1319\n", + "Step= 275, Dmax= 2.5e-02 nm, Epot= -5.98978e+04 Fmax= 2.94874e+02, atom= 1319\n", + "Step= 276, Dmax= 3.0e-02 nm, Epot= -5.99062e+04 Fmax= 2.35808e+02, atom= 1319\n", + "Step= 277, Dmax= 3.6e-02 nm, Epot= -5.99087e+04 Fmax= 4.06924e+02, atom= 1319\n", + "Step= 278, Dmax= 4.4e-02 nm, Epot= -5.99171e+04 Fmax= 3.61301e+02, atom= 1319\n", + "Step= 280, Dmax= 2.6e-02 nm, Epot= -5.99307e+04 Fmax= 8.87213e+01, atom= 1319\n", + "Step= 281, Dmax= 3.2e-02 nm, Epot= -5.99414e+04 Fmax= 4.18033e+02, atom= 1319\n", + "Step= 282, Dmax= 3.8e-02 nm, Epot= -5.99546e+04 Fmax= 2.32465e+02, atom= 1319\n", + "Step= 284, Dmax= 2.3e-02 nm, Epot= -5.99621e+04 Fmax= 1.65416e+02, atom= 1319\n", + "Step= 285, Dmax= 2.7e-02 nm, Epot= -5.99676e+04 Fmax= 3.08849e+02, atom= 1319\n", + "Step= 286, Dmax= 3.3e-02 nm, Epot= -5.99752e+04 Fmax= 2.63161e+02, atom= 1319\n", + "Step= 287, Dmax= 3.9e-02 nm, Epot= -5.99774e+04 Fmax= 4.18453e+02, atom= 1319\n", + "Step= 288, Dmax= 4.7e-02 nm, Epot= -5.99840e+04 Fmax= 4.04201e+02, atom= 1319\n", + "Step= 290, Dmax= 2.8e-02 nm, Epot= -5.99987e+04 Fmax= 7.64403e+01, atom= 1319\n", + "Step= 291, Dmax= 3.4e-02 nm, Epot= -6.00103e+04 Fmax= 4.72924e+02, atom= 1319\n", + "Step= 292, Dmax= 4.1e-02 nm, Epot= -6.00260e+04 Fmax= 2.28258e+02, atom= 1319\n", + "Step= 294, Dmax= 2.4e-02 nm, Epot= -6.00327e+04 Fmax= 2.01055e+02, atom= 1319\n", + "Step= 295, Dmax= 2.9e-02 nm, Epot= -6.00376e+04 Fmax= 3.03494e+02, atom= 1319\n", + "Step= 296, Dmax= 3.5e-02 nm, Epot= -6.00436e+04 Fmax= 3.08345e+02, atom= 1319\n", + "Step= 297, Dmax= 4.2e-02 nm, Epot= -6.00463e+04 Fmax= 4.17414e+02, atom= 1319\n", + "Step= 298, Dmax= 5.1e-02 nm, Epot= -6.00499e+04 Fmax= 4.61089e+02, atom= 1319\n", + "Step= 299, Dmax= 6.1e-02 nm, Epot= -6.00500e+04 Fmax= 5.76279e+02, atom= 1319\n", + "Step= 301, Dmax= 3.6e-02 nm, Epot= -6.00740e+04 Fmax= 6.92350e+01, atom= 1318\n", + "Step= 303, Dmax= 2.2e-02 nm, Epot= -6.00849e+04 Fmax= 2.97816e+02, atom= 1319\n", + "Step= 304, Dmax= 2.6e-02 nm, Epot= -6.00940e+04 Fmax= 1.74488e+02, atom= 1319\n", + "Step= 305, Dmax= 3.1e-02 nm, Epot= -6.00963e+04 Fmax= 3.76278e+02, atom= 1319\n", + "Step= 306, Dmax= 3.8e-02 nm, Epot= -6.01053e+04 Fmax= 2.84534e+02, atom= 1319\n", + "Step= 308, Dmax= 2.3e-02 nm, Epot= -6.01145e+04 Fmax= 1.02150e+02, atom= 1319\n", + "Step= 309, Dmax= 2.7e-02 nm, Epot= -6.01210e+04 Fmax= 3.51456e+02, atom= 1319\n", + "Step= 310, Dmax= 3.3e-02 nm, Epot= -6.01310e+04 Fmax= 2.05725e+02, atom= 1319\n", + "Step= 312, Dmax= 2.0e-02 nm, Epot= -6.01375e+04 Fmax= 1.32276e+02, atom= 1319\n", + "Step= 313, Dmax= 2.3e-02 nm, Epot= -6.01429e+04 Fmax= 2.71747e+02, atom= 1319\n", + "Step= 314, Dmax= 2.8e-02 nm, Epot= -6.01498e+04 Fmax= 2.17193e+02, atom= 1319\n", + "Step= 315, Dmax= 3.4e-02 nm, Epot= -6.01523e+04 Fmax= 3.63914e+02, atom= 1319\n", + "Step= 316, Dmax= 4.1e-02 nm, Epot= -6.01588e+04 Fmax= 3.39846e+02, atom= 1319\n", + "Step= 318, Dmax= 2.4e-02 nm, Epot= -6.01697e+04 Fmax= 7.37318e+01, atom= 1319\n", + "Step= 319, Dmax= 2.9e-02 nm, Epot= -6.01788e+04 Fmax= 4.13958e+02, atom= 1319\n", + "Step= 320, Dmax= 3.5e-02 nm, Epot= -6.01916e+04 Fmax= 1.86138e+02, atom= 1319\n", + "Step= 322, Dmax= 2.1e-02 nm, Epot= -6.01974e+04 Fmax= 1.78388e+02, atom= 1319\n", + "Step= 323, Dmax= 2.5e-02 nm, Epot= -6.02022e+04 Fmax= 2.51869e+02, atom= 1319\n", + "Step= 324, Dmax= 3.0e-02 nm, Epot= -6.02074e+04 Fmax= 2.70618e+02, atom= 1319\n", + "Step= 325, Dmax= 3.6e-02 nm, Epot= -6.02108e+04 Fmax= 3.49031e+02, atom= 1319\n", + "Step= 326, Dmax= 4.4e-02 nm, Epot= -6.02141e+04 Fmax= 4.02081e+02, atom= 1319\n", + "Step= 327, Dmax= 5.2e-02 nm, Epot= -6.02156e+04 Fmax= 4.86209e+02, atom= 1319\n", + "Step= 329, Dmax= 3.1e-02 nm, Epot= -6.02336e+04 Fmax= 5.71155e+01, atom= 1319\n", + "Step= 330, Dmax= 3.8e-02 nm, Epot= -6.02368e+04 Fmax= 6.64340e+02, atom= 1318\n", + "Step= 331, Dmax= 4.5e-02 nm, Epot= -6.02655e+04 Fmax= 1.83676e+02, atom= 1319\n", + "Step= 333, Dmax= 2.7e-02 nm, Epot= -6.02695e+04 Fmax= 2.91250e+02, atom= 1319\n", + "Step= 334, Dmax= 3.3e-02 nm, Epot= -6.02756e+04 Fmax= 2.63202e+02, atom= 1319\n", + "Step= 335, Dmax= 3.9e-02 nm, Epot= -6.02765e+04 Fmax= 4.03992e+02, atom= 1319\n", + "Step= 336, Dmax= 4.7e-02 nm, Epot= -6.02819e+04 Fmax= 3.98621e+02, atom= 1319\n", + "Step= 338, Dmax= 2.8e-02 nm, Epot= -6.02956e+04 Fmax= 7.60762e+01, atom= 1319\n", + "Step= 339, Dmax= 3.4e-02 nm, Epot= -6.03017e+04 Fmax= 4.77231e+02, atom= 1319\n", + "Step= 340, Dmax= 4.1e-02 nm, Epot= -6.03171e+04 Fmax= 2.15730e+02, atom= 1319\n", + "Step= 342, Dmax= 2.4e-02 nm, Epot= -6.03227e+04 Fmax= 2.03128e+02, atom= 1319\n", + "Step= 343, Dmax= 2.9e-02 nm, Epot= -6.03264e+04 Fmax= 2.89043e+02, atom= 1319\n", + "Step= 344, Dmax= 3.5e-02 nm, Epot= -6.03312e+04 Fmax= 3.08965e+02, atom= 1319\n", + "Step= 345, Dmax= 4.2e-02 nm, Epot= -6.03330e+04 Fmax= 4.00348e+02, atom= 1319\n", + "Step= 346, Dmax= 5.0e-02 nm, Epot= -6.03353e+04 Fmax= 4.58882e+02, atom= 1319\n", + "Step= 348, Dmax= 3.0e-02 nm, Epot= -6.03520e+04 Fmax= 5.05216e+01, atom= 1319\n", + "Step= 349, Dmax= 3.6e-02 nm, Epot= -6.03634e+04 Fmax= 5.51052e+02, atom= 1319\n", + "Step= 350, Dmax= 4.4e-02 nm, Epot= -6.03847e+04 Fmax= 2.08449e+02, atom= 1319\n", + "Step= 352, Dmax= 2.6e-02 nm, Epot= -6.03894e+04 Fmax= 2.48168e+02, atom= 1319\n", + "Step= 353, Dmax= 3.1e-02 nm, Epot= -6.03939e+04 Fmax= 2.78026e+02, atom= 1319\n", + "Step= 354, Dmax= 3.8e-02 nm, Epot= -6.03962e+04 Fmax= 3.63994e+02, atom= 1319\n", + "Step= 355, Dmax= 4.5e-02 nm, Epot= -6.04000e+04 Fmax= 3.95144e+02, atom= 1319\n", + "Step= 357, Dmax= 2.7e-02 nm, Epot= -6.04132e+04 Fmax= 6.51975e+01, atom= 1319\n", + "Step= 358, Dmax= 3.3e-02 nm, Epot= -6.04186e+04 Fmax= 4.91131e+02, atom= 1319\n", + "Step= 359, Dmax= 3.9e-02 nm, Epot= -6.04361e+04 Fmax= 1.93860e+02, atom= 1319\n", + "Step= 361, Dmax= 2.3e-02 nm, Epot= -6.04414e+04 Fmax= 2.04614e+02, atom= 1319\n", + "Step= 362, Dmax= 2.8e-02 nm, Epot= -6.04453e+04 Fmax= 2.67362e+02, atom= 1319\n", + "Step= 363, Dmax= 3.4e-02 nm, Epot= -6.04495e+04 Fmax= 3.00671e+02, atom= 1319\n", + "Step= 364, Dmax= 4.0e-02 nm, Epot= -6.04514e+04 Fmax= 3.83352e+02, atom= 1319\n", + "Step= 365, Dmax= 4.9e-02 nm, Epot= -6.04542e+04 Fmax= 4.30970e+02, atom= 1319\n", + "Step= 367, Dmax= 2.9e-02 nm, Epot= -6.04695e+04 Fmax= 6.18336e+01, atom= 1319\n", + "Step= 368, Dmax= 3.5e-02 nm, Epot= -6.04722e+04 Fmax= 5.46742e+02, atom= 1319\n", + "Step= 369, Dmax= 4.2e-02 nm, Epot= -6.04944e+04 Fmax= 1.96927e+02, atom= 1319\n", + "Step= 371, Dmax= 2.5e-02 nm, Epot= -6.04991e+04 Fmax= 2.32225e+02, atom= 1319\n", + "Step= 372, Dmax= 3.0e-02 nm, Epot= -6.05030e+04 Fmax= 2.73007e+02, atom= 1319\n", + "Step= 373, Dmax= 3.6e-02 nm, Epot= -6.05060e+04 Fmax= 3.36710e+02, atom= 1319\n", + "Step= 374, Dmax= 4.4e-02 nm, Epot= -6.05082e+04 Fmax= 3.96413e+02, atom= 1319\n", + "Step= 375, Dmax= 5.2e-02 nm, Epot= -6.05088e+04 Fmax= 4.76611e+02, atom= 1319\n", + "Step= 377, Dmax= 3.1e-02 nm, Epot= -6.05272e+04 Fmax= 5.16323e+01, atom= 1319\n", + "Step= 378, Dmax= 3.8e-02 nm, Epot= -6.05276e+04 Fmax= 6.14499e+02, atom= 1319\n", + "Step= 379, Dmax= 4.5e-02 nm, Epot= -6.05569e+04 Fmax= 2.03659e+02, atom= 1319\n", + "Step= 381, Dmax= 2.7e-02 nm, Epot= -6.05610e+04 Fmax= 2.60531e+02, atom= 1319\n", + "Step= 382, Dmax= 3.2e-02 nm, Epot= -6.05650e+04 Fmax= 2.79866e+02, atom= 1319\n", + "Step= 383, Dmax= 3.9e-02 nm, Epot= -6.05663e+04 Fmax= 3.74775e+02, atom= 1319\n", + "Step= 384, Dmax= 4.7e-02 nm, Epot= -6.05691e+04 Fmax= 4.11038e+02, atom= 1319\n", + "Step= 386, Dmax= 2.8e-02 nm, Epot= -6.05838e+04 Fmax= 5.79211e+01, atom= 1319\n", + "Step= 387, Dmax= 3.4e-02 nm, Epot= -6.05889e+04 Fmax= 4.89873e+02, atom= 1319\n", + "Step= 388, Dmax= 4.0e-02 nm, Epot= -6.06071e+04 Fmax= 1.97414e+02, atom= 1319\n", + "Step= 390, Dmax= 2.4e-02 nm, Epot= -6.06115e+04 Fmax= 2.17537e+02, atom= 1319\n", + "Step= 391, Dmax= 2.9e-02 nm, Epot= -6.06147e+04 Fmax= 2.68041e+02, atom= 1319\n", + "Step= 392, Dmax= 3.5e-02 nm, Epot= -6.06174e+04 Fmax= 3.21251e+02, atom= 1319\n", + "Step= 393, Dmax= 4.2e-02 nm, Epot= -6.06190e+04 Fmax= 3.79032e+02, atom= 1319\n", + "Step= 395, Dmax= 2.5e-02 nm, Epot= -6.06328e+04 Fmax= 4.36223e+01, atom= 1319\n", + "Step= 396, Dmax= 3.0e-02 nm, Epot= -6.06401e+04 Fmax= 4.74855e+02, atom= 1319\n", + "Step= 397, Dmax= 3.6e-02 nm, Epot= -6.06604e+04 Fmax= 1.57750e+02, atom= 1319\n", + "Step= 399, Dmax= 2.2e-02 nm, Epot= -6.06641e+04 Fmax= 2.12313e+02, atom= 1319\n", + "Step= 400, Dmax= 2.6e-02 nm, Epot= -6.06682e+04 Fmax= 2.24630e+02, atom= 1319\n", + "Step= 401, Dmax= 3.1e-02 nm, Epot= -6.06700e+04 Fmax= 3.00293e+02, atom= 1319\n", + "Step= 402, Dmax= 3.8e-02 nm, Epot= -6.06728e+04 Fmax= 3.31786e+02, atom= 1319\n", + "Step= 404, Dmax= 2.3e-02 nm, Epot= -6.06847e+04 Fmax= 4.53620e+01, atom= 1319\n", + "Step= 405, Dmax= 2.7e-02 nm, Epot= -6.06914e+04 Fmax= 4.01247e+02, atom= 1319\n", + "Step= 406, Dmax= 3.2e-02 nm, Epot= -6.07079e+04 Fmax= 1.48220e+02, atom= 1319\n", + "Step= 408, Dmax= 1.9e-02 nm, Epot= -6.07116e+04 Fmax= 1.84527e+02, atom= 1319\n", + "Step= 409, Dmax= 2.3e-02 nm, Epot= -6.07151e+04 Fmax= 2.06689e+02, atom= 1319\n", + "Step= 410, Dmax= 2.8e-02 nm, Epot= -6.07169e+04 Fmax= 2.67366e+02, atom= 1319\n", + "Step= 411, Dmax= 3.4e-02 nm, Epot= -6.07192e+04 Fmax= 2.96362e+02, atom= 1319\n", + "Step= 413, Dmax= 2.0e-02 nm, Epot= -6.07315e+04 Fmax= 4.34829e+01, atom= 1319\n", + "Step= 414, Dmax= 2.4e-02 nm, Epot= -6.07318e+04 Fmax= 3.67845e+02, atom= 1319\n", + "Step= 415, Dmax= 2.9e-02 nm, Epot= -6.07518e+04 Fmax= 1.31639e+02, atom= 1319\n", + "Step= 417, Dmax= 1.7e-02 nm, Epot= -6.07548e+04 Fmax= 1.63602e+02, atom= 1319\n", + "Step= 418, Dmax= 2.1e-02 nm, Epot= -6.07572e+04 Fmax= 1.88990e+02, atom= 1319\n", + "Step= 419, Dmax= 2.5e-02 nm, Epot= -6.07577e+04 Fmax= 2.32875e+02, atom= 1319\n", + "Step= 421, Dmax= 1.5e-02 nm, Epot= -6.07708e+04 Fmax= 3.30466e+01, atom= 2326\n", + "Step= 422, Dmax= 1.8e-02 nm, Epot= -6.07767e+04 Fmax= 3.04932e+02, atom= 2326\n", + "Step= 423, Dmax= 2.2e-02 nm, Epot= -6.07912e+04 Fmax= 9.78066e+01, atom= 1223\n", + "Step= 425, Dmax= 1.3e-02 nm, Epot= -6.07950e+04 Fmax= 1.25476e+02, atom= 1223\n", + "Step= 426, Dmax= 1.6e-02 nm, Epot= -6.07985e+04 Fmax= 1.45130e+02, atom= 1223\n", + "Step= 427, Dmax= 1.9e-02 nm, Epot= -6.08015e+04 Fmax= 1.89108e+02, atom= 1223\n", + "Step= 428, Dmax= 2.2e-02 nm, Epot= -6.08046e+04 Fmax= 2.04297e+02, atom= 1223\n", + "Step= 429, Dmax= 2.7e-02 nm, Epot= -6.08059e+04 Fmax= 2.74445e+02, atom= 1223\n", + "Step= 430, Dmax= 3.2e-02 nm, Epot= -6.08084e+04 Fmax= 2.93029e+02, atom= 1223\n", + "Step= 432, Dmax= 1.9e-02 nm, Epot= -6.08203e+04 Fmax= 4.92068e+01, atom= 1223\n", + "Step= 433, Dmax= 2.3e-02 nm, Epot= -6.08255e+04 Fmax= 3.74352e+02, atom= 1223\n", + "Step= 434, Dmax= 2.8e-02 nm, Epot= -6.08374e+04 Fmax= 1.59570e+02, atom= 1223\n", + "Step= 436, Dmax= 1.7e-02 nm, Epot= -6.08415e+04 Fmax= 1.18581e+02, atom= 1223\n", + "Step= 437, Dmax= 2.0e-02 nm, Epot= -6.08439e+04 Fmax= 2.38973e+02, atom= 1223\n", + "Step= 438, Dmax= 2.4e-02 nm, Epot= -6.08490e+04 Fmax= 1.78082e+02, atom= 1223\n", + "Step= 440, Dmax= 1.4e-02 nm, Epot= -6.08539e+04 Fmax= 7.59461e+01, atom= 1223\n", + "Step= 441, Dmax= 1.7e-02 nm, Epot= -6.08580e+04 Fmax= 2.27286e+02, atom= 1223\n", + "Step= 442, Dmax= 2.1e-02 nm, Epot= -6.08635e+04 Fmax= 1.44711e+02, atom= 1223\n", + "Step= 443, Dmax= 2.5e-02 nm, Epot= -6.08645e+04 Fmax= 2.95004e+02, atom= 1223\n", + "Step= 444, Dmax= 3.0e-02 nm, Epot= -6.08700e+04 Fmax= 2.32901e+02, atom= 1223\n", + "Step= 446, Dmax= 1.8e-02 nm, Epot= -6.08762e+04 Fmax= 7.04377e+01, atom= 1223\n", + "Step= 447, Dmax= 2.2e-02 nm, Epot= -6.08777e+04 Fmax= 3.43073e+02, atom= 1223\n", + "Step= 448, Dmax= 2.6e-02 nm, Epot= -6.08879e+04 Fmax= 1.24836e+02, atom= 1223\n", + "Step= 450, Dmax= 1.6e-02 nm, Epot= -6.08917e+04 Fmax= 1.42072e+02, atom= 1223\n", + "Step= 451, Dmax= 1.9e-02 nm, Epot= -6.08948e+04 Fmax= 1.81305e+02, atom= 1223\n", + "Step= 452, Dmax= 2.2e-02 nm, Epot= -6.08980e+04 Fmax= 2.14994e+02, atom= 1223\n", + "Step= 453, Dmax= 2.7e-02 nm, Epot= -6.09003e+04 Fmax= 2.53778e+02, atom= 1223\n", + "Step= 454, Dmax= 3.2e-02 nm, Epot= -6.09020e+04 Fmax= 3.13246e+02, atom= 1223\n", + "Step= 455, Dmax= 3.9e-02 nm, Epot= -6.09029e+04 Fmax= 3.64355e+02, atom= 1223\n", + "Step= 457, Dmax= 2.3e-02 nm, Epot= -6.09160e+04 Fmax= 4.65659e+01, atom= 1223\n", + "Step= 458, Dmax= 2.8e-02 nm, Epot= -6.09208e+04 Fmax= 4.79801e+02, atom= 1223\n", + "Step= 459, Dmax= 3.4e-02 nm, Epot= -6.09356e+04 Fmax= 1.97644e+02, atom= 1223\n", + "Step= 461, Dmax= 2.0e-02 nm, Epot= -6.09399e+04 Fmax= 1.28547e+02, atom= 1223\n", + "Step= 462, Dmax= 2.4e-02 nm, Epot= -6.09409e+04 Fmax= 3.01190e+02, atom= 1223\n", + "Step= 463, Dmax= 2.9e-02 nm, Epot= -6.09471e+04 Fmax= 1.97468e+02, atom= 1223\n", + "Step= 465, Dmax= 1.7e-02 nm, Epot= -6.09522e+04 Fmax= 1.00804e+02, atom= 1223\n", + "Step= 466, Dmax= 2.1e-02 nm, Epot= -6.09543e+04 Fmax= 2.63690e+02, atom= 1223\n", + "Step= 467, Dmax= 2.5e-02 nm, Epot= -6.09602e+04 Fmax= 1.78006e+02, atom= 1223\n", + "Step= 469, Dmax= 1.5e-02 nm, Epot= -6.09647e+04 Fmax= 7.47557e+01, atom= 1223\n", + "Step= 470, Dmax= 1.8e-02 nm, Epot= -6.09677e+04 Fmax= 2.55234e+02, atom= 1223\n", + "Step= 471, Dmax= 2.2e-02 nm, Epot= -6.09741e+04 Fmax= 1.22540e+02, atom= 1223\n", + "Step= 473, Dmax= 1.3e-02 nm, Epot= -6.09779e+04 Fmax= 1.02993e+02, atom= 1223\n", + "Step= 474, Dmax= 1.6e-02 nm, Epot= -6.09811e+04 Fmax= 1.64853e+02, atom= 1223\n", + "Step= 475, Dmax= 1.9e-02 nm, Epot= -6.09848e+04 Fmax= 1.64522e+02, atom= 1223\n", + "Step= 476, Dmax= 2.2e-02 nm, Epot= -6.09870e+04 Fmax= 2.23727e+02, atom= 1223\n", + "Step= 477, Dmax= 2.7e-02 nm, Epot= -6.09899e+04 Fmax= 2.47590e+02, atom= 1223\n", + "Step= 478, Dmax= 3.2e-02 nm, Epot= -6.09907e+04 Fmax= 3.14368e+02, atom= 1223\n", + "Step= 479, Dmax= 3.9e-02 nm, Epot= -6.09921e+04 Fmax= 3.58548e+02, atom= 1223\n", + "Step= 481, Dmax= 2.3e-02 nm, Epot= -6.10042e+04 Fmax= 6.45564e+01, atom= 2326\n", + "Step= 482, Dmax= 2.8e-02 nm, Epot= -6.10077e+04 Fmax= 4.22201e+02, atom= 2326\n", + "Step= 483, Dmax= 3.3e-02 nm, Epot= -6.10168e+04 Fmax= 1.82764e+02, atom= 1223\n", + "Step= 485, Dmax= 2.0e-02 nm, Epot= -6.10212e+04 Fmax= 1.44877e+02, atom= 1223\n", + "Step= 487, Dmax= 1.2e-02 nm, Epot= -6.10253e+04 Fmax= 6.19955e+01, atom= 1223\n", + "Step= 488, Dmax= 1.4e-02 nm, Epot= -6.10291e+04 Fmax= 2.01341e+02, atom= 1223\n", + "Step= 489, Dmax= 1.7e-02 nm, Epot= -6.10341e+04 Fmax= 1.01983e+02, atom= 1223\n", + "Step= 490, Dmax= 2.1e-02 nm, Epot= -6.10347e+04 Fmax= 2.78053e+02, atom= 1223\n", + "Step= 491, Dmax= 2.5e-02 nm, Epot= -6.10412e+04 Fmax= 1.59365e+02, atom= 1223\n", + "Step= 493, Dmax= 1.5e-02 nm, Epot= -6.10456e+04 Fmax= 9.52809e+01, atom= 1223\n", + "Step= 494, Dmax= 1.8e-02 nm, Epot= -6.10477e+04 Fmax= 2.16944e+02, atom= 1223\n", + "Step= 495, Dmax= 2.2e-02 nm, Epot= -6.10526e+04 Fmax= 1.62664e+02, atom= 1223\n", + "Step= 497, Dmax= 1.3e-02 nm, Epot= -6.10568e+04 Fmax= 5.81613e+01, atom= 1223\n", + "Step= 498, Dmax= 1.6e-02 nm, Epot= -6.10605e+04 Fmax= 2.30065e+02, atom= 1223\n", + "Step= 499, Dmax= 1.9e-02 nm, Epot= -6.10663e+04 Fmax= 9.80535e+01, atom= 1223\n", + "Step= 501, Dmax= 1.1e-02 nm, Epot= -6.10697e+04 Fmax= 9.64444e+01, atom= 1223\n", + "Step= 502, Dmax= 1.3e-02 nm, Epot= -6.10728e+04 Fmax= 1.33882e+02, atom= 1223\n", + "Step= 503, Dmax= 1.6e-02 nm, Epot= -6.10759e+04 Fmax= 1.50261e+02, atom= 1223\n", + "Step= 504, Dmax= 1.9e-02 nm, Epot= -6.10785e+04 Fmax= 1.83555e+02, atom= 1223\n", + "Step= 505, Dmax= 2.3e-02 nm, Epot= -6.10809e+04 Fmax= 2.23775e+02, atom= 1223\n", + "Step= 506, Dmax= 2.8e-02 nm, Epot= -6.10828e+04 Fmax= 2.58840e+02, atom= 1223\n", + "Step= 507, Dmax= 3.3e-02 nm, Epot= -6.10835e+04 Fmax= 3.24092e+02, atom= 1223\n", + "Step= 508, Dmax= 4.0e-02 nm, Epot= -6.10837e+04 Fmax= 3.73191e+02, atom= 1223\n", + "Step= 510, Dmax= 2.4e-02 nm, Epot= -6.10974e+04 Fmax= 4.94931e+01, atom= 2002\n", + "Step= 511, Dmax= 2.9e-02 nm, Epot= -6.10982e+04 Fmax= 4.71037e+02, atom= 1223\n", + "Step= 512, Dmax= 3.5e-02 nm, Epot= -6.11131e+04 Fmax= 2.19061e+02, atom= 1223\n", + "Step= 514, Dmax= 2.1e-02 nm, Epot= -6.11176e+04 Fmax= 1.18684e+02, atom= 1223\n", + "Step= 516, Dmax= 1.2e-02 nm, Epot= -6.11210e+04 Fmax= 9.84646e+01, atom= 1223\n", + "Step= 517, Dmax= 1.5e-02 nm, Epot= -6.11240e+04 Fmax= 1.54585e+02, atom= 1223\n", + "Step= 518, Dmax= 1.8e-02 nm, Epot= -6.11271e+04 Fmax= 1.58661e+02, atom= 1223\n", + "Step= 519, Dmax= 2.2e-02 nm, Epot= -6.11292e+04 Fmax= 2.11798e+02, atom= 1223\n", + "Step= 520, Dmax= 2.6e-02 nm, Epot= -6.11315e+04 Fmax= 2.37670e+02, atom= 1223\n", + "Step= 521, Dmax= 3.1e-02 nm, Epot= -6.11322e+04 Fmax= 2.99094e+02, atom= 1223\n", + "Step= 522, Dmax= 3.7e-02 nm, Epot= -6.11330e+04 Fmax= 3.44767e+02, atom= 1223\n", + "Step= 524, Dmax= 2.2e-02 nm, Epot= -6.11447e+04 Fmax= 5.97056e+01, atom= 2326\n", + "Step= 525, Dmax= 2.7e-02 nm, Epot= -6.11474e+04 Fmax= 4.00193e+02, atom= 2326\n", + "Step= 526, Dmax= 3.2e-02 nm, Epot= -6.11562e+04 Fmax= 1.77130e+02, atom= 1223\n", + "Step= 528, Dmax= 1.9e-02 nm, Epot= -6.11602e+04 Fmax= 1.38647e+02, atom= 1223\n", + "Step= 530, Dmax= 1.2e-02 nm, Epot= -6.11639e+04 Fmax= 6.03498e+01, atom= 1223\n", + "Step= 531, Dmax= 1.4e-02 nm, Epot= -6.11672e+04 Fmax= 1.89772e+02, atom= 1223\n", + "Step= 532, Dmax= 1.7e-02 nm, Epot= -6.11718e+04 Fmax= 1.00613e+02, atom= 1223\n", + "Step= 533, Dmax= 2.0e-02 nm, Epot= -6.11721e+04 Fmax= 2.60538e+02, atom= 1223\n", + "Step= 534, Dmax= 2.4e-02 nm, Epot= -6.11779e+04 Fmax= 1.57938e+02, atom= 1223\n", + "Step= 536, Dmax= 1.4e-02 nm, Epot= -6.11822e+04 Fmax= 8.63103e+01, atom= 1223\n", + "Step= 537, Dmax= 1.7e-02 nm, Epot= -6.11839e+04 Fmax= 2.13303e+02, atom= 1223\n", + "Step= 538, Dmax= 2.1e-02 nm, Epot= -6.11888e+04 Fmax= 1.49692e+02, atom= 1223\n", + "Step= 540, Dmax= 1.2e-02 nm, Epot= -6.11926e+04 Fmax= 6.22881e+01, atom= 1223\n", + "Step= 541, Dmax= 1.5e-02 nm, Epot= -6.11953e+04 Fmax= 2.08925e+02, atom= 1223\n", + "Step= 542, Dmax= 1.8e-02 nm, Epot= -6.12004e+04 Fmax= 1.03819e+02, atom= 1223\n", + "Step= 544, Dmax= 1.1e-02 nm, Epot= -6.12036e+04 Fmax= 8.21175e+01, atom= 1223\n", + "Step= 545, Dmax= 1.3e-02 nm, Epot= -6.12064e+04 Fmax= 1.39020e+02, atom= 1223\n", + "Step= 546, Dmax= 1.5e-02 nm, Epot= -6.12096e+04 Fmax= 1.32133e+02, atom= 1223\n", + "Step= 547, Dmax= 1.9e-02 nm, Epot= -6.12115e+04 Fmax= 1.88047e+02, atom= 1223\n", + "Step= 548, Dmax= 2.2e-02 nm, Epot= -6.12142e+04 Fmax= 2.00684e+02, atom= 1223\n", + "Step= 549, Dmax= 2.7e-02 nm, Epot= -6.12150e+04 Fmax= 2.62648e+02, atom= 1223\n", + "Step= 550, Dmax= 3.2e-02 nm, Epot= -6.12166e+04 Fmax= 2.94405e+02, atom= 1223\n", + "Step= 552, Dmax= 1.9e-02 nm, Epot= -6.12259e+04 Fmax= 5.23357e+01, atom= 2326\n", + "Step= 553, Dmax= 2.3e-02 nm, Epot= -6.12293e+04 Fmax= 3.43597e+02, atom= 2326\n", + "Step= 554, Dmax= 2.8e-02 nm, Epot= -6.12373e+04 Fmax= 1.53810e+02, atom= 1223\n", + "Step= 556, Dmax= 1.7e-02 nm, Epot= -6.12409e+04 Fmax= 1.21731e+02, atom= 1223\n", + "Step= 557, Dmax= 2.0e-02 nm, Epot= -6.12416e+04 Fmax= 2.24143e+02, atom= 1223\n", + "Step= 558, Dmax= 2.4e-02 nm, Epot= -6.12460e+04 Fmax= 1.91440e+02, atom= 1223\n", + "Step= 560, Dmax= 1.4e-02 nm, Epot= -6.12510e+04 Fmax= 5.48196e+01, atom= 1223\n", + "Step= 561, Dmax= 1.7e-02 nm, Epot= -6.12531e+04 Fmax= 2.69031e+02, atom= 1223\n", + "Step= 562, Dmax= 2.1e-02 nm, Epot= -6.12605e+04 Fmax= 1.00313e+02, atom= 1223\n", + "Step= 564, Dmax= 1.2e-02 nm, Epot= -6.12635e+04 Fmax= 1.10796e+02, atom= 1223\n", + "Step= 565, Dmax= 1.5e-02 nm, Epot= -6.12661e+04 Fmax= 1.44672e+02, atom= 1223\n", + "Step= 566, Dmax= 1.8e-02 nm, Epot= -6.12687e+04 Fmax= 1.67308e+02, atom= 1223\n", + "Step= 567, Dmax= 2.1e-02 nm, Epot= -6.12706e+04 Fmax= 2.02282e+02, atom= 1223\n", + "Step= 568, Dmax= 2.6e-02 nm, Epot= -6.12724e+04 Fmax= 2.45964e+02, atom= 1223\n", + "Step= 569, Dmax= 3.1e-02 nm, Epot= -6.12732e+04 Fmax= 2.88150e+02, atom= 1223\n", + "Step= 571, Dmax= 1.9e-02 nm, Epot= -6.12828e+04 Fmax= 3.52276e+01, atom= 2002\n", + "Step= 572, Dmax= 2.2e-02 nm, Epot= -6.12895e+04 Fmax= 3.37060e+02, atom= 1223\n", + "Step= 573, Dmax= 2.7e-02 nm, Epot= -6.12994e+04 Fmax= 1.66757e+02, atom= 1223\n", + "Step= 575, Dmax= 1.6e-02 nm, Epot= -6.13033e+04 Fmax= 9.76431e+01, atom= 1223\n", + "Step= 576, Dmax= 1.9e-02 nm, Epot= -6.13042e+04 Fmax= 2.41500e+02, atom= 1223\n", + "Step= 577, Dmax= 2.3e-02 nm, Epot= -6.13096e+04 Fmax= 1.55215e+02, atom= 1223\n", + "Step= 579, Dmax= 1.4e-02 nm, Epot= -6.13136e+04 Fmax= 8.21985e+01, atom= 1223\n", + "Step= 580, Dmax= 1.7e-02 nm, Epot= -6.13156e+04 Fmax= 2.05423e+02, atom= 1223\n", + "Step= 581, Dmax= 2.0e-02 nm, Epot= -6.13203e+04 Fmax= 1.41518e+02, atom= 1223\n", + "Step= 583, Dmax= 1.2e-02 nm, Epot= -6.13241e+04 Fmax= 6.04040e+01, atom= 1223\n", + "Step= 584, Dmax= 1.4e-02 nm, Epot= -6.13270e+04 Fmax= 1.96301e+02, atom= 1223\n", + "Step= 585, Dmax= 1.7e-02 nm, Epot= -6.13321e+04 Fmax= 1.02305e+02, atom= 1223\n", + "Step= 587, Dmax= 1.0e-02 nm, Epot= -6.13353e+04 Fmax= 7.60511e+01, atom= 1223\n", + "Step= 588, Dmax= 1.2e-02 nm, Epot= -6.13383e+04 Fmax= 1.36678e+02, atom= 1223\n", + "Step= 589, Dmax= 1.5e-02 nm, Epot= -6.13417e+04 Fmax= 1.22432e+02, atom= 1223\n", + "Step= 590, Dmax= 1.8e-02 nm, Epot= -6.13436e+04 Fmax= 1.85066e+02, atom= 1223\n", + "Step= 591, Dmax= 2.1e-02 nm, Epot= -6.13467e+04 Fmax= 1.86598e+02, atom= 1223\n", + "Step= 592, Dmax= 2.6e-02 nm, Epot= -6.13471e+04 Fmax= 2.58182e+02, atom= 1223\n", + "Step= 593, Dmax= 3.1e-02 nm, Epot= -6.13494e+04 Fmax= 2.74523e+02, atom= 1223\n", + "Step= 595, Dmax= 1.9e-02 nm, Epot= -6.13585e+04 Fmax= 5.13218e+01, atom= 2326\n", + "Step= 596, Dmax= 2.2e-02 nm, Epot= -6.13605e+04 Fmax= 3.35681e+02, atom= 2326\n", + "Step= 597, Dmax= 2.7e-02 nm, Epot= -6.13702e+04 Fmax= 1.48336e+02, atom= 1223\n", + "Step= 599, Dmax= 1.6e-02 nm, Epot= -6.13739e+04 Fmax= 1.16013e+02, atom= 1223\n", + "Step= 600, Dmax= 1.9e-02 nm, Epot= -6.13748e+04 Fmax= 2.15015e+02, atom= 1223\n", + "Step= 601, Dmax= 2.3e-02 nm, Epot= -6.13792e+04 Fmax= 1.82102e+02, atom= 1223\n", + "Step= 603, Dmax= 1.4e-02 nm, Epot= -6.13843e+04 Fmax= 5.32855e+01, atom= 1223\n", + "Step= 604, Dmax= 1.7e-02 nm, Epot= -6.13867e+04 Fmax= 2.51868e+02, atom= 1223\n", + "Step= 605, Dmax= 2.0e-02 nm, Epot= -6.13940e+04 Fmax= 9.92775e+01, atom= 1223\n", + "Step= 607, Dmax= 1.2e-02 nm, Epot= -6.13972e+04 Fmax= 1.03082e+02, atom= 1223\n", + "Step= 608, Dmax= 1.4e-02 nm, Epot= -6.13998e+04 Fmax= 1.41508e+02, atom= 1223\n", + "Step= 609, Dmax= 1.7e-02 nm, Epot= -6.14026e+04 Fmax= 1.55968e+02, atom= 1223\n", + "Step= 610, Dmax= 2.1e-02 nm, Epot= -6.14045e+04 Fmax= 1.97491e+02, atom= 1223\n", + "Step= 611, Dmax= 2.5e-02 nm, Epot= -6.14066e+04 Fmax= 2.30065e+02, atom= 1223\n", + "Step= 612, Dmax= 3.0e-02 nm, Epot= -6.14071e+04 Fmax= 2.80509e+02, atom= 1223\n", + "Step= 613, Dmax= 3.6e-02 nm, Epot= -6.14073e+04 Fmax= 3.32363e+02, atom= 1223\n", + "Step= 615, Dmax= 2.1e-02 nm, Epot= -6.14204e+04 Fmax= 5.60515e+01, atom= 2326\n", + "Step= 616, Dmax= 2.6e-02 nm, Epot= -6.14238e+04 Fmax= 3.65824e+02, atom= 2326\n", + "Step= 617, Dmax= 3.1e-02 nm, Epot= -6.14322e+04 Fmax= 1.67807e+02, atom= 1223\n", + "Step= 619, Dmax= 1.8e-02 nm, Epot= -6.14361e+04 Fmax= 1.34038e+02, atom= 1223\n", + "Step= 621, Dmax= 1.1e-02 nm, Epot= -6.14401e+04 Fmax= 5.50527e+01, atom= 1223\n", + "Step= 622, Dmax= 1.3e-02 nm, Epot= -6.14435e+04 Fmax= 1.78651e+02, atom= 1223\n", + "Step= 623, Dmax= 1.6e-02 nm, Epot= -6.14483e+04 Fmax= 9.60041e+01, atom= 1223\n", + "Step= 624, Dmax= 1.9e-02 nm, Epot= -6.14486e+04 Fmax= 2.41824e+02, atom= 1223\n", + "Step= 625, Dmax= 2.3e-02 nm, Epot= -6.14546e+04 Fmax= 1.53190e+02, atom= 1223\n", + "Step= 627, Dmax= 1.4e-02 nm, Epot= -6.14590e+04 Fmax= 7.78358e+01, atom= 1223\n", + "Step= 628, Dmax= 1.7e-02 nm, Epot= -6.14606e+04 Fmax= 2.05742e+02, atom= 1223\n", + "Step= 629, Dmax= 2.0e-02 nm, Epot= -6.14660e+04 Fmax= 1.35763e+02, atom= 1223\n", + "Step= 631, Dmax= 1.2e-02 nm, Epot= -6.14699e+04 Fmax= 6.48805e+01, atom= 1223\n", + "Step= 632, Dmax= 1.4e-02 nm, Epot= -6.14724e+04 Fmax= 1.86673e+02, atom= 1223\n", + "Step= 633, Dmax= 1.7e-02 nm, Epot= -6.14775e+04 Fmax= 1.07111e+02, atom= 1223\n", + "Step= 635, Dmax= 1.0e-02 nm, Epot= -6.14809e+04 Fmax= 6.79335e+01, atom= 1223\n", + "Step= 636, Dmax= 1.2e-02 nm, Epot= -6.14839e+04 Fmax= 1.41408e+02, atom= 1223\n", + "Step= 637, Dmax= 1.5e-02 nm, Epot= -6.14877e+04 Fmax= 1.13284e+02, atom= 1223\n", + "Step= 638, Dmax= 1.8e-02 nm, Epot= -6.14891e+04 Fmax= 1.89173e+02, atom= 1223\n", + "Step= 639, Dmax= 2.1e-02 nm, Epot= -6.14928e+04 Fmax= 1.76115e+02, atom= 1223\n", + "Step= 641, Dmax= 1.3e-02 nm, Epot= -6.14983e+04 Fmax= 3.97391e+01, atom= 1223\n", + "Step= 642, Dmax= 1.5e-02 nm, Epot= -6.15019e+04 Fmax= 2.42423e+02, atom= 1223\n", + "Step= 643, Dmax= 1.8e-02 nm, Epot= -6.15104e+04 Fmax= 8.07222e+01, atom= 1223\n", + "Step= 645, Dmax= 1.1e-02 nm, Epot= -6.15136e+04 Fmax= 1.05926e+02, atom= 1223\n", + "Step= 646, Dmax= 1.3e-02 nm, Epot= -6.15166e+04 Fmax= 1.17903e+02, atom= 1223\n", + "Step= 647, Dmax= 1.6e-02 nm, Epot= -6.15191e+04 Fmax= 1.55289e+02, atom= 1223\n", + "Step= 648, Dmax= 1.9e-02 nm, Epot= -6.15218e+04 Fmax= 1.67975e+02, atom= 1223\n", + "Step= 649, Dmax= 2.3e-02 nm, Epot= -6.15228e+04 Fmax= 2.24444e+02, atom= 1223\n", + "Step= 650, Dmax= 2.8e-02 nm, Epot= -6.15247e+04 Fmax= 2.41343e+02, atom= 1223\n", + "Step= 652, Dmax= 1.7e-02 nm, Epot= -6.15343e+04 Fmax= 4.47053e+01, atom= 2002\n", + "Step= 653, Dmax= 2.0e-02 nm, Epot= -6.15378e+04 Fmax= 2.82850e+02, atom= 2002\n", + "Step= 654, Dmax= 2.4e-02 nm, Epot= -6.15469e+04 Fmax= 1.28913e+02, atom= 2003\n", + "Step= 656, Dmax= 1.4e-02 nm, Epot= -6.15506e+04 Fmax= 1.11679e+02, atom= 2003\n", + "Step= 657, Dmax= 1.7e-02 nm, Epot= -6.15523e+04 Fmax= 1.81701e+02, atom= 2003\n", + "Step= 658, Dmax= 2.1e-02 nm, Epot= -6.15561e+04 Fmax= 1.61320e+02, atom= 2003\n", + "Step= 660, Dmax= 1.2e-02 nm, Epot= -6.15613e+04 Fmax= 5.08633e+01, atom= 2003\n", + "Step= 661, Dmax= 1.5e-02 nm, Epot= -6.15649e+04 Fmax= 1.95413e+02, atom= 2003\n", + "Step= 662, Dmax= 1.8e-02 nm, Epot= -6.15705e+04 Fmax= 1.14628e+02, atom= 2003\n", + "Step= 664, Dmax= 1.1e-02 nm, Epot= -6.15742e+04 Fmax= 6.40345e+01, atom= 2003\n", + "Step= 665, Dmax= 1.3e-02 nm, Epot= -6.15775e+04 Fmax= 1.54010e+02, atom= 2003\n", + "Step= 666, Dmax= 1.5e-02 nm, Epot= -6.15816e+04 Fmax= 1.01478e+02, atom= 2003\n", + "Step= 667, Dmax= 1.8e-02 nm, Epot= -6.15825e+04 Fmax= 2.14265e+02, atom= 2003\n", + "Step= 668, Dmax= 2.2e-02 nm, Epot= -6.15877e+04 Fmax= 1.53961e+02, atom= 2003\n", + "Step= 670, Dmax= 1.3e-02 nm, Epot= -6.15923e+04 Fmax= 7.17153e+01, atom= 2003\n", + "Step= 671, Dmax= 1.6e-02 nm, Epot= -6.15944e+04 Fmax= 1.94172e+02, atom= 2003\n", + "Step= 672, Dmax= 1.9e-02 nm, Epot= -6.15995e+04 Fmax= 1.34465e+02, atom= 2003\n", + "Step= 674, Dmax= 1.1e-02 nm, Epot= -6.16035e+04 Fmax= 5.76225e+01, atom= 2003\n", + "Step= 675, Dmax= 1.4e-02 nm, Epot= -6.16069e+04 Fmax= 1.72810e+02, atom= 2003\n", + "Step= 676, Dmax= 1.7e-02 nm, Epot= -6.16116e+04 Fmax= 1.01823e+02, atom= 2003\n", + "Step= 677, Dmax= 2.0e-02 nm, Epot= -6.16117e+04 Fmax= 2.34006e+02, atom= 2003\n", + "Step= 678, Dmax= 2.4e-02 nm, Epot= -6.16176e+04 Fmax= 1.61353e+02, atom= 2003\n", + "Step= 680, Dmax= 1.4e-02 nm, Epot= -6.16223e+04 Fmax= 7.88245e+01, atom= 2003\n", + "Step= 681, Dmax= 1.7e-02 nm, Epot= -6.16237e+04 Fmax= 2.08074e+02, atom= 2003\n", + "Step= 682, Dmax= 2.1e-02 nm, Epot= -6.16290e+04 Fmax= 1.42235e+02, atom= 2003\n", + "Step= 684, Dmax= 1.2e-02 nm, Epot= -6.16332e+04 Fmax= 6.41023e+01, atom= 2003\n", + "Step= 685, Dmax= 1.5e-02 nm, Epot= -6.16361e+04 Fmax= 1.80185e+02, atom= 2003\n", + "Step= 686, Dmax= 1.8e-02 nm, Epot= -6.16408e+04 Fmax= 1.14791e+02, atom= 2003\n", + "Step= 688, Dmax= 1.1e-02 nm, Epot= -6.16442e+04 Fmax= 6.38684e+01, atom= 2003\n", + "Step= 689, Dmax= 1.3e-02 nm, Epot= -6.16473e+04 Fmax= 1.49940e+02, atom= 2003\n", + "Step= 690, Dmax= 1.5e-02 nm, Epot= -6.16512e+04 Fmax= 1.09117e+02, atom= 2003\n", + "Step= 691, Dmax= 1.8e-02 nm, Epot= -6.16525e+04 Fmax= 1.97989e+02, atom= 2003\n", + "Step= 692, Dmax= 2.2e-02 nm, Epot= -6.16564e+04 Fmax= 1.75100e+02, atom= 2003\n", + "Step= 694, Dmax= 1.3e-02 nm, Epot= -6.16616e+04 Fmax= 4.58183e+01, atom= 2003\n", + "Step= 695, Dmax= 1.6e-02 nm, Epot= -6.16655e+04 Fmax= 2.11814e+02, atom= 2003\n", + "Step= 696, Dmax= 1.9e-02 nm, Epot= -6.16717e+04 Fmax= 1.04387e+02, atom= 2003\n", + "Step= 698, Dmax= 1.1e-02 nm, Epot= -6.16749e+04 Fmax= 8.76908e+01, atom= 2003\n", + "Step= 699, Dmax= 1.4e-02 nm, Epot= -6.16773e+04 Fmax= 1.41051e+02, atom= 2003\n", + "Step= 700, Dmax= 1.6e-02 nm, Epot= -6.16805e+04 Fmax= 1.35624e+02, atom= 2003\n", + "Step= 701, Dmax= 2.0e-02 nm, Epot= -6.16816e+04 Fmax= 1.93555e+02, atom= 2003\n", + "Step= 702, Dmax= 2.4e-02 nm, Epot= -6.16840e+04 Fmax= 2.05078e+02, atom= 2003\n", + "Step= 704, Dmax= 1.4e-02 nm, Epot= -6.16913e+04 Fmax= 3.17197e+01, atom= 2003\n", + "Step= 705, Dmax= 1.7e-02 nm, Epot= -6.16949e+04 Fmax= 2.39624e+02, atom= 2003\n", + "Step= 706, Dmax= 2.1e-02 nm, Epot= -6.17050e+04 Fmax= 1.16014e+02, atom= 368\n", + "Step= 708, Dmax= 1.2e-02 nm, Epot= -6.17085e+04 Fmax= 9.90791e+01, atom= 368\n", + "Step= 709, Dmax= 1.5e-02 nm, Epot= -6.17102e+04 Fmax= 1.58602e+02, atom= 368\n", + "Step= 710, Dmax= 1.8e-02 nm, Epot= -6.17137e+04 Fmax= 1.48940e+02, atom= 368\n", + "Step= 711, Dmax= 2.1e-02 nm, Epot= -6.17142e+04 Fmax= 2.22296e+02, atom= 368\n", + "Step= 712, Dmax= 2.6e-02 nm, Epot= -6.17176e+04 Fmax= 2.19836e+02, atom= 368\n", + "Step= 714, Dmax= 1.5e-02 nm, Epot= -6.17245e+04 Fmax= 4.82357e+01, atom= 368\n", + "Step= 715, Dmax= 1.8e-02 nm, Epot= -6.17270e+04 Fmax= 2.75294e+02, atom= 368\n", + "Step= 716, Dmax= 2.2e-02 nm, Epot= -6.17349e+04 Fmax= 1.21547e+02, atom= 368\n", + "Step= 718, Dmax= 1.3e-02 nm, Epot= -6.17380e+04 Fmax= 1.10529e+02, atom= 368\n", + "Step= 719, Dmax= 1.6e-02 nm, Epot= -6.17404e+04 Fmax= 1.64026e+02, atom= 368\n", + "Step= 720, Dmax= 1.9e-02 nm, Epot= -6.17433e+04 Fmax= 1.66327e+02, atom= 368\n", + "Step= 721, Dmax= 2.3e-02 nm, Epot= -6.17447e+04 Fmax= 2.30901e+02, atom= 368\n", + "Step= 722, Dmax= 2.7e-02 nm, Epot= -6.17474e+04 Fmax= 2.43478e+02, atom= 368\n", + "Step= 724, Dmax= 1.6e-02 nm, Epot= -6.17534e+04 Fmax= 4.37707e+01, atom= 368\n", + "Step= 725, Dmax= 2.0e-02 nm, Epot= -6.17569e+04 Fmax= 3.06569e+02, atom= 368\n", + "Step= 726, Dmax= 2.4e-02 nm, Epot= -6.17655e+04 Fmax= 1.23357e+02, atom= 368\n", + "Step= 728, Dmax= 1.4e-02 nm, Epot= -6.17685e+04 Fmax= 1.27029e+02, atom= 368\n", + "Step= 729, Dmax= 1.7e-02 nm, Epot= -6.17709e+04 Fmax= 1.66765e+02, atom= 368\n", + "Step= 730, Dmax= 2.0e-02 nm, Epot= -6.17735e+04 Fmax= 1.88374e+02, atom= 368\n", + "Step= 731, Dmax= 2.5e-02 nm, Epot= -6.17750e+04 Fmax= 2.37119e+02, atom= 368\n", + "Step= 732, Dmax= 2.9e-02 nm, Epot= -6.17770e+04 Fmax= 2.72256e+02, atom= 368\n", + "Step= 734, Dmax= 1.8e-02 nm, Epot= -6.17841e+04 Fmax= 3.70225e+01, atom= 369\n", + "Step= 735, Dmax= 2.1e-02 nm, Epot= -6.17883e+04 Fmax= 3.60829e+02, atom= 369\n", + "Step= 736, Dmax= 2.5e-02 nm, Epot= -6.17994e+04 Fmax= 1.03095e+02, atom= 368\n", + "Step= 738, Dmax= 1.5e-02 nm, Epot= -6.18018e+04 Fmax= 1.70097e+02, atom= 368\n", + "Step= 739, Dmax= 1.8e-02 nm, Epot= -6.18051e+04 Fmax= 1.48555e+02, atom= 368\n", + "Step= 740, Dmax= 2.2e-02 nm, Epot= -6.18063e+04 Fmax= 2.35406e+02, atom= 368\n", + "Step= 741, Dmax= 2.6e-02 nm, Epot= -6.18094e+04 Fmax= 2.23330e+02, atom= 368\n", + "Step= 743, Dmax= 1.6e-02 nm, Epot= -6.18151e+04 Fmax= 4.97477e+01, atom= 368\n", + "Step= 744, Dmax= 1.9e-02 nm, Epot= -6.18197e+04 Fmax= 2.62392e+02, atom= 368\n", + "Step= 745, Dmax= 2.3e-02 nm, Epot= -6.18258e+04 Fmax= 1.29486e+02, atom= 368\n", + "Step= 747, Dmax= 1.4e-02 nm, Epot= -6.18288e+04 Fmax= 1.08641e+02, atom= 368\n", + "Step= 748, Dmax= 1.6e-02 nm, Epot= -6.18312e+04 Fmax= 1.74175e+02, atom= 368\n", + "Step= 749, Dmax= 2.0e-02 nm, Epot= -6.18341e+04 Fmax= 1.67198e+02, atom= 368\n", + "Step= 750, Dmax= 2.4e-02 nm, Epot= -6.18353e+04 Fmax= 2.41594e+02, atom= 368\n", + "Step= 751, Dmax= 2.8e-02 nm, Epot= -6.18378e+04 Fmax= 2.49320e+02, atom= 368\n", + "Step= 753, Dmax= 1.7e-02 nm, Epot= -6.18443e+04 Fmax= 4.28431e+01, atom= 368\n", + "Step= 754, Dmax= 2.0e-02 nm, Epot= -6.18492e+04 Fmax= 2.97137e+02, atom= 368\n", + "Step= 755, Dmax= 2.5e-02 nm, Epot= -6.18571e+04 Fmax= 1.26726e+02, atom= 368\n", + "Step= 757, Dmax= 1.5e-02 nm, Epot= -6.18600e+04 Fmax= 1.29646e+02, atom= 368\n", + "Step= 758, Dmax= 1.8e-02 nm, Epot= -6.18621e+04 Fmax= 1.73592e+02, atom= 368\n", + "Step= 759, Dmax= 2.1e-02 nm, Epot= -6.18645e+04 Fmax= 1.92137e+02, atom= 368\n", + "Step= 760, Dmax= 2.5e-02 nm, Epot= -6.18657e+04 Fmax= 2.46347e+02, atom= 368\n", + "Step= 761, Dmax= 3.1e-02 nm, Epot= -6.18670e+04 Fmax= 2.79095e+02, atom= 368\n", + "Step= 763, Dmax= 1.8e-02 nm, Epot= -6.18756e+04 Fmax= 3.45257e+01, atom= 368\n", + "Step= 764, Dmax= 2.2e-02 nm, Epot= -6.18806e+04 Fmax= 3.31107e+02, atom= 368\n", + "Step= 765, Dmax= 2.6e-02 nm, Epot= -6.18916e+04 Fmax= 1.29041e+02, atom= 368\n", + "Step= 767, Dmax= 1.6e-02 nm, Epot= -6.18942e+04 Fmax= 1.48210e+02, atom= 368\n", + "Step= 768, Dmax= 1.9e-02 nm, Epot= -6.18964e+04 Fmax= 1.76917e+02, atom= 368\n", + "Step= 769, Dmax= 2.3e-02 nm, Epot= -6.18979e+04 Fmax= 2.15149e+02, atom= 368\n", + "Step= 770, Dmax= 2.7e-02 nm, Epot= -6.18991e+04 Fmax= 2.55259e+02, atom= 368\n", + "Step= 772, Dmax= 1.6e-02 nm, Epot= -6.19071e+04 Fmax= 2.75736e+01, atom= 368\n", + "Step= 773, Dmax= 2.0e-02 nm, Epot= -6.19079e+04 Fmax= 3.44267e+02, atom= 2750\n", + "Step= 774, Dmax= 2.4e-02 nm, Epot= -6.19247e+04 Fmax= 1.08612e+02, atom= 2750\n", + "Step= 776, Dmax= 1.4e-02 nm, Epot= -6.19271e+04 Fmax= 1.35035e+02, atom= 2750\n", + "Step= 777, Dmax= 1.7e-02 nm, Epot= -6.19289e+04 Fmax= 1.61560e+02, atom= 2750\n", + "Step= 778, Dmax= 2.0e-02 nm, Epot= -6.19307e+04 Fmax= 2.00973e+02, atom= 2750\n", + "Step= 779, Dmax= 2.4e-02 nm, Epot= -6.19318e+04 Fmax= 2.24575e+02, atom= 2750\n", + "Step= 781, Dmax= 1.5e-02 nm, Epot= -6.19398e+04 Fmax= 1.91633e+01, atom= 1037\n", + "Step= 782, Dmax= 1.8e-02 nm, Epot= -6.19463e+04 Fmax= 2.75170e+02, atom= 1037\n", + "Step= 783, Dmax= 2.1e-02 nm, Epot= -6.19616e+04 Fmax= 1.25706e+02, atom= 2750\n", + "Step= 785, Dmax= 1.3e-02 nm, Epot= -6.19646e+04 Fmax= 9.91287e+01, atom= 2750\n", + "Step= 786, Dmax= 1.5e-02 nm, Epot= -6.19660e+04 Fmax= 1.77579e+02, atom= 2750\n", + "Step= 787, Dmax= 1.8e-02 nm, Epot= -6.19693e+04 Fmax= 1.46723e+02, atom= 2750\n", + "Step= 789, Dmax= 1.1e-02 nm, Epot= -6.19733e+04 Fmax= 3.79304e+01, atom= 2750\n", + "Step= 790, Dmax= 1.3e-02 nm, Epot= -6.19767e+04 Fmax= 1.93656e+02, atom= 2750\n", + "Step= 791, Dmax= 1.6e-02 nm, Epot= -6.19827e+04 Fmax= 8.18299e+01, atom= 2750\n", + "Step= 793, Dmax= 9.5e-03 nm, Epot= -6.19852e+04 Fmax= 8.65966e+01, atom= 2750\n", + "Step= 794, Dmax= 1.1e-02 nm, Epot= -6.19878e+04 Fmax= 1.16394e+02, atom= 2750\n", + "Step= 795, Dmax= 1.4e-02 nm, Epot= -6.19901e+04 Fmax= 1.24825e+02, atom= 2750\n", + "Step= 796, Dmax= 1.6e-02 nm, Epot= -6.19921e+04 Fmax= 1.68551e+02, atom= 2750\n", + "Step= 797, Dmax= 2.0e-02 nm, Epot= -6.19942e+04 Fmax= 1.76615e+02, atom= 2750\n", + "Step= 798, Dmax= 2.4e-02 nm, Epot= -6.19950e+04 Fmax= 2.48557e+02, atom= 2750\n", + "Step= 799, Dmax= 2.8e-02 nm, Epot= -6.19967e+04 Fmax= 2.45580e+02, atom= 2750\n", + "Step= 801, Dmax= 1.7e-02 nm, Epot= -6.20046e+04 Fmax= 3.22618e+01, atom= 2750\n", + "Step= 803, Dmax= 1.0e-02 nm, Epot= -6.20090e+04 Fmax= 1.51622e+02, atom= 2750\n", + "Step= 804, Dmax= 1.2e-02 nm, Epot= -6.20134e+04 Fmax= 6.78330e+01, atom= 2750\n", + "Step= 805, Dmax= 1.5e-02 nm, Epot= -6.20151e+04 Fmax= 1.80441e+02, atom= 2750\n", + "Step= 806, Dmax= 1.8e-02 nm, Epot= -6.20194e+04 Fmax= 1.23844e+02, atom= 2750\n", + "Step= 808, Dmax= 1.1e-02 nm, Epot= -6.20226e+04 Fmax= 6.75862e+01, atom= 2750\n", + "Step= 809, Dmax= 1.3e-02 nm, Epot= -6.20249e+04 Fmax= 1.62270e+02, atom= 2750\n", + "Step= 810, Dmax= 1.5e-02 nm, Epot= -6.20282e+04 Fmax= 1.10923e+02, atom= 2750\n", + "Step= 811, Dmax= 1.8e-02 nm, Epot= -6.20290e+04 Fmax= 2.22463e+02, atom= 2750\n", + "Step= 812, Dmax= 2.2e-02 nm, Epot= -6.20326e+04 Fmax= 1.67805e+02, atom= 2750\n", + "Step= 814, Dmax= 1.3e-02 nm, Epot= -6.20368e+04 Fmax= 5.20848e+01, atom= 2750\n", + "Step= 815, Dmax= 1.6e-02 nm, Epot= -6.20387e+04 Fmax= 2.22083e+02, atom= 2750\n", + "Step= 816, Dmax= 1.9e-02 nm, Epot= -6.20448e+04 Fmax= 1.07316e+02, atom= 2750\n", + "Step= 818, Dmax= 1.1e-02 nm, Epot= -6.20474e+04 Fmax= 9.50686e+01, atom= 2750\n", + "Step= 819, Dmax= 1.4e-02 nm, Epot= -6.20496e+04 Fmax= 1.49584e+02, atom= 2750\n", + "Step= 820, Dmax= 1.6e-02 nm, Epot= -6.20522e+04 Fmax= 1.39899e+02, atom= 2750\n", + "Step= 821, Dmax= 2.0e-02 nm, Epot= -6.20535e+04 Fmax= 2.13977e+02, atom= 2750\n", + "Step= 822, Dmax= 2.4e-02 nm, Epot= -6.20560e+04 Fmax= 2.00165e+02, atom= 2750\n", + "Step= 824, Dmax= 1.4e-02 nm, Epot= -6.20613e+04 Fmax= 3.38868e+01, atom= 2750\n", + "Step= 825, Dmax= 1.7e-02 nm, Epot= -6.20648e+04 Fmax= 2.65216e+02, atom= 2750\n", + "Step= 826, Dmax= 2.0e-02 nm, Epot= -6.20738e+04 Fmax= 9.39634e+01, atom= 2750\n", + "Step= 828, Dmax= 1.2e-02 nm, Epot= -6.20762e+04 Fmax= 1.19392e+02, atom= 2750\n", + "Step= 829, Dmax= 1.5e-02 nm, Epot= -6.20786e+04 Fmax= 1.40910e+02, atom= 2750\n", + "Step= 830, Dmax= 1.8e-02 nm, Epot= -6.20805e+04 Fmax= 1.67102e+02, atom= 2750\n", + "Step= 831, Dmax= 2.1e-02 nm, Epot= -6.20824e+04 Fmax= 2.10474e+02, atom= 2750\n", + "Step= 832, Dmax= 2.5e-02 nm, Epot= -6.20837e+04 Fmax= 2.30599e+02, atom= 2750\n", + "Step= 833, Dmax= 3.0e-02 nm, Epot= -6.20837e+04 Fmax= 3.17050e+02, atom= 2750\n", + "Step= 834, Dmax= 3.6e-02 nm, Epot= -6.20844e+04 Fmax= 3.14592e+02, atom= 2750\n", + "Step= 836, Dmax= 2.2e-02 nm, Epot= -6.20957e+04 Fmax= 4.04836e+01, atom= 1037\n", + "Step= 838, Dmax= 1.3e-02 nm, Epot= -6.20990e+04 Fmax= 1.77233e+02, atom= 2750\n", + "Step= 839, Dmax= 1.6e-02 nm, Epot= -6.21040e+04 Fmax= 1.12088e+02, atom= 2750\n", + "Step= 840, Dmax= 1.9e-02 nm, Epot= -6.21041e+04 Fmax= 2.09887e+02, atom= 2750\n", + "Step= 841, Dmax= 2.3e-02 nm, Epot= -6.21080e+04 Fmax= 1.85533e+02, atom= 2750\n", + "Step= 843, Dmax= 1.4e-02 nm, Epot= -6.21124e+04 Fmax= 6.45958e+01, atom= 2750\n", + "Step= 844, Dmax= 1.6e-02 nm, Epot= -6.21141e+04 Fmax= 2.37687e+02, atom= 2750\n", + "Step= 845, Dmax= 2.0e-02 nm, Epot= -6.21189e+04 Fmax= 1.20446e+02, atom= 2750\n", + "Step= 847, Dmax= 1.2e-02 nm, Epot= -6.21217e+04 Fmax= 7.95349e+01, atom= 2750\n", + "Step= 848, Dmax= 1.4e-02 nm, Epot= -6.21236e+04 Fmax= 1.65943e+02, atom= 2750\n", + "Step= 849, Dmax= 1.7e-02 nm, Epot= -6.21269e+04 Fmax= 1.29655e+02, atom= 2750\n", + "Step= 850, Dmax= 2.0e-02 nm, Epot= -6.21272e+04 Fmax= 2.19874e+02, atom= 2750\n", + "Step= 851, Dmax= 2.4e-02 nm, Epot= -6.21305e+04 Fmax= 2.08640e+02, atom= 2750\n", + "Step= 853, Dmax= 1.5e-02 nm, Epot= -6.21354e+04 Fmax= 6.09002e+01, atom= 2750\n", + "Step= 854, Dmax= 1.8e-02 nm, Epot= -6.21369e+04 Fmax= 2.68250e+02, atom= 2750\n", + "Step= 855, Dmax= 2.1e-02 nm, Epot= -6.21425e+04 Fmax= 1.20175e+02, atom= 2750\n", + "Step= 857, Dmax= 1.3e-02 nm, Epot= -6.21452e+04 Fmax= 9.50631e+01, atom= 2750\n", + "Step= 858, Dmax= 1.5e-02 nm, Epot= -6.21470e+04 Fmax= 1.68258e+02, atom= 2750\n", + "Step= 859, Dmax= 1.8e-02 nm, Epot= -6.21500e+04 Fmax= 1.50537e+02, atom= 2750\n", + "Step= 860, Dmax= 2.2e-02 nm, Epot= -6.21502e+04 Fmax= 2.25493e+02, atom= 2750\n", + "Step= 861, Dmax= 2.6e-02 nm, Epot= -6.21529e+04 Fmax= 2.37605e+02, atom= 2750\n", + "Step= 863, Dmax= 1.6e-02 nm, Epot= -6.21587e+04 Fmax= 5.47983e+01, atom= 2750\n", + "Step= 864, Dmax= 1.9e-02 nm, Epot= -6.21603e+04 Fmax= 3.04818e+02, atom= 2750\n", + "Step= 865, Dmax= 2.3e-02 nm, Epot= -6.21669e+04 Fmax= 1.19078e+02, atom= 2750\n", + "Step= 867, Dmax= 1.4e-02 nm, Epot= -6.21695e+04 Fmax= 1.12533e+02, atom= 2750\n", + "Step= 868, Dmax= 1.6e-02 nm, Epot= -6.21711e+04 Fmax= 1.70236e+02, atom= 2750\n", + "Step= 869, Dmax= 2.0e-02 nm, Epot= -6.21737e+04 Fmax= 1.73636e+02, atom= 2750\n", + "Step= 870, Dmax= 2.3e-02 nm, Epot= -6.21739e+04 Fmax= 2.31386e+02, atom= 2750\n", + "Step= 871, Dmax= 2.8e-02 nm, Epot= -6.21758e+04 Fmax= 2.68993e+02, atom= 2750\n", + "Step= 873, Dmax= 1.7e-02 nm, Epot= -6.21826e+04 Fmax= 4.84076e+01, atom= 2750\n", + "Step= 874, Dmax= 2.0e-02 nm, Epot= -6.21844e+04 Fmax= 3.47355e+02, atom= 2750\n", + "Step= 875, Dmax= 2.4e-02 nm, Epot= -6.21921e+04 Fmax= 1.17833e+02, atom= 2750\n", + "Step= 877, Dmax= 1.5e-02 nm, Epot= -6.21944e+04 Fmax= 1.31259e+02, atom= 2750\n", + "Step= 878, Dmax= 1.8e-02 nm, Epot= -6.21958e+04 Fmax= 1.72611e+02, atom= 2750\n", + "Step= 879, Dmax= 2.1e-02 nm, Epot= -6.21978e+04 Fmax= 1.98336e+02, atom= 2750\n", + "Step= 880, Dmax= 2.5e-02 nm, Epot= -6.21983e+04 Fmax= 2.37885e+02, atom= 2750\n", + "Step= 881, Dmax= 3.0e-02 nm, Epot= -6.21991e+04 Fmax= 3.02513e+02, atom= 2750\n", + "Step= 883, Dmax= 1.8e-02 nm, Epot= -6.22073e+04 Fmax= 4.21541e+01, atom= 2750\n", + "Step= 884, Dmax= 2.2e-02 nm, Epot= -6.22094e+04 Fmax= 3.98904e+02, atom= 2750\n", + "Step= 885, Dmax= 2.6e-02 nm, Epot= -6.22184e+04 Fmax= 1.17094e+02, atom= 2750\n", + "Step= 887, Dmax= 1.6e-02 nm, Epot= -6.22204e+04 Fmax= 1.50826e+02, atom= 2750\n", + "Step= 888, Dmax= 1.9e-02 nm, Epot= -6.22220e+04 Fmax= 1.75637e+02, atom= 2750\n", + "Step= 889, Dmax= 2.3e-02 nm, Epot= -6.22234e+04 Fmax= 2.24598e+02, atom= 2750\n", + "Step= 890, Dmax= 2.7e-02 nm, Epot= -6.22242e+04 Fmax= 2.45050e+02, atom= 2750\n", + "Step= 892, Dmax= 1.6e-02 nm, Epot= -6.22309e+04 Fmax= 2.27688e+01, atom= 1037\n", + "Step= 893, Dmax= 2.0e-02 nm, Epot= -6.22355e+04 Fmax= 3.11486e+02, atom= 2750\n", + "Step= 894, Dmax= 2.3e-02 nm, Epot= -6.22485e+04 Fmax= 1.37326e+02, atom= 2750\n", + "Step= 896, Dmax= 1.4e-02 nm, Epot= -6.22508e+04 Fmax= 1.12125e+02, atom= 2750\n", + "Step= 897, Dmax= 1.7e-02 nm, Epot= -6.22521e+04 Fmax= 1.91929e+02, atom= 2750\n", + "Step= 898, Dmax= 2.0e-02 nm, Epot= -6.22546e+04 Fmax= 1.66074e+02, atom= 2750\n", + "Step= 900, Dmax= 1.2e-02 nm, Epot= -6.22583e+04 Fmax= 3.72284e+01, atom= 2750\n", + "Step= 901, Dmax= 1.5e-02 nm, Epot= -6.22612e+04 Fmax= 2.21501e+02, atom= 2750\n", + "Step= 902, Dmax= 1.7e-02 nm, Epot= -6.22671e+04 Fmax= 8.47179e+01, atom= 2750\n", + "Step= 904, Dmax= 1.0e-02 nm, Epot= -6.22694e+04 Fmax= 1.01163e+02, atom= 2750\n", + "Step= 905, Dmax= 1.3e-02 nm, Epot= -6.22715e+04 Fmax= 1.22760e+02, atom= 2750\n", + "Step= 906, Dmax= 1.5e-02 nm, Epot= -6.22732e+04 Fmax= 1.43909e+02, atom= 2750\n", + "Step= 907, Dmax= 1.8e-02 nm, Epot= -6.22749e+04 Fmax= 1.80170e+02, atom= 2750\n", + "Step= 908, Dmax= 2.2e-02 nm, Epot= -6.22762e+04 Fmax= 2.01256e+02, atom= 2750\n", + "Step= 909, Dmax= 2.6e-02 nm, Epot= -6.22768e+04 Fmax= 2.68729e+02, atom= 2750\n", + "Step= 910, Dmax= 3.1e-02 nm, Epot= -6.22773e+04 Fmax= 2.77247e+02, atom= 2750\n", + "Step= 912, Dmax= 1.9e-02 nm, Epot= -6.22860e+04 Fmax= 3.04031e+01, atom= 1037\n", + "Step= 914, Dmax= 1.1e-02 nm, Epot= -6.22899e+04 Fmax= 1.66516e+02, atom= 2750\n", + "Step= 915, Dmax= 1.4e-02 nm, Epot= -6.22944e+04 Fmax= 8.28680e+01, atom= 2750\n", + "Step= 916, Dmax= 1.6e-02 nm, Epot= -6.22951e+04 Fmax= 1.92190e+02, atom= 2750\n", + "Step= 917, Dmax= 1.9e-02 nm, Epot= -6.22987e+04 Fmax= 1.44973e+02, atom= 2750\n", + "Step= 919, Dmax= 1.2e-02 nm, Epot= -6.23019e+04 Fmax= 6.82966e+01, atom= 2750\n", + "Step= 920, Dmax= 1.4e-02 nm, Epot= -6.23035e+04 Fmax= 1.87706e+02, atom= 2750\n", + "Step= 921, Dmax= 1.7e-02 nm, Epot= -6.23068e+04 Fmax= 1.17433e+02, atom= 2750\n", + "Step= 923, Dmax= 1.0e-02 nm, Epot= -6.23094e+04 Fmax= 5.49337e+01, atom= 2750\n", + "Step= 924, Dmax= 1.2e-02 nm, Epot= -6.23116e+04 Fmax= 1.58267e+02, atom= 2750\n", + "Step= 925, Dmax= 1.5e-02 nm, Epot= -6.23149e+04 Fmax= 9.58326e+01, atom= 2750\n", + "Step= 926, Dmax= 1.7e-02 nm, Epot= -6.23151e+04 Fmax= 2.06015e+02, atom= 2750\n", + "Step= 927, Dmax= 2.1e-02 nm, Epot= -6.23189e+04 Fmax= 1.60837e+02, atom= 2750\n", + "Step= 929, Dmax= 1.3e-02 nm, Epot= -6.23223e+04 Fmax= 6.87621e+01, atom= 2750\n", + "Step= 930, Dmax= 1.5e-02 nm, Epot= -6.23235e+04 Fmax= 2.08350e+02, atom= 2750\n", + "Step= 931, Dmax= 1.8e-02 nm, Epot= -6.23272e+04 Fmax= 1.20806e+02, atom= 2750\n", + "Step= 933, Dmax= 1.1e-02 nm, Epot= -6.23299e+04 Fmax= 6.43351e+01, atom= 2750\n", + "Step= 934, Dmax= 1.3e-02 nm, Epot= -6.23316e+04 Fmax= 1.64205e+02, atom= 2750\n", + "Step= 935, Dmax= 1.6e-02 nm, Epot= -6.23349e+04 Fmax= 1.09254e+02, atom= 2750\n", + "Step= 937, Dmax= 9.4e-03 nm, Epot= -6.23373e+04 Fmax= 6.08007e+01, atom= 2750\n", + "Step= 938, Dmax= 1.1e-02 nm, Epot= -6.23395e+04 Fmax= 1.41628e+02, atom= 2750\n", + "Step= 939, Dmax= 1.4e-02 nm, Epot= -6.23421e+04 Fmax= 1.01490e+02, atom= 2750\n", + "Step= 940, Dmax= 1.6e-02 nm, Epot= -6.23430e+04 Fmax= 1.92695e+02, atom= 2750\n", + "Step= 941, Dmax= 1.9e-02 nm, Epot= -6.23457e+04 Fmax= 1.54793e+02, atom= 2750\n", + "Step= 943, Dmax= 1.2e-02 nm, Epot= -6.23491e+04 Fmax= 4.20879e+01, atom= 2750\n", + "Step= 944, Dmax= 1.4e-02 nm, Epot= -6.23513e+04 Fmax= 2.05820e+02, atom= 2750\n", + "Step= 945, Dmax= 1.7e-02 nm, Epot= -6.23565e+04 Fmax= 8.83032e+01, atom= 2750\n", + "Step= 947, Dmax= 1.0e-02 nm, Epot= -6.23586e+04 Fmax= 9.22018e+01, atom= 2750\n", + "Step= 948, Dmax= 1.2e-02 nm, Epot= -6.23605e+04 Fmax= 1.23843e+02, atom= 2750\n", + "Step= 949, Dmax= 1.5e-02 nm, Epot= -6.23624e+04 Fmax= 1.34223e+02, atom= 2750\n", + "Step= 950, Dmax= 1.7e-02 nm, Epot= -6.23638e+04 Fmax= 1.78374e+02, atom= 2750\n", + "Step= 951, Dmax= 2.1e-02 nm, Epot= -6.23652e+04 Fmax= 1.90476e+02, atom= 2750\n", + "Step= 952, Dmax= 2.5e-02 nm, Epot= -6.23655e+04 Fmax= 2.62860e+02, atom= 2750\n", + "Step= 953, Dmax= 3.0e-02 nm, Epot= -6.23664e+04 Fmax= 2.64834e+02, atom= 2750\n", + "Step= 955, Dmax= 1.8e-02 nm, Epot= -6.23743e+04 Fmax= 3.04993e+01, atom= 2750\n", + "Step= 957, Dmax= 1.1e-02 nm, Epot= -6.23775e+04 Fmax= 1.70863e+02, atom= 2750\n", + "Step= 958, Dmax= 1.3e-02 nm, Epot= -6.23821e+04 Fmax= 6.69715e+01, atom= 2750\n", + "Step= 959, Dmax= 1.6e-02 nm, Epot= -6.23830e+04 Fmax= 1.95303e+02, atom= 2750\n", + "Step= 960, Dmax= 1.9e-02 nm, Epot= -6.23869e+04 Fmax= 1.25988e+02, atom= 2750\n", + "Step= 962, Dmax= 1.1e-02 nm, Epot= -6.23895e+04 Fmax= 7.82270e+01, atom= 2750\n", + "Step= 963, Dmax= 1.3e-02 nm, Epot= -6.23909e+04 Fmax= 1.66084e+02, atom= 2750\n", + "Step= 964, Dmax= 1.6e-02 nm, Epot= -6.23936e+04 Fmax= 1.25696e+02, atom= 2750\n", + "Step= 965, Dmax= 1.9e-02 nm, Epot= -6.23936e+04 Fmax= 2.28743e+02, atom= 2750\n", + "Step= 966, Dmax= 2.3e-02 nm, Epot= -6.23963e+04 Fmax= 1.87346e+02, atom= 2750\n", + "Step= 968, Dmax= 1.4e-02 nm, Epot= -6.24007e+04 Fmax= 4.61115e+01, atom= 2750\n", + "Step= 970, Dmax= 8.4e-03 nm, Epot= -6.24030e+04 Fmax= 1.06144e+02, atom= 2750\n", + "Step= 971, Dmax= 1.0e-02 nm, Epot= -6.24054e+04 Fmax= 7.16916e+01, atom= 2750\n", + "Step= 972, Dmax= 1.2e-02 nm, Epot= -6.24069e+04 Fmax= 1.41454e+02, atom= 2750\n", + "Step= 973, Dmax= 1.5e-02 nm, Epot= -6.24095e+04 Fmax= 1.13761e+02, atom= 2750\n", + "Step= 974, Dmax= 1.7e-02 nm, Epot= -6.24098e+04 Fmax= 1.90679e+02, atom= 2750\n", + "Step= 975, Dmax= 2.1e-02 nm, Epot= -6.24125e+04 Fmax= 1.79039e+02, atom= 2750\n", + "Step= 977, Dmax= 1.3e-02 nm, Epot= -6.24163e+04 Fmax= 5.29980e+01, atom= 2750\n", + "Step= 978, Dmax= 1.5e-02 nm, Epot= -6.24178e+04 Fmax= 2.26140e+02, atom= 2750\n", + "Step= 979, Dmax= 1.8e-02 nm, Epot= -6.24220e+04 Fmax= 1.06989e+02, atom= 2750\n", + "Step= 981, Dmax= 1.1e-02 nm, Epot= -6.24242e+04 Fmax= 7.87776e+01, atom= 2750\n", + "Step= 982, Dmax= 1.3e-02 nm, Epot= -6.24255e+04 Fmax= 1.49557e+02, atom= 2750\n", + "Step= 983, Dmax= 1.6e-02 nm, Epot= -6.24281e+04 Fmax= 1.24449e+02, atom= 2750\n", + "Step= 984, Dmax= 1.9e-02 nm, Epot= -6.24282e+04 Fmax= 2.01481e+02, atom= 2750\n", + "Step= 985, Dmax= 2.2e-02 nm, Epot= -6.24308e+04 Fmax= 1.95733e+02, atom= 2750\n", + "Step= 987, Dmax= 1.3e-02 nm, Epot= -6.24351e+04 Fmax= 5.41248e+01, atom= 2750\n", + "Step= 988, Dmax= 1.6e-02 nm, Epot= -6.24361e+04 Fmax= 2.48590e+02, atom= 2750\n", + "Step= 989, Dmax= 1.9e-02 nm, Epot= -6.24409e+04 Fmax= 1.11541e+02, atom= 2750\n", + "Step= 991, Dmax= 1.2e-02 nm, Epot= -6.24432e+04 Fmax= 8.77878e+01, atom= 2750\n", + "Step= 992, Dmax= 1.4e-02 nm, Epot= -6.24444e+04 Fmax= 1.57307e+02, atom= 2750\n", + "Step= 993, Dmax= 1.7e-02 nm, Epot= -6.24469e+04 Fmax= 1.37498e+02, atom= 2750\n", + "Step= 995, Dmax= 1.0e-02 nm, Epot= -6.24497e+04 Fmax= 4.70264e+01, atom= 2750\n", + "Step= 996, Dmax= 1.2e-02 nm, Epot= -6.24521e+04 Fmax= 1.72199e+02, atom= 2750\n", + "Step= 997, Dmax= 1.4e-02 nm, Epot= -6.24552e+04 Fmax= 9.22409e+01, atom= 2750\n", + "Step= 998, Dmax= 1.7e-02 nm, Epot= -6.24554e+04 Fmax= 2.27634e+02, atom= 2750\n", + "Step= 999, Dmax= 2.1e-02 nm, Epot= -6.24590e+04 Fmax= 1.49093e+02, atom= 2750\n", + "Step= 1000, Dmax= 2.5e-02 nm, Epot= -6.24568e+04 Fmax= 3.15809e+02, atom= 2750\n", + "Energy minimization reached the maximum number of steps before the forces\n", + "reached the requested precision Fmax < 10.\n", + "\n", + "writing lowest energy coordinates.\n", + "\n", + "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n", + "Potential Energy = -6.2459031e+04\n", + "Maximum force = 1.4909303e+02 on atom 2750\n", + "Norm of force = 4.0432186e+00\n", + "\n", + "GROMACS reminds you: \"The aim of science is not to open the door to infinite wisdom, but to set a limit to infinite error.\" (Bertolt Brecht, Life of Galileo)\n", + "\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top\n", + "\n", + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "GROMACS reminds you: \"If we knew what it was we were doing, it would not be called research, would it?\" (Albert Einstein)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] All files set up for a run time of 1000 ps (dt=0.01, nsteps=100000)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -554193827\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.125 nm, buffer size 0.025 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.100 nm, buffer size 0.000 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "data": { + "text/plain": [ + "{'struct': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro',\n", + " 'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top',\n", + " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx',\n", + " 'qscript': ['./local.sh'],\n", + " 'mainselection': None,\n", + " 'deffnm': 'md',\n", + " 'includes': ['/home/awsm/MDPOW/mdpow/top',\n", + " '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top']}" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from mdpow.equil import OctanolSimulation\n", + "\n", + "oct_sim = OctanolSimulation(\n", + " molecule=\"BENZ\",\n", + " ff_class=MARTINI,\n", + " mdp={\n", + " \"energy_minimize\": str(EM_FILE.absolute()),\n", + " \"MD_relaxed\": str(EQ_FILE.absolute()),\n", + " \"MD_NPT\": str(EQ_FILE.absolute()),\n", + " \"MD_restrained\": str(RUN_FILE.absolute()),\n", + " },\n", + " distance=4.0,\n", + ")\n", + "oct_sim.topology(str(BENZENE_ITP))\n", + "oct_sim.solvate(struct=MARTINI_BENZENE, maxwarn=1)\n", + "oct_sim.energy_minimize(maxwarn=1)\n", + "oct_sim.MD_relaxed(runtime=1e3, dt=0.01)" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 10 to 50, rlist from 1.1 to 1.233\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the GPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "100000 steps, 1000.0 ps.\n", + "\n", + "Step 0 Warning: pressure scaling more than 1%, mu: 0.971025 0.971025 0.971025\n", + "step 0\n", + "Step 50 Warning: pressure scaling more than 1%, mu: 1.01107 1.01107 1.01107\n", + "step 99900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 100000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 297.037 74.259 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1163.502 0.021\n", + "\n", + "GROMACS reminds you: \"There's so many shades of black\" (The Raconteurs)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + }, + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "r = gromacs.run.MDrunner(\n", + " dirname=oct_sim.dirs[\"MD_relaxed\"],\n", + " deffnm=\"md\",\n", + " c=\"md.pdb\",\n", + " cpi=True,\n", + " v=True,\n", + ")\n", + "r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.equil : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro').\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 't']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -t /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt\n", + "\n", + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "Last frame -1 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"I was told I'd never make it to VP rank because I was too outspoken. Maybe so, but I think men will always find an excuse for keeping women in their 'place.' So, let's make that place the executive suite and start more of our own companies.\" (Jean Bartik, ENIAC developer)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] All files set up for a run time of 10000 ps (dt=0.02, nsteps=500000)\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -989987098\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.168 nm, buffer size 0.068 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.109 nm, buffer size 0.009 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "Reading Coordinates, Velocities and Box size from old trajectory\n", + "\n", + "Will read whole trajectory\n", + "\n", + "Using frame at t = 1000 ps\n", + "\n", + "Starting time for run is 0 ps\n", + "\n", + "This run will generate roughly 15 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 10 to 25, rlist from 1.108 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the GPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "500000 steps, 10000.0 ps.\n", + "step 499900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 500000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 1247.510 311.878 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2770.319 0.009\n", + "\n", + "GROMACS reminds you: \"Garbage Collecting...\" (GNU Emacs)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + }, + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "oct_sim.MD(\n", + " runtime=10e3, qscript=[\"local.sh\"], dt=0.02\n", + ")\n", + "\n", + "r = gromacs.run.MDrunner(\n", + " dirname=oct_sim.dirs[\"MD_NPT\"], deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True\n", + ")\n", + "r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.gro').\n", + "mdpow.fep : INFO Solvation free energy calculation for molecule BENZ in solvent octanol.\n", + "mdpow.fep : INFO Base directory is '/home/awsm/MDPOW/doc/examples/martini'\n", + "mdpow.fep : INFO Using setup directories under 'FEP/octanol': {'coulomb': 'FEP/octanol/Coulomb', 'vdw': 'FEP/octanol/VDW'}\n", + "mdpow.fep : INFO Default checkpoint file is '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep'\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n", + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"I had trouble with physics in college. When I signed up I thought it said psychics.\" (Greg Tamblyn)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.25\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1610694785\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"Your theory is crazy, but it's not crazy enough to be true.\" (Niels Bohr)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.5\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -102842532\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"Your theory is crazy, but it's not crazy enough to be true.\" (Niels Bohr)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.75\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -16979715\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"But I always say, one's company, two's a crowd, and three's a party.\" (Andy Warhol)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=1\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -322961413\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"No matter how important you are, you are not as important as lunch.\" (Randy Pausch)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", + "mdpow.fep : INFO [coulomb] Wrote array job scripts [None]\n", + "mdpow.fep : INFO Preparing vdw for lambda=0\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -176234568\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"No matter how important you are, you are not as important as lunch.\" (Randy Pausch)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.05\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1878318079\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"Numbers have life; they’re not just symbols on paper.\" (Shakuntala Devi)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.1\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1209184641\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"Numbers have life; they’re not just symbols on paper.\" (Shakuntala Devi)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.2\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -589374473\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"All Work and No Play Makes Jack a Dull Boy\" (The Shining)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.3\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -187252737\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"All Work and No Play Makes Jack a Dull Boy\" (The Shining)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.4\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 331345371\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"It is a cute toxin.\" (Rebecca Howard)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.5\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 2006891771\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"It is a cute toxin.\" (Rebecca Howard)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.6\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1110644929\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"It's So Fast It's Slow\" (F. Black)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.65\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -9461789\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"It's So Fast It's Slow\" (F. Black)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.7\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -297900070\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"It takes money to make money, they say\" (Lou Reed)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.75\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1093150214\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"It takes money to make money, they say\" (Lou Reed)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.8\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -24248510\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"Kissing You is Like Kissing Gravel\" (Throwing Muses)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.85\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 1256396671\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"Kissing You is Like Kissing Gravel\" (Throwing Muses)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.9\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -6310919\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"Some of these pro-drug messages come from popular culture.\" (John Walters)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.95\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1208987793\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"Some of these pro-drug messages come from popular culture.\" (John Walters)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=1\n", + "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "NOTE 3 [file md.mdp]:\n", + " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -35661570\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "There was 1 WARNING\n", + "\n", + "GROMACS reminds you: \"Science and everyday life cannot and should not be separated.\" (Rosalind Franklin)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", + "mdpow.fep : INFO [vdw] Wrote array job scripts [None]\n", + "mdpow.fep : INFO Saved state information to '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep'; reload later with G = Goct(filename='/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep').\n", + "mdpow.fep : INFO Finished setting up all individual simulations. Now run them...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -109805585\n", + "\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Coupling 1 copies of molecule type 'BENZ'\n", + "\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 8 Mb of data\n" + ] + }, + { + "data": { + "text/plain": [ + "{'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top',\n", + " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx',\n", + " 'qscript': ['./local.sh'],\n", + " 'mainselection': None,\n", + " 'deffnm': 'md',\n", + " 'includes': ['/home/awsm/MDPOW/mdpow/top'],\n", + " 'maxwarn': 1,\n", + " 'couple-intramol': 'no',\n", + " 'couple_lambda0': 'vdw',\n", + " 'couple_lambda1': 'none',\n", + " 'sc_alpha': 0.5,\n", + " 'sc_power': 1,\n", + " 'sc_sigma': 0.3,\n", + " 'separate-dhdl-file': 'yes',\n", + " 'ref_t': 300.0,\n", + " 'gen_temp': 300.0,\n", + " 'free_energy': 'yes',\n", + " 'couple_moltype': 'BENZ',\n", + " 'init_lambda_state': 15,\n", + " 'fep_lambdas': array([0. , 0.05, 0.1 , 0.2 , 0.3 , 0.4 , 0.5 , 0.6 , 0.65, 0.7 , 0.75,\n", + " 0.8 , 0.85, 0.9 , 0.95, 1. ]),\n", + " 'calc_lambda_neighbors': -1}" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "goct = mdpow.fep.Goct(simulation=oct_sim, runtime=1e+3, mdp=str(RUN_FILE.absolute()))\n", + "goct.setup(dt=0.02, edr=False)" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 155.428 38.857 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2223.565 0.011\n", + "\n", + "GROMACS reminds you: \"The greatest shortcoming of the human race is our inability to understand the exponential function.\" (Albert Bartlett)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 115.908 28.977 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2981.738 0.008\n", + "\n", + "GROMACS reminds you: \"Microsecond Here I Come\" (P.J. Van Maaren)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 147.410 36.853 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2344.525 0.010\n", + "\n", + "GROMACS reminds you: \"I see they found out the universe is 80 million years older than we thought. It's also been lying about its weight.\" (Bill Maher)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s , remaining wall clock time: 15 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 177.267 44.317 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1949.639 0.012\n", + "\n", + "GROMACS reminds you: \"In the processing of models we must be especially cautious of the human weakness to think that models can be verified or validated. Especially one's own.\" (Roald Hoffmann)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 119.299 29.825 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2896.969 0.008\n", + "\n", + "GROMACS reminds you: \"Here's Another Useful Quote\" (S. Boot)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 179.663 44.916 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1923.637 0.012\n", + "\n", + "GROMACS reminds you: \"The historical meaning of QM/MM: Quanto Mangi, Mamma Mia!\" (Attilio Vittorio Vargiu, at BioExcel 2022 Summer School in Sardinia)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 190.598 47.650 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1813.274 0.013\n", + "\n", + "GROMACS reminds you: \"I Am a Wonderful Thing\" (Kid Creole)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 120.687 30.172 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2863.642 0.008\n", + "\n", + "GROMACS reminds you: \"For the first time we can now mechanically simulate the cognitive process. We can make studies in artificial intelligence. Beyond that, this mechanism can be used to assist humans in learning. As we are going to have more mature students in greater numbers as time goes on, this type of teaching will probably be increasingly important.\" (Sister Mary Kenneth Keller)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 125.666 31.417 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2750.194 0.009\n", + "\n", + "GROMACS reminds you: \"Try to calculate the numbers that have been\" (The Smoke Fairies)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 125.003 31.251 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2764.782 0.009\n", + "\n", + "GROMACS reminds you: \"I see they found out the universe is 80 million years older than we thought. It's also been lying about its weight.\" (Bill Maher)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 124.501 31.125 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2775.941 0.009\n", + "\n", + "GROMACS reminds you: \"Well, I am a dilettante. It's only in England that dilettantism is considered a bad thing. In other countries it's called interdisciplinary research.\" (Brian Eno)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 125.453 31.363 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2754.873 0.009\n", + "\n", + "GROMACS reminds you: \"Good Music Saves your Soul\" (Lemmy)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 125.507 31.377 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2753.682 0.009\n", + "\n", + "GROMACS reminds you: \"Your assumptions are your windows on the world. Scrub them off every once in a while, or the light won't come in.\" (Isaac Asimov)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 127.829 31.957 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2703.654 0.009\n", + "\n", + "GROMACS reminds you: \"Everybody's Good Enough For Some Change\" (LIVE)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 131.403 32.851 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2630.119 0.009\n", + "\n", + "GROMACS reminds you: \"Would You Like to Be the Monster Tonight ?\" (Captain Beefheart)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 131.139 32.785 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2635.427 0.009\n", + "\n", + "GROMACS reminds you: \"GROMACS First : Making MD Great Again\" (Vedran Miletic)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 129.744 32.436 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2663.753 0.009\n", + "\n", + "GROMACS reminds you: \"Erwin with his psi can do / Calculations quite a few. / But one thing has not been seen / Just what psi really mean.\" (Felix Bloch)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 130.443 32.611 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2649.482 0.009\n", + "\n", + "GROMACS reminds you: \"The only place success comes before work is in the dictionary\" (Vince Lombardi)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 130.377 32.594 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2650.831 0.009\n", + "\n", + "GROMACS reminds you: \"Here are all the 'gmx' tools... but no gmx writethesis\" (Christian Blau)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 136.588 34.147 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2530.279 0.009\n", + "\n", + "GROMACS reminds you: \"I was detained, I was restrained\" (The Smiths)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 129.204 32.301 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 2674.882 0.009\n", + "\n", + "GROMACS reminds you: \"We ignore public understanding of science at our peril.\" (Eugenie Clark)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + } + ], + "source": [ + "for dir_ in goct.fep_dirs():\n", + " r = gromacs.run.MDrunner(\n", + " dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=\"md.xvg\"\n", + " )\n", + " r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Finding dgdl xvg files, reading with stride=1 permissive=False.\n", + "mdpow.fep : INFO Analysis stride is 1.\n", + "mdpow.fep : INFO Analyzing stored data.\n", + "mdpow.fep : INFO [BENZ coulomb] Computing averages and errors for 5 lambda values.\n", + "numkit.integration: WARNING Approximating Simpson integration statistical error with the average spacing.\n", + "mdpow.fep : INFO [BENZ vdw] Computing averages and errors for 16 lambda values.\n", + "numkit.integration: WARNING Approximating Simpson integration statistical error with the average spacing.\n", + "mdpow.fep : INFO DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n", + "mdpow.fep : INFO [BENZ] Octanol solvation free energy (coulomb) -25109.1 (13.01) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Octanol solvation free energy (vdw) -25105.4 (6.33) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Octanol solvation free energy (Gibbs) 50214.5 (14.47) kJ/mol\n" + ] + }, + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "goct.collect()\n", + "goct.analyze()\n", + "goct.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [BENZ] transfer free energy water --> octanol calculation\n", + "mdpow.fep : INFO The solvent is water .\n", + "mdpow.fep : INFO Using already calculated free energy DeltaA\n", + "mdpow.fep : INFO The solvent is octanol .\n", + "mdpow.fep : INFO Using already calculated free energy DeltaA\n", + "mdpow.fep : INFO [BENZ] Values at T = 300 K\n", + "mdpow.fep : INFO [BENZ] Free energy of transfer water --> octanol: -17812.254 (15.182) kJ/mol\n", + "mdpow.fep : INFO [BENZ] log P_ow: 3101.325 (2.643)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "log P_ow = 3101.324683550301 ± 2.643399588149987\n" + ] + } + ], + "source": [ + "delta_G, p_OW = mdpow.fep.pOW(gwat, goct)\n", + "print(f\"log P_ow = {p_OW.value} ± {p_OW.error}\")" ] } ], diff --git a/doc/examples/martini/run.mdp b/doc/examples/martini/run.mdp index 3b1f95ed..8802883e 100644 --- a/doc/examples/martini/run.mdp +++ b/doc/examples/martini/run.mdp @@ -11,14 +11,16 @@ comm-mode = Linear ; number of steps for center of mass motion removal = nstcomm = 10 -; Output frequency for energies to log file and energy file = nstxout = 0 nstvout = 0 nstfout = 0 -nstlog = 10000 -nstenergy = 10000 +; Output frequency for energies to log file and energy file +nstlog = 500 +nstenergy = 200 nstcalcenergy = 10 -nstxtcout = 10000 +; Output frequency and precisi500on for xtc file +nstxtcout = 250 +xtc-precision = 1000 cutoff-scheme = Verlet nstlist = 20 @@ -41,7 +43,8 @@ rvdw = 1.1 ;rvdw = 1.2 -gen-vel = no +gen-vel = yes +gen-temp = 300 gen_seed = 175547 tc-grps = System tcoupl = v-rescale @@ -61,15 +64,17 @@ ref_p = 1.0 free-energy = yes sc-power = 1 sc-alpha = 0.5 +sc-sigma = 0.3 sc-r-power = 6 ; Which intermediate state do we start with? Doesn't really matter, it leaves soon -------- -init-lambda-state = 0 +;------- +init-lambda-state = sedstate ; What are the values of lambda at the intermediate states? ;------- vdw-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 +; fep_lambdas = 0.0 0.25 0.5 0.75 1.0 ; This makes sure we print out the differences in Hamiltonians between all states, and not just the neighboring states ;-------- @@ -87,6 +92,8 @@ dhdl-print-energy = yes ; We are doing free energies with the solute molecule alone couple-moltype = SOLUTE +separate-dhdl-file = yes + ; decharging free energy ; couple-lambda0 = vdw-q ; couple-lambda1 = vdw From b739c883eaef573b3e5856a0ab17dd934cdfce6d Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 4 Sep 2023 22:30:23 +0100 Subject: [PATCH 32/38] Working example --- doc/examples/martini/martini-benzene.ipynb | 7122 ++++++++++---------- doc/examples/martini/run.mdp | 3 +- 2 files changed, 3475 insertions(+), 3650 deletions(-) diff --git a/doc/examples/martini/martini-benzene.ipynb b/doc/examples/martini/martini-benzene.ipynb index f8478852..d4c775bc 100644 --- a/doc/examples/martini/martini-benzene.ipynb +++ b/doc/examples/martini/martini-benzene.ipynb @@ -117,9 +117,22 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow : INFO MDPOW 0+untagged.603.ge92ffd8.dirty starting.\n", + "mdpow : INFO Copyright (c) 2010-2023 Shujie Fan, Ian Kenney, Alia Lescoulie, Cade Duckworth, Bogdan Iorga, and Oliver Beckstein\n", + "mdpow : INFO Released under the GNU Public Licence, version 3.\n", + "mdpow : INFO For bug reports and help: https://github.com/Becksteinlab/MDPOW/issues\n", + "mdpow.config: INFO Using the bundled force fields from GMXLIB='/home/awsm/MDPOW/mdpow/top'.\n", + "mdpow.config: INFO If required, override this behaviour by setting the environment variable GMXLIB yourself.\n" + ] + } + ], "source": [ "from mdpow.forcefields import Forcefield, GromacsSolventModel\n", "\n", @@ -158,7 +171,7 @@ "output_type": "stream", "text": [ "octanol\n", - "{'identifier': 'octanol', 'name': 'OCTANOL', 'itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_solvents_v1.itp'), 'coordinates': PosixPath('/home/awsm/MDPOW/doc/examples/martini/octanol.gro'), 'description': None, 'forcefield': 'Martini'}\n" + "{'identifier': 'octanol', 'name': 'OCTANOL', 'itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_solvents_v1.itp'), 'coordinates': '/home/awsm/MDPOW/doc/examples/martini/octanol.gro', 'description': None, 'forcefield': 'Martini'}\n" ] } ], @@ -179,7 +192,9 @@ "name": "stderr", "output_type": "stream", "text": [ + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top' (newly created)...\n", "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation' (newly created)...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/water.gro'...\n", " :-) GROMACS - gmx editconf, 2023.2 (-:\n", "\n", @@ -190,9 +205,7 @@ " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 3.0\n", "\n", "\n", - "Back Off! I just backed up boxed.gro to ./#boxed.gro.11#\n", - "\n", - "GROMACS reminds you: \"The loveliest theories are being overthrown by these damned experiments; it is no fun being a chemist any more.\" (Justus von Liebig, letter to J.J. Berzelius 1834)\n", + "GROMACS reminds you: \"According to my computations we're overdue for a transformation.\" (Jackson Browne)\n", "\n", " :-) GROMACS - gmx solvate, 2023.2 (-:\n", "\n", @@ -217,8 +230,6 @@ "Generated solvent containing 1633 atoms in 1633 residues\n", "Writing generated configuration to solvated.gro\n", "\n", - "Back Off! I just backed up solvated.gro to ./#solvated.gro.11#\n", - "\n", "Output configuration contains 1636 atoms in 1634 residues\n", "Volume : 174.316 (nm^3)\n", "Density : 2860.16 (g/l)\n", @@ -226,9 +237,9 @@ "\n", "Processing topology\n", "\n", - "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#system.top.12#\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#system.top.1#\n", "\n", - "GROMACS reminds you: \"The loveliest theories are being overthrown by these damned experiments; it is no fun being a chemist any more.\" (Justus von Liebig, letter to J.J. Berzelius 1834)\n", + "GROMACS reminds you: \"According to my computations we're overdue for a transformation.\" (Jackson Browne)\n", "\n", "gromacs.setup: INFO Solvated system with /home/awsm/MDPOW/doc/examples/martini/water.gro\n" ] @@ -296,9 +307,7 @@ "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "\n", - "Back Off! I just backed up main.ndx to ./#main.ndx.22#\n", - "\n", - "GROMACS reminds you: \"You still have to climb to the shoulders of the giants\" (Vedran Miletic)\n", + "GROMACS reminds you: \"Expertise is not inherently good.\" (Joe Jordan)\n", "\n", " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", "\n", @@ -313,9 +322,9 @@ "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "\n", - "Back Off! I just backed up main.ndx to ./#main.ndx.23#\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.1#\n", "\n", - "GROMACS reminds you: \"You still have to climb to the shoulders of the giants\" (Vedran Miletic)\n", + "GROMACS reminds you: \"Expertise is not inherently good.\" (Joe Jordan)\n", "\n", " :-) GROMACS - gmx trjconv, 2023.2 (-:\n", "\n", @@ -343,14 +352,12 @@ "Select a group: Reading frames from gro file 'This is an auto generated system', 1636 atoms.\n", "Reading frame 0 time 0.000 \n", "Precision of ionized.gro is 0.001 (nm)\n", - "\n", - "Back Off! I just backed up compact.pdb to ./#compact.pdb.11#\n", "Last frame 0 time 0.000 \n", " -> frame 0 time 0.000 \n", "Last written: frame 0 time 0.000\n", "\n", "\n", - "GROMACS reminds you: \"You still have to climb to the shoulders of the giants\" (Vedran Miletic)\n", + "GROMACS reminds you: \"Expertise is not inherently good.\" (Joe Jordan)\n", "\n", " :-) GROMACS - gmx grompp, 2023.2 (-:\n", "\n", @@ -358,15 +365,13 @@ "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -f /tmp/tmpev4lqv00.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -nov\n", + " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -f /tmp/tmpec_ojnsf.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -nov\n", "\n", "\n", - "NOTE 1 [file /tmp/tmpev4lqv00.mdp]:\n", + "NOTE 1 [file /tmp/tmpec_ojnsf.mdp]:\n", " For a correct single-point energy evaluation with nsteps = 0, use\n", " continuation = yes to avoid constraining the input coordinates.\n", - "\n", - "\n", - "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#pp_system.top.11#\n" + "\n" ] }, { @@ -444,7 +449,7 @@ "Number of degrees of freedom in T-Coupling group rest is 4902.00\n", "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", "\n", - "NOTE 3 [file /tmp/tmpev4lqv00.mdp]:\n", + "NOTE 3 [file /tmp/tmpec_ojnsf.mdp]:\n", " NVE simulation with an initial temperature of zero: will use a Verlet\n", " buffer of 10%. Check your energy drift!\n", "\n", @@ -453,9 +458,10 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"You still have to climb to the shoulders of the giants\" (Vedran Miletic)\n", + "GROMACS reminds you: \"Expertise is not inherently good.\" (Joe Jordan)\n", "\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top', mdp='em.mdp' ...\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'em.mdp': ['maxwarn', 'pp']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -472,16 +478,14 @@ " gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -maxwarn 1 -pp processed.top\n", "\n", "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", - "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.11#\n" + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1853841179\n", + "Setting the LD random seed to -1526990921\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -598,9 +602,7 @@ "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up em.tpr to ./#em.tpr.11#\n", - "\n", - "GROMACS reminds you: \"I'm Only Faking When I Get It Right\" (Soundgarden)\n", + "GROMACS reminds you: \"Ludwig Boltzmann, who spent much of his life studying statistical mechanics, died in 1906, by his own hand. Paul Ehrenfest, carrying on the same work, died similarly in 1933. Now it is our turn to study statistical mechanics. Perhaps it will be wise to approach the subject cautiously.\" (David Goodstein)\n", "\n", "gromacs.run : WARNING No 'mdrun_d' binary found so trying 'mdrun' instead.\n", "(Note that energy minimization runs better with mdrun_d.)\n", @@ -621,7 +623,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -561519253\n", + "Setting the LD random seed to 2013264681\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -681,8 +683,6 @@ "name": "stderr", "output_type": "stream", "text": [ - "\n", - "Back Off! I just backed up em.log to ./#em.log.11#\n", "Reading file em.tpr, VERSION 2023.2 (single precision)\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -693,10 +693,6 @@ "Using 4 OpenMP threads \n", "\n", "\n", - "Back Off! I just backed up em.trr to ./#em.trr.11#\n", - "\n", - "Back Off! I just backed up em.edr to ./#em.edr.11#\n", - "\n", "Steepest Descents:\n", " Tolerance (Fmax) = 1.00000e+01\n", " Number of steps = 1000\n", @@ -712,7 +708,7 @@ "Step= 9, Dmax= 4.3e-02 nm, Epot= 1.57693e+05 Fmax= 1.98551e+05, atom= 544\n", "Step= 10, Dmax= 5.2e-02 nm, Epot= 1.29573e+05 Fmax= 6.97811e+04, atom= 1043\n", "Step= 11, Dmax= 6.2e-02 nm, Epot= 8.43732e+04 Fmax= 2.96444e+05, atom= 200\n", - "Step= 12, Dmax= 7.4e-02 nm, Epot= 7.16053e+04 Fmax= 2.00454e+04, atom= 200\n", + "Step= 12, Dmax= 7.4e-02 nm, Epot= 7.16052e+04 Fmax= 2.00454e+04, atom= 200\n", "Step= 13, Dmax= 8.9e-02 nm, Epot= 1.52005e+04 Fmax= 5.75866e+04, atom= 200\n", "Step= 14, Dmax= 1.1e-01 nm, Epot= 7.52938e+03 Fmax= 2.23148e+04, atom= 200\n", "Step= 15, Dmax= 1.3e-01 nm, Epot= -2.26040e+03 Fmax= 3.65168e+04, atom= 1107\n", @@ -722,794 +718,793 @@ "Step= 20, Dmax= 1.3e-01 nm, Epot= -1.44389e+04 Fmax= 1.77137e+04, atom= 1591\n", "Step= 22, Dmax= 8.0e-02 nm, Epot= -1.69180e+04 Fmax= 2.36072e+04, atom= 1591\n", "Step= 23, Dmax= 9.6e-02 nm, Epot= -1.85682e+04 Fmax= 1.69728e+04, atom= 1267\n", - "Step= 24, Dmax= 1.2e-01 nm, Epot= -2.05149e+04 Fmax= 1.35048e+04, atom= 1586\n", - "Step= 26, Dmax= 6.9e-02 nm, Epot= -2.22957e+04 Fmax= 7.78835e+03, atom= 1606\n", - "Step= 27, Dmax= 8.3e-02 nm, Epot= -2.46065e+04 Fmax= 8.23715e+03, atom= 1606\n", - "Step= 28, Dmax= 9.9e-02 nm, Epot= -2.60463e+04 Fmax= 2.03931e+04, atom= 1586\n", - "Step= 29, Dmax= 1.2e-01 nm, Epot= -2.71109e+04 Fmax= 8.51185e+03, atom= 1267\n", + "Step= 24, Dmax= 1.2e-01 nm, Epot= -2.05149e+04 Fmax= 1.35047e+04, atom= 1586\n", + "Step= 26, Dmax= 6.9e-02 nm, Epot= -2.22957e+04 Fmax= 7.78833e+03, atom= 1606\n", + "Step= 27, Dmax= 8.3e-02 nm, Epot= -2.46065e+04 Fmax= 8.23724e+03, atom= 1606\n", + "Step= 28, Dmax= 9.9e-02 nm, Epot= -2.60463e+04 Fmax= 2.03930e+04, atom= 1586\n", + "Step= 29, Dmax= 1.2e-01 nm, Epot= -2.71109e+04 Fmax= 8.51178e+03, atom= 1267\n", "Step= 30, Dmax= 1.4e-01 nm, Epot= -2.77852e+04 Fmax= 5.10263e+04, atom= 1490\n", - "Step= 31, Dmax= 1.7e-01 nm, Epot= -2.89093e+04 Fmax= 8.58700e+03, atom= 1446\n", - "Step= 32, Dmax= 2.1e-01 nm, Epot= -3.02287e+04 Fmax= 2.27403e+04, atom= 1550\n", - "Step= 34, Dmax= 1.2e-01 nm, Epot= -3.08777e+04 Fmax= 1.66822e+04, atom= 1550\n", + "Step= 31, Dmax= 1.7e-01 nm, Epot= -2.89093e+04 Fmax= 8.58695e+03, atom= 1446\n", + "Step= 32, Dmax= 2.1e-01 nm, Epot= -3.02288e+04 Fmax= 2.27389e+04, atom= 1550\n", + "Step= 34, Dmax= 1.2e-01 nm, Epot= -3.08778e+04 Fmax= 1.66821e+04, atom= 1550\n", "Step= 35, Dmax= 1.5e-01 nm, Epot= -3.15210e+04 Fmax= 7.84232e+03, atom= 468\n", - "Step= 36, Dmax= 1.8e-01 nm, Epot= -3.26742e+04 Fmax= 4.75751e+03, atom= 1596\n", - "Step= 37, Dmax= 2.1e-01 nm, Epot= -3.33775e+04 Fmax= 3.33247e+04, atom= 1461\n", - "Step= 38, Dmax= 2.6e-01 nm, Epot= -3.44663e+04 Fmax= 4.50562e+03, atom= 1596\n", - "Step= 40, Dmax= 1.5e-01 nm, Epot= -3.54502e+04 Fmax= 1.55012e+03, atom= 430\n", + "Step= 36, Dmax= 1.8e-01 nm, Epot= -3.26742e+04 Fmax= 4.75748e+03, atom= 1596\n", + "Step= 37, Dmax= 2.1e-01 nm, Epot= -3.33775e+04 Fmax= 3.33249e+04, atom= 1461\n", + "Step= 38, Dmax= 2.6e-01 nm, Epot= -3.44663e+04 Fmax= 4.50564e+03, atom= 1596\n", + "Step= 40, Dmax= 1.5e-01 nm, Epot= -3.54502e+04 Fmax= 1.55013e+03, atom= 430\n", "Step= 41, Dmax= 1.8e-01 nm, Epot= -3.68978e+04 Fmax= 1.01688e+04, atom= 430\n", - "Step= 43, Dmax= 1.1e-01 nm, Epot= -3.73994e+04 Fmax= 2.71564e+03, atom= 1090\n", - "Step= 44, Dmax= 1.3e-01 nm, Epot= -3.78345e+04 Fmax= 2.32950e+03, atom= 1200\n", - "Step= 45, Dmax= 1.6e-01 nm, Epot= -3.80154e+04 Fmax= 6.23586e+03, atom= 1363\n", - "Step= 47, Dmax= 9.6e-02 nm, Epot= -3.85621e+04 Fmax= 2.23179e+03, atom= 867\n", - "Step= 48, Dmax= 1.1e-01 nm, Epot= -3.89186e+04 Fmax= 1.51574e+03, atom= 666\n", - "Step= 50, Dmax= 6.9e-02 nm, Epot= -3.92438e+04 Fmax= 1.20399e+03, atom= 1190\n", - "Step= 52, Dmax= 4.1e-02 nm, Epot= -3.94257e+04 Fmax= 1.81706e+03, atom= 1190\n", - "Step= 53, Dmax= 5.0e-02 nm, Epot= -3.95622e+04 Fmax= 1.81324e+03, atom= 1190\n", - "Step= 54, Dmax= 6.0e-02 nm, Epot= -3.96129e+04 Fmax= 3.55332e+03, atom= 1190\n", - "Step= 55, Dmax= 7.1e-02 nm, Epot= -3.97856e+04 Fmax= 1.91005e+03, atom= 652\n", - "Step= 57, Dmax= 4.3e-02 nm, Epot= -3.99184e+04 Fmax= 1.12243e+03, atom= 1469\n", - "Step= 58, Dmax= 5.1e-02 nm, Epot= -4.00827e+04 Fmax= 1.67429e+03, atom= 652\n", - "Step= 59, Dmax= 6.2e-02 nm, Epot= -4.01536e+04 Fmax= 2.68805e+03, atom= 652\n", - "Step= 60, Dmax= 7.4e-02 nm, Epot= -4.02827e+04 Fmax= 2.17712e+03, atom= 1190\n", - "Step= 61, Dmax= 8.9e-02 nm, Epot= -4.03035e+04 Fmax= 2.90934e+03, atom= 1190\n", - "Step= 63, Dmax= 5.3e-02 nm, Epot= -4.05244e+04 Fmax= 7.06731e+02, atom= 5920\n", - "Step= 64, Dmax= 6.4e-02 nm, Epot= -4.07516e+04 Fmax= 1.27359e+03, atom= 620\n", - "Step= 66, Dmax= 3.8e-02 nm, Epot= -4.08794e+04 Fmax= 1.05973e+03, atom= 620\n", - "Step= 67, Dmax= 4.6e-02 nm, Epot= -4.09734e+04 Fmax= 1.25287e+03, atom= 1190\n", - "Step= 68, Dmax= 5.5e-02 nm, Epot= -4.10696e+04 Fmax= 1.23286e+03, atom= 652\n", - "Step= 69, Dmax= 6.6e-02 nm, Epot= -4.10934e+04 Fmax= 2.04140e+03, atom= 652\n", - "Step= 70, Dmax= 8.0e-02 nm, Epot= -4.11782e+04 Fmax= 2.16374e+03, atom= 652\n", - "Step= 72, Dmax= 4.8e-02 nm, Epot= -4.13409e+04 Fmax= 5.23621e+02, atom= 1469\n", - "Step= 73, Dmax= 5.7e-02 nm, Epot= -4.14399e+04 Fmax= 4.60012e+03, atom= 113\n", - "Step= 74, Dmax= 6.9e-02 nm, Epot= -4.15766e+04 Fmax= 1.02818e+03, atom= 170\n", - "Step= 75, Dmax= 8.3e-02 nm, Epot= -4.16145e+04 Fmax= 4.11463e+03, atom= 170\n", - "Step= 76, Dmax= 9.9e-02 nm, Epot= -4.17154e+04 Fmax= 1.43780e+03, atom= 113\n", - "Step= 77, Dmax= 1.2e-01 nm, Epot= -4.17179e+04 Fmax= 4.52138e+03, atom= 113\n", - "Step= 78, Dmax= 1.4e-01 nm, Epot= -4.17574e+04 Fmax= 5.42849e+03, atom= 170\n", - "Step= 80, Dmax= 8.6e-02 nm, Epot= -4.18853e+04 Fmax= 1.57744e+03, atom= 1281\n", - "Step= 81, Dmax= 1.0e-01 nm, Epot= -4.20080e+04 Fmax= 1.11946e+03, atom= 712\n", - "Step= 83, Dmax= 6.2e-02 nm, Epot= -4.21195e+04 Fmax= 4.11103e+02, atom= 1541\n", - "Step= 84, Dmax= 7.4e-02 nm, Epot= -4.21928e+04 Fmax= 1.94301e+03, atom= 712\n", - "Step= 85, Dmax= 8.9e-02 nm, Epot= -4.23274e+04 Fmax= 1.32241e+03, atom= 1589\n", - "Step= 87, Dmax= 5.3e-02 nm, Epot= -4.24331e+04 Fmax= 8.97786e+02, atom= 434\n", - "Step= 88, Dmax= 6.4e-02 nm, Epot= -4.24949e+04 Fmax= 1.14063e+03, atom= 434\n", - "Step= 90, Dmax= 3.8e-02 nm, Epot= -4.25673e+04 Fmax= 3.36942e+02, atom= 1589\n", - "Step= 91, Dmax= 4.6e-02 nm, Epot= -4.26762e+04 Fmax= 1.27605e+03, atom= 1589\n", - "Step= 92, Dmax= 5.5e-02 nm, Epot= -4.27289e+04 Fmax= 8.00429e+02, atom= 434\n", - "Step= 93, Dmax= 6.6e-02 nm, Epot= -4.27805e+04 Fmax= 1.06524e+03, atom= 434\n", - "Step= 95, Dmax= 4.0e-02 nm, Epot= -4.28472e+04 Fmax= 3.14248e+02, atom= 1589\n", - "Step= 96, Dmax= 4.8e-02 nm, Epot= -4.29489e+04 Fmax= 1.02626e+03, atom= 1589\n", - "Step= 97, Dmax= 5.7e-02 nm, Epot= -4.29942e+04 Fmax= 8.66540e+02, atom= 434\n", - "Step= 98, Dmax= 6.9e-02 nm, Epot= -4.30311e+04 Fmax= 9.53738e+02, atom= 434\n", - "Step= 100, Dmax= 4.1e-02 nm, Epot= -4.30996e+04 Fmax= 2.93202e+02, atom= 1589\n", - "Step= 101, Dmax= 4.9e-02 nm, Epot= -4.31753e+04 Fmax= 1.10153e+03, atom= 1589\n", - "Step= 102, Dmax= 5.9e-02 nm, Epot= -4.32252e+04 Fmax= 9.34391e+02, atom= 434\n", - "Step= 103, Dmax= 7.1e-02 nm, Epot= -4.32587e+04 Fmax= 9.34787e+02, atom= 317\n", - "Step= 104, Dmax= 8.5e-02 nm, Epot= -4.32610e+04 Fmax= 1.64631e+03, atom= 317\n", - "Step= 105, Dmax= 1.0e-01 nm, Epot= -4.33016e+04 Fmax= 1.28613e+03, atom= 317\n", - "Step= 107, Dmax= 6.2e-02 nm, Epot= -4.33906e+04 Fmax= 3.85737e+02, atom= 1589\n", - "Step= 108, Dmax= 7.4e-02 nm, Epot= -4.34217e+04 Fmax= 1.00007e+03, atom= 1310\n", - "Step= 110, Dmax= 4.4e-02 nm, Epot= -4.35166e+04 Fmax= 3.28319e+02, atom= 317\n", - "Step= 111, Dmax= 5.3e-02 nm, Epot= -4.35425e+04 Fmax= 6.75626e+02, atom= 317\n", - "Step= 113, Dmax= 3.2e-02 nm, Epot= -4.36161e+04 Fmax= 2.61455e+02, atom= 983\n", - "Step= 114, Dmax= 3.8e-02 nm, Epot= -4.36370e+04 Fmax= 1.02704e+03, atom= 983\n", - "Step= 115, Dmax= 4.6e-02 nm, Epot= -4.36909e+04 Fmax= 4.75666e+02, atom= 983\n", - "Step= 117, Dmax= 2.8e-02 nm, Epot= -4.37182e+04 Fmax= 3.08316e+02, atom= 292\n", - "Step= 118, Dmax= 3.3e-02 nm, Epot= -4.37412e+04 Fmax= 9.12164e+02, atom= 983\n", - "Step= 119, Dmax= 4.0e-02 nm, Epot= -4.37713e+04 Fmax= 4.20075e+02, atom= 983\n", - "Step= 120, Dmax= 4.8e-02 nm, Epot= -4.37839e+04 Fmax= 1.34372e+03, atom= 983\n", - "Step= 121, Dmax= 5.7e-02 nm, Epot= -4.38167e+04 Fmax= 5.46838e+02, atom= 983\n", - "Step= 123, Dmax= 3.4e-02 nm, Epot= -4.38482e+04 Fmax= 2.66963e+02, atom= 939\n", - "Step= 124, Dmax= 4.1e-02 nm, Epot= -4.38560e+04 Fmax= 1.05569e+03, atom= 983\n", - "Step= 125, Dmax= 4.9e-02 nm, Epot= -4.38997e+04 Fmax= 8.25245e+02, atom= 983\n", - "Step= 126, Dmax= 5.9e-02 nm, Epot= -4.39091e+04 Fmax= 8.54830e+02, atom= 983\n", - "Step= 128, Dmax= 3.6e-02 nm, Epot= -4.39503e+04 Fmax= 1.83632e+02, atom= 939\n", - "Step= 129, Dmax= 4.3e-02 nm, Epot= -4.39908e+04 Fmax= 6.90661e+02, atom= 1550\n", - "Step= 130, Dmax= 5.1e-02 nm, Epot= -4.39914e+04 Fmax= 1.60360e+03, atom= 983\n", - "Step= 131, Dmax= 6.1e-02 nm, Epot= -4.40363e+04 Fmax= 5.69990e+02, atom= 292\n", - "Step= 133, Dmax= 3.7e-02 nm, Epot= -4.40661e+04 Fmax= 2.55382e+02, atom= 939\n", - "Step= 134, Dmax= 4.4e-02 nm, Epot= -4.40729e+04 Fmax= 8.77303e+02, atom= 983\n", - "Step= 135, Dmax= 5.3e-02 nm, Epot= -4.40907e+04 Fmax= 1.33513e+03, atom= 983\n", - "Step= 136, Dmax= 6.4e-02 nm, Epot= -4.41246e+04 Fmax= 6.23039e+02, atom= 983\n", - "Step= 138, Dmax= 3.8e-02 nm, Epot= -4.41545e+04 Fmax= 2.58181e+02, atom= 1550\n", - "Step= 139, Dmax= 4.6e-02 nm, Epot= -4.41686e+04 Fmax= 8.33654e+02, atom= 983\n", - "Step= 140, Dmax= 5.5e-02 nm, Epot= -4.41853e+04 Fmax= 1.00435e+03, atom= 983\n", - "Step= 141, Dmax= 6.6e-02 nm, Epot= -4.42000e+04 Fmax= 7.38560e+02, atom= 292\n", - "Step= 143, Dmax= 4.0e-02 nm, Epot= -4.42394e+04 Fmax= 2.83898e+02, atom= 939\n", - "Step= 144, Dmax= 4.8e-02 nm, Epot= -4.42475e+04 Fmax= 6.70825e+02, atom= 939\n", - "Step= 146, Dmax= 2.9e-02 nm, Epot= -4.42901e+04 Fmax= 1.91053e+02, atom= 983\n", - "Step= 147, Dmax= 3.4e-02 nm, Epot= -4.43094e+04 Fmax= 6.79625e+02, atom= 983\n", - "Step= 148, Dmax= 4.1e-02 nm, Epot= -4.43327e+04 Fmax= 3.76758e+02, atom= 1550\n", - "Step= 150, Dmax= 2.5e-02 nm, Epot= -4.43506e+04 Fmax= 2.59805e+02, atom= 681\n", - "Step= 151, Dmax= 3.0e-02 nm, Epot= -4.43633e+04 Fmax= 5.66457e+02, atom= 681\n", - "Step= 152, Dmax= 3.5e-02 nm, Epot= -4.43787e+04 Fmax= 3.98318e+02, atom= 681\n", - "Step= 153, Dmax= 4.3e-02 nm, Epot= -4.43800e+04 Fmax= 8.90609e+02, atom= 681\n", - "Step= 154, Dmax= 5.1e-02 nm, Epot= -4.44011e+04 Fmax= 5.19996e+02, atom= 681\n", - "Step= 156, Dmax= 3.1e-02 nm, Epot= -4.44244e+04 Fmax= 1.34639e+02, atom= 1059\n", - "Step= 158, Dmax= 1.8e-02 nm, Epot= -4.44403e+04 Fmax= 3.69269e+02, atom= 681\n", - "Step= 159, Dmax= 2.2e-02 nm, Epot= -4.44568e+04 Fmax= 2.25993e+02, atom= 681\n", - "Step= 160, Dmax= 2.6e-02 nm, Epot= -4.44657e+04 Fmax= 4.53948e+02, atom= 681\n", - "Step= 161, Dmax= 3.2e-02 nm, Epot= -4.44808e+04 Fmax= 3.59969e+02, atom= 681\n", - "Step= 163, Dmax= 1.9e-02 nm, Epot= -4.44951e+04 Fmax= 1.48568e+02, atom= 681\n", - "Step= 164, Dmax= 2.3e-02 nm, Epot= -4.45087e+04 Fmax= 4.81990e+02, atom= 681\n", - "Step= 165, Dmax= 2.7e-02 nm, Epot= -4.45221e+04 Fmax= 2.76160e+02, atom= 681\n", - "Step= 166, Dmax= 3.3e-02 nm, Epot= -4.45262e+04 Fmax= 6.54042e+02, atom= 681\n", - "Step= 167, Dmax= 4.0e-02 nm, Epot= -4.45405e+04 Fmax= 3.98719e+02, atom= 681\n", - "Step= 169, Dmax= 2.4e-02 nm, Epot= -4.45557e+04 Fmax= 1.08335e+02, atom= 681\n", - "Step= 171, Dmax= 1.4e-02 nm, Epot= -4.45678e+04 Fmax= 2.85478e+02, atom= 681\n", - "Step= 172, Dmax= 1.7e-02 nm, Epot= -4.45791e+04 Fmax= 1.47014e+02, atom= 681\n", - "Step= 173, Dmax= 2.1e-02 nm, Epot= -4.45873e+04 Fmax= 3.79193e+02, atom= 681\n", - "Step= 174, Dmax= 2.5e-02 nm, Epot= -4.46000e+04 Fmax= 2.34392e+02, atom= 681\n", - "Step= 176, Dmax= 1.5e-02 nm, Epot= -4.46093e+04 Fmax= 1.49891e+02, atom= 681\n", - "Step= 177, Dmax= 1.8e-02 nm, Epot= -4.46186e+04 Fmax= 3.00452e+02, atom= 681\n", - "Step= 178, Dmax= 2.1e-02 nm, Epot= -4.46270e+04 Fmax= 2.48382e+02, atom= 681\n", - "Step= 179, Dmax= 2.6e-02 nm, Epot= -4.46328e+04 Fmax= 4.13687e+02, atom= 681\n", - "Step= 180, Dmax= 3.1e-02 nm, Epot= -4.46405e+04 Fmax= 3.58339e+02, atom= 681\n", - "Step= 181, Dmax= 3.7e-02 nm, Epot= -4.46421e+04 Fmax= 6.04580e+02, atom= 681\n", - "Step= 182, Dmax= 4.4e-02 nm, Epot= -4.46500e+04 Fmax= 4.85753e+02, atom= 681\n", - "Step= 184, Dmax= 2.6e-02 nm, Epot= -4.46687e+04 Fmax= 9.81433e+01, atom= 983\n", - "Step= 186, Dmax= 1.6e-02 nm, Epot= -4.46795e+04 Fmax= 2.40466e+02, atom= 681\n", - "Step= 187, Dmax= 1.9e-02 nm, Epot= -4.46874e+04 Fmax= 2.53126e+02, atom= 681\n", - "Step= 188, Dmax= 2.3e-02 nm, Epot= -4.46931e+04 Fmax= 3.08779e+02, atom= 681\n", - "Step= 189, Dmax= 2.7e-02 nm, Epot= -4.46993e+04 Fmax= 3.64428e+02, atom= 681\n", - "Step= 190, Dmax= 3.3e-02 nm, Epot= -4.47026e+04 Fmax= 4.24388e+02, atom= 681\n", - "Step= 191, Dmax= 3.9e-02 nm, Epot= -4.47059e+04 Fmax= 5.46354e+02, atom= 681\n", - "Step= 192, Dmax= 4.7e-02 nm, Epot= -4.47069e+04 Fmax= 5.62949e+02, atom= 681\n", - "Step= 194, Dmax= 2.8e-02 nm, Epot= -4.47327e+04 Fmax= 7.49773e+01, atom= 260\n", - "Step= 196, Dmax= 1.7e-02 nm, Epot= -4.47447e+04 Fmax= 2.33328e+02, atom= 983\n", - "Step= 197, Dmax= 2.0e-02 nm, Epot= -4.47513e+04 Fmax= 2.55777e+02, atom= 681\n", - "Step= 198, Dmax= 2.5e-02 nm, Epot= -4.47535e+04 Fmax= 3.28205e+02, atom= 681\n", - "Step= 199, Dmax= 2.9e-02 nm, Epot= -4.47564e+04 Fmax= 3.79900e+02, atom= 681\n", - "Step= 201, Dmax= 1.8e-02 nm, Epot= -4.47764e+04 Fmax= 7.24967e+01, atom= 681\n", - "Step= 202, Dmax= 2.1e-02 nm, Epot= -4.47823e+04 Fmax= 4.44399e+02, atom= 681\n", - "Step= 203, Dmax= 2.5e-02 nm, Epot= -4.47984e+04 Fmax= 2.05731e+02, atom= 681\n", - "Step= 205, Dmax= 1.5e-02 nm, Epot= -4.48056e+04 Fmax= 1.63623e+02, atom= 401\n", - "Step= 206, Dmax= 1.8e-02 nm, Epot= -4.48074e+04 Fmax= 3.37522e+02, atom= 401\n", - "Step= 207, Dmax= 2.2e-02 nm, Epot= -4.48169e+04 Fmax= 2.37977e+02, atom= 401\n", - "Step= 209, Dmax= 1.3e-02 nm, Epot= -4.48244e+04 Fmax= 1.01416e+02, atom= 401\n", - "Step= 210, Dmax= 1.6e-02 nm, Epot= -4.48304e+04 Fmax= 3.15960e+02, atom= 401\n", - "Step= 211, Dmax= 1.9e-02 nm, Epot= -4.48383e+04 Fmax= 1.91451e+02, atom= 401\n", - "Step= 212, Dmax= 2.3e-02 nm, Epot= -4.48402e+04 Fmax= 4.12632e+02, atom= 401\n", - "Step= 213, Dmax= 2.7e-02 nm, Epot= -4.48481e+04 Fmax= 3.09859e+02, atom= 401\n", - "Step= 215, Dmax= 1.6e-02 nm, Epot= -4.48559e+04 Fmax= 1.00911e+02, atom= 401\n", - "Step= 216, Dmax= 2.0e-02 nm, Epot= -4.48583e+04 Fmax= 5.16413e+02, atom= 401\n", - "Step= 217, Dmax= 2.4e-02 nm, Epot= -4.48718e+04 Fmax= 1.67997e+02, atom= 401\n", - "Step= 219, Dmax= 1.4e-02 nm, Epot= -4.48771e+04 Fmax= 1.91015e+02, atom= 401\n", - "Step= 220, Dmax= 1.7e-02 nm, Epot= -4.48818e+04 Fmax= 2.45644e+02, atom= 401\n", - "Step= 221, Dmax= 2.0e-02 nm, Epot= -4.48863e+04 Fmax= 2.90142e+02, atom= 401\n", - "Step= 222, Dmax= 2.5e-02 nm, Epot= -4.48898e+04 Fmax= 3.52635e+02, atom= 401\n", - "Step= 223, Dmax= 2.9e-02 nm, Epot= -4.48928e+04 Fmax= 4.25211e+02, atom= 401\n", - "Step= 224, Dmax= 3.5e-02 nm, Epot= -4.48938e+04 Fmax= 5.23681e+02, atom= 401\n", - "Step= 225, Dmax= 4.2e-02 nm, Epot= -4.48947e+04 Fmax= 6.04656e+02, atom= 401\n", - "Step= 227, Dmax= 2.5e-02 nm, Epot= -4.49131e+04 Fmax= 9.56179e+01, atom= 514\n", - "Step= 229, Dmax= 1.5e-02 nm, Epot= -4.49199e+04 Fmax= 2.78897e+02, atom= 401\n", - "Step= 230, Dmax= 1.8e-02 nm, Epot= -4.49260e+04 Fmax= 2.27570e+02, atom= 401\n", - "Step= 231, Dmax= 2.2e-02 nm, Epot= -4.49292e+04 Fmax= 3.37757e+02, atom= 401\n", - "Step= 232, Dmax= 2.6e-02 nm, Epot= -4.49334e+04 Fmax= 3.42104e+02, atom= 401\n", - "Step= 233, Dmax= 3.2e-02 nm, Epot= -4.49338e+04 Fmax= 4.95014e+02, atom= 401\n", - "Step= 234, Dmax= 3.8e-02 nm, Epot= -4.49364e+04 Fmax= 5.20282e+02, atom= 401\n", - "Step= 236, Dmax= 2.3e-02 nm, Epot= -4.49514e+04 Fmax= 8.81958e+01, atom= 1356\n", - "Step= 237, Dmax= 2.7e-02 nm, Epot= -4.49575e+04 Fmax= 6.14417e+02, atom= 401\n", - "Step= 238, Dmax= 3.3e-02 nm, Epot= -4.49684e+04 Fmax= 3.65380e+02, atom= 401\n", - "Step= 240, Dmax= 2.0e-02 nm, Epot= -4.49757e+04 Fmax= 1.09430e+02, atom= 401\n", - "Step= 242, Dmax= 1.2e-02 nm, Epot= -4.49804e+04 Fmax= 2.28978e+02, atom= 401\n", - "Step= 243, Dmax= 1.4e-02 nm, Epot= -4.49855e+04 Fmax= 1.39363e+02, atom= 401\n", - "Step= 244, Dmax= 1.7e-02 nm, Epot= -4.49892e+04 Fmax= 3.05832e+02, atom= 401\n", - "Step= 245, Dmax= 2.0e-02 nm, Epot= -4.49947e+04 Fmax= 2.18545e+02, atom= 401\n", - "Step= 246, Dmax= 2.4e-02 nm, Epot= -4.49951e+04 Fmax= 4.33387e+02, atom= 401\n", - "Step= 247, Dmax= 2.9e-02 nm, Epot= -4.50012e+04 Fmax= 3.37822e+02, atom= 401\n", - "Step= 249, Dmax= 1.8e-02 nm, Epot= -4.50092e+04 Fmax= 9.95405e+01, atom= 401\n", - "Step= 250, Dmax= 2.1e-02 nm, Epot= -4.50102e+04 Fmax= 5.24716e+02, atom= 401\n", - "Step= 251, Dmax= 2.5e-02 nm, Epot= -4.50224e+04 Fmax= 1.83671e+02, atom= 401\n", - "Step= 253, Dmax= 1.5e-02 nm, Epot= -4.50267e+04 Fmax= 1.70431e+02, atom= 401\n", - "Step= 254, Dmax= 1.8e-02 nm, Epot= -4.50293e+04 Fmax= 3.04775e+02, atom= 401\n", - "Step= 255, Dmax= 2.2e-02 nm, Epot= -4.50341e+04 Fmax= 2.57360e+02, atom= 401\n", - "Step= 257, Dmax= 1.3e-02 nm, Epot= -4.50399e+04 Fmax= 7.50503e+01, atom= 401\n", - "Step= 258, Dmax= 1.6e-02 nm, Epot= -4.50455e+04 Fmax= 3.44605e+02, atom= 401\n", - "Step= 259, Dmax= 1.9e-02 nm, Epot= -4.50525e+04 Fmax= 1.54818e+02, atom= 401\n", - "Step= 261, Dmax= 1.1e-02 nm, Epot= -4.50565e+04 Fmax= 1.20428e+02, atom= 401\n", - "Step= 262, Dmax= 1.4e-02 nm, Epot= -4.50600e+04 Fmax= 2.34153e+02, atom= 401\n", - "Step= 263, Dmax= 1.6e-02 nm, Epot= -4.50644e+04 Fmax= 1.85357e+02, atom= 401\n", - "Step= 264, Dmax= 2.0e-02 nm, Epot= -4.50660e+04 Fmax= 3.24057e+02, atom= 401\n", - "Step= 265, Dmax= 2.4e-02 nm, Epot= -4.50704e+04 Fmax= 2.87728e+02, atom= 401\n", - "Step= 267, Dmax= 1.4e-02 nm, Epot= -4.50769e+04 Fmax= 6.95540e+01, atom= 401\n", - "Step= 268, Dmax= 1.7e-02 nm, Epot= -4.50817e+04 Fmax= 3.94582e+02, atom= 401\n", - "Step= 269, Dmax= 2.0e-02 nm, Epot= -4.50899e+04 Fmax= 1.51428e+02, atom= 401\n", - "Step= 271, Dmax= 1.2e-02 nm, Epot= -4.50936e+04 Fmax= 1.39840e+02, atom= 401\n", - "Step= 272, Dmax= 1.5e-02 nm, Epot= -4.50964e+04 Fmax= 2.34467e+02, atom= 401\n", - "Step= 273, Dmax= 1.8e-02 nm, Epot= -4.51001e+04 Fmax= 2.12492e+02, atom= 401\n", - "Step= 274, Dmax= 2.1e-02 nm, Epot= -4.51013e+04 Fmax= 3.27600e+02, atom= 401\n", - "Step= 275, Dmax= 2.5e-02 nm, Epot= -4.51044e+04 Fmax= 3.28185e+02, atom= 401\n", - "Step= 277, Dmax= 1.5e-02 nm, Epot= -4.51122e+04 Fmax= 5.82710e+01, atom= 1356\n", - "Step= 278, Dmax= 1.8e-02 nm, Epot= -4.51176e+04 Fmax= 4.44603e+02, atom= 401\n", - "Step= 279, Dmax= 2.2e-02 nm, Epot= -4.51267e+04 Fmax= 1.55786e+02, atom= 401\n", - "Step= 281, Dmax= 1.3e-02 nm, Epot= -4.51300e+04 Fmax= 1.53556e+02, atom= 401\n", - "Step= 282, Dmax= 1.6e-02 nm, Epot= -4.51323e+04 Fmax= 2.41408e+02, atom= 401\n", - "Step= 283, Dmax= 1.9e-02 nm, Epot= -4.51355e+04 Fmax= 2.34651e+02, atom= 401\n", - "Step= 284, Dmax= 2.3e-02 nm, Epot= -4.51362e+04 Fmax= 3.36909e+02, atom= 401\n", - "Step= 285, Dmax= 2.7e-02 nm, Epot= -4.51382e+04 Fmax= 3.67313e+02, atom= 401\n", - "Step= 287, Dmax= 1.6e-02 nm, Epot= -4.51473e+04 Fmax= 5.07336e+01, atom= 1356\n", - "Step= 288, Dmax= 2.0e-02 nm, Epot= -4.51541e+04 Fmax= 4.70797e+02, atom= 401\n", - "Step= 289, Dmax= 2.4e-02 nm, Epot= -4.51630e+04 Fmax= 1.77990e+02, atom= 401\n", - "Step= 291, Dmax= 1.4e-02 nm, Epot= -4.51662e+04 Fmax= 1.55265e+02, atom= 401\n", - "Step= 292, Dmax= 1.7e-02 nm, Epot= -4.51677e+04 Fmax= 2.64924e+02, atom= 401\n", - "Step= 293, Dmax= 2.0e-02 nm, Epot= -4.51709e+04 Fmax= 2.44923e+02, atom= 401\n", - "Step= 295, Dmax= 1.2e-02 nm, Epot= -4.51761e+04 Fmax= 5.67225e+01, atom= 401\n", - "Step= 296, Dmax= 1.5e-02 nm, Epot= -4.51807e+04 Fmax= 3.18966e+02, atom= 401\n", - "Step= 297, Dmax= 1.8e-02 nm, Epot= -4.51868e+04 Fmax= 1.26951e+02, atom= 401\n", - "Step= 299, Dmax= 1.1e-02 nm, Epot= -4.51898e+04 Fmax= 1.21747e+02, atom= 401\n", - "Step= 300, Dmax= 1.3e-02 nm, Epot= -4.51922e+04 Fmax= 1.86619e+02, atom= 401\n", - "Step= 301, Dmax= 1.5e-02 nm, Epot= -4.51950e+04 Fmax= 1.89933e+02, atom= 401\n", - "Step= 302, Dmax= 1.8e-02 nm, Epot= -4.51966e+04 Fmax= 2.53997e+02, atom= 401\n", - "Step= 303, Dmax= 2.2e-02 nm, Epot= -4.51982e+04 Fmax= 2.99486e+02, atom= 401\n", - "Step= 304, Dmax= 2.6e-02 nm, Epot= -4.51993e+04 Fmax= 3.39627e+02, atom= 401\n", - "Step= 306, Dmax= 1.6e-02 nm, Epot= -4.52081e+04 Fmax= 6.44718e+01, atom= 732\n", - "Step= 307, Dmax= 1.9e-02 nm, Epot= -4.52102e+04 Fmax= 3.54375e+02, atom= 732\n", - "Step= 308, Dmax= 2.3e-02 nm, Epot= -4.52168e+04 Fmax= 2.67085e+02, atom= 401\n", - "Step= 310, Dmax= 1.4e-02 nm, Epot= -4.52223e+04 Fmax= 7.35888e+01, atom= 401\n", - "Step= 311, Dmax= 1.6e-02 nm, Epot= -4.52252e+04 Fmax= 3.17462e+02, atom= 401\n", - "Step= 312, Dmax= 2.0e-02 nm, Epot= -4.52308e+04 Fmax= 1.48920e+02, atom= 401\n", - "Step= 314, Dmax= 1.2e-02 nm, Epot= -4.52339e+04 Fmax= 1.24568e+02, atom= 401\n", - "Step= 315, Dmax= 1.4e-02 nm, Epot= -4.52356e+04 Fmax= 2.10116e+02, atom= 401\n", - "Step= 316, Dmax= 1.7e-02 nm, Epot= -4.52386e+04 Fmax= 2.07917e+02, atom= 401\n", - "Step= 317, Dmax= 2.0e-02 nm, Epot= -4.52395e+04 Fmax= 2.72514e+02, atom= 401\n", - "Step= 318, Dmax= 2.4e-02 nm, Epot= -4.52402e+04 Fmax= 3.42851e+02, atom= 401\n", - "Step= 319, Dmax= 2.9e-02 nm, Epot= -4.52420e+04 Fmax= 3.49525e+02, atom= 401\n", - "Step= 321, Dmax= 1.8e-02 nm, Epot= -4.52519e+04 Fmax= 9.30597e+01, atom= 732\n", - "Step= 323, Dmax= 1.1e-02 nm, Epot= -4.52552e+04 Fmax= 1.14687e+02, atom= 1356\n", - "Step= 324, Dmax= 1.3e-02 nm, Epot= -4.52573e+04 Fmax= 1.87465e+02, atom= 401\n", - "Step= 325, Dmax= 1.5e-02 nm, Epot= -4.52605e+04 Fmax= 1.65437e+02, atom= 401\n", - "Step= 326, Dmax= 1.8e-02 nm, Epot= -4.52609e+04 Fmax= 2.77895e+02, atom= 401\n", - "Step= 327, Dmax= 2.2e-02 nm, Epot= -4.52649e+04 Fmax= 2.27756e+02, atom= 401\n", - "Step= 329, Dmax= 1.3e-02 nm, Epot= -4.52703e+04 Fmax= 8.33427e+01, atom= 732\n", - "Step= 330, Dmax= 1.6e-02 nm, Epot= -4.52715e+04 Fmax= 2.74829e+02, atom= 732\n", - "Step= 331, Dmax= 1.9e-02 nm, Epot= -4.52768e+04 Fmax= 1.80904e+02, atom= 1356\n", - "Step= 333, Dmax= 1.1e-02 nm, Epot= -4.52807e+04 Fmax= 8.10176e+01, atom= 4016\n", - "Step= 334, Dmax= 1.4e-02 nm, Epot= -4.52828e+04 Fmax= 2.32433e+02, atom= 401\n", - "Step= 335, Dmax= 1.6e-02 nm, Epot= -4.52872e+04 Fmax= 1.43260e+02, atom= 1356\n", - "Step= 337, Dmax= 9.8e-03 nm, Epot= -4.52905e+04 Fmax= 7.93137e+01, atom= 732\n", - "Step= 338, Dmax= 1.2e-02 nm, Epot= -4.52927e+04 Fmax= 1.94381e+02, atom= 1356\n", - "Step= 339, Dmax= 1.4e-02 nm, Epot= -4.52964e+04 Fmax= 1.33096e+02, atom= 1356\n", - "Step= 340, Dmax= 1.7e-02 nm, Epot= -4.52966e+04 Fmax= 2.68275e+02, atom= 1356\n", - "Step= 341, Dmax= 2.0e-02 nm, Epot= -4.53009e+04 Fmax= 2.00702e+02, atom= 1356\n", - "Step= 343, Dmax= 1.2e-02 nm, Epot= -4.53055e+04 Fmax= 7.73948e+01, atom= 401\n", - "Step= 344, Dmax= 1.5e-02 nm, Epot= -4.53070e+04 Fmax= 2.50722e+02, atom= 401\n", - "Step= 345, Dmax= 1.8e-02 nm, Epot= -4.53119e+04 Fmax= 1.53401e+02, atom= 1356\n", - "Step= 347, Dmax= 1.1e-02 nm, Epot= -4.53153e+04 Fmax= 8.46940e+01, atom= 7326\n", - "Step= 348, Dmax= 1.3e-02 nm, Epot= -4.53172e+04 Fmax= 2.01191e+02, atom= 732\n", - "Step= 349, Dmax= 1.5e-02 nm, Epot= -4.53208e+04 Fmax= 1.40161e+02, atom= 1356\n", - "Step= 351, Dmax= 9.1e-03 nm, Epot= -4.53241e+04 Fmax= 5.95074e+01, atom= 401\n", - "Step= 352, Dmax= 1.1e-02 nm, Epot= -4.53266e+04 Fmax= 1.87251e+02, atom= 1356\n", - "Step= 353, Dmax= 1.3e-02 nm, Epot= -4.53306e+04 Fmax= 1.13401e+02, atom= 1356\n", - "Step= 354, Dmax= 1.6e-02 nm, Epot= -4.53308e+04 Fmax= 2.37663e+02, atom= 1356\n", - "Step= 355, Dmax= 1.9e-02 nm, Epot= -4.53347e+04 Fmax= 1.91627e+02, atom= 1356\n", - "Step= 357, Dmax= 1.1e-02 nm, Epot= -4.53392e+04 Fmax= 6.85218e+01, atom= 7326\n", - "Step= 358, Dmax= 1.4e-02 nm, Epot= -4.53414e+04 Fmax= 2.28151e+02, atom= 732\n", - "Step= 359, Dmax= 1.6e-02 nm, Epot= -4.53455e+04 Fmax= 1.32929e+02, atom= 732\n", - "Step= 361, Dmax= 9.8e-03 nm, Epot= -4.53484e+04 Fmax= 7.51858e+01, atom= 732\n", - "Step= 362, Dmax= 1.2e-02 nm, Epot= -4.53500e+04 Fmax= 1.84048e+02, atom= 732\n", - "Step= 363, Dmax= 1.4e-02 nm, Epot= -4.53536e+04 Fmax= 1.32221e+02, atom= 732\n", - "Step= 365, Dmax= 8.4e-03 nm, Epot= -4.53566e+04 Fmax= 5.64467e+01, atom= 732\n", - "Step= 366, Dmax= 1.0e-02 nm, Epot= -4.53593e+04 Fmax= 1.64438e+02, atom= 732\n", - "Step= 367, Dmax= 1.2e-02 nm, Epot= -4.53625e+04 Fmax= 1.01697e+02, atom= 732\n", - "Step= 368, Dmax= 1.5e-02 nm, Epot= -4.53629e+04 Fmax= 2.30214e+02, atom= 732\n", - "Step= 369, Dmax= 1.7e-02 nm, Epot= -4.53669e+04 Fmax= 1.52216e+02, atom= 732\n", - "Step= 371, Dmax= 1.0e-02 nm, Epot= -4.53701e+04 Fmax= 6.64692e+01, atom= 732\n", - "Step= 372, Dmax= 1.3e-02 nm, Epot= -4.53705e+04 Fmax= 2.16511e+02, atom= 732\n", - "Step= 373, Dmax= 1.5e-02 nm, Epot= -4.53755e+04 Fmax= 1.22384e+02, atom= 732\n", - "Step= 375, Dmax= 9.1e-03 nm, Epot= -4.53782e+04 Fmax= 7.43448e+01, atom= 732\n", - "Step= 376, Dmax= 1.1e-02 nm, Epot= -4.53798e+04 Fmax= 1.61537e+02, atom= 732\n", - "Step= 377, Dmax= 1.3e-02 nm, Epot= -4.53827e+04 Fmax= 1.20142e+02, atom= 732\n", - "Step= 379, Dmax= 7.8e-03 nm, Epot= -4.53855e+04 Fmax= 4.46628e+01, atom= 732\n", - "Step= 380, Dmax= 9.4e-03 nm, Epot= -4.53873e+04 Fmax= 1.63830e+02, atom= 732\n", - "Step= 381, Dmax= 1.1e-02 nm, Epot= -4.53914e+04 Fmax= 8.44229e+01, atom= 732\n", - "Step= 383, Dmax= 6.8e-03 nm, Epot= -4.53937e+04 Fmax= 6.03527e+01, atom= 732\n", - "Step= 384, Dmax= 8.1e-03 nm, Epot= -4.53953e+04 Fmax= 1.14338e+02, atom= 732\n", - "Step= 385, Dmax= 9.7e-03 nm, Epot= -4.53976e+04 Fmax= 9.84215e+01, atom= 1264\n", - "Step= 386, Dmax= 1.2e-02 nm, Epot= -4.53977e+04 Fmax= 1.64252e+02, atom= 1264\n", - "Step= 387, Dmax= 1.4e-02 nm, Epot= -4.54000e+04 Fmax= 1.49182e+02, atom= 787\n", - "Step= 389, Dmax= 8.4e-03 nm, Epot= -4.54049e+04 Fmax= 3.60901e+01, atom= 718\n", - "Step= 390, Dmax= 1.0e-02 nm, Epot= -4.54064e+04 Fmax= 1.66410e+02, atom= 718\n", - "Step= 391, Dmax= 1.2e-02 nm, Epot= -4.54110e+04 Fmax= 1.05040e+02, atom= 1264\n", - "Step= 393, Dmax= 7.3e-03 nm, Epot= -4.54139e+04 Fmax= 6.61495e+01, atom= 1156\n", - "Step= 394, Dmax= 8.7e-03 nm, Epot= -4.54148e+04 Fmax= 1.47879e+02, atom= 1156\n", - "Step= 395, Dmax= 1.0e-02 nm, Epot= -4.54178e+04 Fmax= 1.02769e+02, atom= 1156\n", - "Step= 396, Dmax= 1.3e-02 nm, Epot= -4.54180e+04 Fmax= 2.06505e+02, atom= 1156\n", - "Step= 397, Dmax= 1.5e-02 nm, Epot= -4.54212e+04 Fmax= 1.53777e+02, atom= 1156\n", - "Step= 399, Dmax= 9.0e-03 nm, Epot= -4.54244e+04 Fmax= 5.19430e+01, atom= 1156\n", - "Step= 400, Dmax= 1.1e-02 nm, Epot= -4.54263e+04 Fmax= 2.09038e+02, atom= 1156\n", - "Step= 401, Dmax= 1.3e-02 nm, Epot= -4.54300e+04 Fmax= 1.01438e+02, atom= 1156\n", - "Step= 402, Dmax= 1.6e-02 nm, Epot= -4.54301e+04 Fmax= 2.62119e+02, atom= 1156\n", - "Step= 403, Dmax= 1.9e-02 nm, Epot= -4.54338e+04 Fmax= 1.79294e+02, atom= 1156\n", - "Step= 405, Dmax= 1.1e-02 nm, Epot= -4.54364e+04 Fmax= 8.25895e+01, atom= 1156\n", - "Step= 406, Dmax= 1.4e-02 nm, Epot= -4.54373e+04 Fmax= 2.61566e+02, atom= 1156\n", - "Step= 407, Dmax= 1.6e-02 nm, Epot= -4.54407e+04 Fmax= 1.34431e+02, atom= 1156\n", - "Step= 409, Dmax= 9.7e-03 nm, Epot= -4.54428e+04 Fmax= 8.56312e+01, atom= 1156\n", - "Step= 410, Dmax= 1.2e-02 nm, Epot= -4.54443e+04 Fmax= 1.86190e+02, atom= 1156\n", - "Step= 411, Dmax= 1.4e-02 nm, Epot= -4.54467e+04 Fmax= 1.41469e+02, atom= 1156\n", - "Step= 412, Dmax= 1.7e-02 nm, Epot= -4.54473e+04 Fmax= 2.46066e+02, atom= 1156\n", - "Step= 413, Dmax= 2.0e-02 nm, Epot= -4.54496e+04 Fmax= 2.26702e+02, atom= 1156\n", - "Step= 415, Dmax= 1.2e-02 nm, Epot= -4.54528e+04 Fmax= 6.13745e+01, atom= 1066\n", - "Step= 416, Dmax= 1.5e-02 nm, Epot= -4.54545e+04 Fmax= 3.11539e+02, atom= 1156\n", - "Step= 417, Dmax= 1.7e-02 nm, Epot= -4.54584e+04 Fmax= 1.31022e+02, atom= 1156\n", - "Step= 419, Dmax= 1.0e-02 nm, Epot= -4.54604e+04 Fmax= 1.03603e+02, atom= 1156\n", - "Step= 420, Dmax= 1.3e-02 nm, Epot= -4.54619e+04 Fmax= 1.85451e+02, atom= 1156\n", - "Step= 421, Dmax= 1.5e-02 nm, Epot= -4.54640e+04 Fmax= 1.63973e+02, atom= 1156\n", - "Step= 422, Dmax= 1.8e-02 nm, Epot= -4.54647e+04 Fmax= 2.48883e+02, atom= 1156\n", - "Step= 423, Dmax= 2.2e-02 nm, Epot= -4.54666e+04 Fmax= 2.56839e+02, atom= 1156\n", - "Step= 425, Dmax= 1.3e-02 nm, Epot= -4.54703e+04 Fmax= 5.82463e+01, atom= 1066\n", - "Step= 426, Dmax= 1.6e-02 nm, Epot= -4.54726e+04 Fmax= 3.14469e+02, atom= 1156\n", - "Step= 427, Dmax= 1.9e-02 nm, Epot= -4.54763e+04 Fmax= 1.59195e+02, atom= 1156\n", - "Step= 429, Dmax= 1.1e-02 nm, Epot= -4.54786e+04 Fmax= 8.89682e+01, atom= 1156\n", - "Step= 430, Dmax= 1.3e-02 nm, Epot= -4.54799e+04 Fmax= 2.22102e+02, atom= 1156\n", - "Step= 431, Dmax= 1.6e-02 nm, Epot= -4.54828e+04 Fmax= 1.50545e+02, atom= 1156\n", - "Step= 433, Dmax= 9.7e-03 nm, Epot= -4.54849e+04 Fmax= 7.03927e+01, atom= 1156\n", - "Step= 434, Dmax= 1.2e-02 nm, Epot= -4.54869e+04 Fmax= 2.13873e+02, atom= 1156\n", - "Step= 435, Dmax= 1.4e-02 nm, Epot= -4.54895e+04 Fmax= 1.15643e+02, atom= 1156\n", - "Step= 436, Dmax= 1.7e-02 nm, Epot= -4.54900e+04 Fmax= 2.96026e+02, atom= 1156\n", - "Step= 437, Dmax= 2.0e-02 nm, Epot= -4.54933e+04 Fmax= 1.75966e+02, atom= 1156\n", - "Step= 439, Dmax= 1.2e-02 nm, Epot= -4.54960e+04 Fmax= 8.59731e+01, atom= 1156\n", - "Step= 440, Dmax= 1.4e-02 nm, Epot= -4.54972e+04 Fmax= 2.49303e+02, atom= 1156\n", - "Step= 441, Dmax= 1.7e-02 nm, Epot= -4.55007e+04 Fmax= 1.49656e+02, atom= 1156\n", - "Step= 443, Dmax= 1.0e-02 nm, Epot= -4.55029e+04 Fmax= 8.37383e+01, atom= 1156\n", - "Step= 444, Dmax= 1.3e-02 nm, Epot= -4.55046e+04 Fmax= 2.16624e+02, atom= 1156\n", - "Step= 445, Dmax= 1.5e-02 nm, Epot= -4.55072e+04 Fmax= 1.30897e+02, atom= 1156\n", - "Step= 446, Dmax= 1.8e-02 nm, Epot= -4.55076e+04 Fmax= 3.03976e+02, atom= 1156\n", - "Step= 447, Dmax= 2.2e-02 nm, Epot= -4.55108e+04 Fmax= 1.94901e+02, atom= 1156\n", - "Step= 449, Dmax= 1.3e-02 nm, Epot= -4.55139e+04 Fmax= 8.18339e+01, atom= 1156\n", - "Step= 450, Dmax= 1.6e-02 nm, Epot= -4.55150e+04 Fmax= 2.81635e+02, atom= 1156\n", - "Step= 451, Dmax= 1.9e-02 nm, Epot= -4.55191e+04 Fmax= 1.46740e+02, atom= 1156\n", - "Step= 453, Dmax= 1.1e-02 nm, Epot= -4.55213e+04 Fmax= 9.88467e+01, atom= 1156\n", - "Step= 454, Dmax= 1.3e-02 nm, Epot= -4.55229e+04 Fmax= 2.17986e+02, atom= 1156\n", - "Step= 455, Dmax= 1.6e-02 nm, Epot= -4.55255e+04 Fmax= 1.48312e+02, atom= 1156\n", - "Step= 456, Dmax= 1.9e-02 nm, Epot= -4.55257e+04 Fmax= 3.11856e+02, atom= 1156\n", - "Step= 457, Dmax= 2.3e-02 nm, Epot= -4.55288e+04 Fmax= 2.14631e+02, atom= 1156\n", - "Step= 459, Dmax= 1.4e-02 nm, Epot= -4.55323e+04 Fmax= 7.71938e+01, atom= 1156\n", - "Step= 460, Dmax= 1.7e-02 nm, Epot= -4.55330e+04 Fmax= 3.21334e+02, atom= 1156\n", - "Step= 461, Dmax= 2.0e-02 nm, Epot= -4.55381e+04 Fmax= 1.41615e+02, atom= 1156\n", - "Step= 463, Dmax= 1.2e-02 nm, Epot= -4.55403e+04 Fmax= 1.15698e+02, atom= 1156\n", - "Step= 464, Dmax= 1.4e-02 nm, Epot= -4.55418e+04 Fmax= 2.17832e+02, atom= 1156\n", - "Step= 465, Dmax= 1.7e-02 nm, Epot= -4.55442e+04 Fmax= 1.67154e+02, atom= 1156\n", - "Step= 466, Dmax= 2.1e-02 nm, Epot= -4.55444e+04 Fmax= 3.17514e+02, atom= 1156\n", - "Step= 467, Dmax= 2.5e-02 nm, Epot= -4.55473e+04 Fmax= 2.36436e+02, atom= 1156\n", - "Step= 469, Dmax= 1.5e-02 nm, Epot= -4.55513e+04 Fmax= 7.12272e+01, atom= 1156\n", - "Step= 470, Dmax= 1.8e-02 nm, Epot= -4.55515e+04 Fmax= 3.70785e+02, atom= 1156\n", - "Step= 471, Dmax= 2.2e-02 nm, Epot= -4.55580e+04 Fmax= 1.35358e+02, atom= 1156\n", - "Step= 473, Dmax= 1.3e-02 nm, Epot= -4.55602e+04 Fmax= 1.33076e+02, atom= 1156\n", - "Step= 474, Dmax= 1.6e-02 nm, Epot= -4.55617e+04 Fmax= 2.16578e+02, atom= 1156\n", - "Step= 475, Dmax= 1.9e-02 nm, Epot= -4.55639e+04 Fmax= 1.86607e+02, atom= 1156\n", - "Step= 476, Dmax= 2.2e-02 nm, Epot= -4.55641e+04 Fmax= 3.24494e+02, atom= 1156\n", - "Step= 477, Dmax= 2.7e-02 nm, Epot= -4.55667e+04 Fmax= 2.59519e+02, atom= 1156\n", - "Step= 479, Dmax= 1.6e-02 nm, Epot= -4.55715e+04 Fmax= 6.55095e+01, atom= 1156\n", - "Step= 481, Dmax= 9.7e-03 nm, Epot= -4.55741e+04 Fmax= 1.50405e+02, atom= 1156\n", - "Step= 482, Dmax= 1.2e-02 nm, Epot= -4.55766e+04 Fmax= 1.03609e+02, atom= 1156\n", - "Step= 483, Dmax= 1.4e-02 nm, Epot= -4.55781e+04 Fmax= 1.92464e+02, atom= 1156\n", - "Step= 484, Dmax= 1.7e-02 nm, Epot= -4.55806e+04 Fmax= 1.70362e+02, atom= 1156\n", - "Step= 485, Dmax= 2.0e-02 nm, Epot= -4.55808e+04 Fmax= 2.57242e+02, atom= 1156\n", - "Step= 486, Dmax= 2.4e-02 nm, Epot= -4.55825e+04 Fmax= 2.66114e+02, atom= 1156\n", - "Step= 488, Dmax= 1.4e-02 nm, Epot= -4.55879e+04 Fmax= 6.06032e+01, atom= 1066\n", - "Step= 489, Dmax= 1.7e-02 nm, Epot= -4.55881e+04 Fmax= 3.13496e+02, atom= 1156\n", - "Step= 490, Dmax= 2.1e-02 nm, Epot= -4.55935e+04 Fmax= 1.78824e+02, atom= 1156\n", - "Step= 492, Dmax= 1.2e-02 nm, Epot= -4.55970e+04 Fmax= 8.06860e+01, atom= 1129\n", - "Step= 494, Dmax= 7.5e-03 nm, Epot= -4.55990e+04 Fmax= 9.39491e+01, atom= 1129\n", - "Step= 495, Dmax= 9.0e-03 nm, Epot= -4.56008e+04 Fmax= 1.15327e+02, atom= 1129\n", - "Step= 496, Dmax= 1.1e-02 nm, Epot= -4.56026e+04 Fmax= 1.33503e+02, atom= 1129\n", - "Step= 497, Dmax= 1.3e-02 nm, Epot= -4.56041e+04 Fmax= 1.68267e+02, atom= 1129\n", - "Step= 498, Dmax= 1.6e-02 nm, Epot= -4.56056e+04 Fmax= 1.89476e+02, atom= 1129\n", - "Step= 499, Dmax= 1.9e-02 nm, Epot= -4.56064e+04 Fmax= 2.45543e+02, atom= 1129\n", - "Step= 500, Dmax= 2.2e-02 nm, Epot= -4.56076e+04 Fmax= 2.67980e+02, atom= 1129\n", - "Step= 502, Dmax= 1.3e-02 nm, Epot= -4.56126e+04 Fmax= 4.69913e+01, atom= 9499\n", - "Step= 503, Dmax= 1.6e-02 nm, Epot= -4.56147e+04 Fmax= 3.20608e+02, atom= 949\n", - "Step= 504, Dmax= 1.9e-02 nm, Epot= -4.56193e+04 Fmax= 1.80850e+02, atom= 1129\n", - "Step= 506, Dmax= 1.2e-02 nm, Epot= -4.56217e+04 Fmax= 7.40528e+01, atom= 1129\n", - "Step= 507, Dmax= 1.4e-02 nm, Epot= -4.56220e+04 Fmax= 2.82158e+02, atom= 1129\n", - "Step= 508, Dmax= 1.7e-02 nm, Epot= -4.56260e+04 Fmax= 1.16116e+02, atom= 1129\n", - "Step= 510, Dmax= 1.0e-02 nm, Epot= -4.56277e+04 Fmax= 1.03945e+02, atom= 1129\n", - "Step= 511, Dmax= 1.2e-02 nm, Epot= -4.56289e+04 Fmax= 1.71334e+02, atom= 1129\n", - "Step= 512, Dmax= 1.4e-02 nm, Epot= -4.56306e+04 Fmax= 1.61667e+02, atom= 1129\n", - "Step= 513, Dmax= 1.7e-02 nm, Epot= -4.56310e+04 Fmax= 2.34953e+02, atom= 1129\n", - "Step= 514, Dmax= 2.1e-02 nm, Epot= -4.56324e+04 Fmax= 2.43803e+02, atom= 1129\n", - "Step= 516, Dmax= 1.2e-02 nm, Epot= -4.56362e+04 Fmax= 4.91039e+01, atom= 1287\n", - "Step= 517, Dmax= 1.5e-02 nm, Epot= -4.56380e+04 Fmax= 3.06609e+02, atom= 1129\n", - "Step= 518, Dmax= 1.8e-02 nm, Epot= -4.56418e+04 Fmax= 1.35994e+02, atom= 1129\n", - "Step= 520, Dmax= 1.1e-02 nm, Epot= -4.56436e+04 Fmax= 9.97900e+01, atom= 1129\n", - "Step= 521, Dmax= 1.3e-02 nm, Epot= -4.56442e+04 Fmax= 1.97176e+02, atom= 1129\n", - "Step= 522, Dmax= 1.6e-02 nm, Epot= -4.56463e+04 Fmax= 1.58407e+02, atom= 1129\n", - "Step= 524, Dmax= 9.3e-03 nm, Epot= -4.56484e+04 Fmax= 5.35071e+01, atom= 1129\n", - "Step= 525, Dmax= 1.1e-02 nm, Epot= -4.56500e+04 Fmax= 2.12661e+02, atom= 1129\n", - "Step= 526, Dmax= 1.3e-02 nm, Epot= -4.56525e+04 Fmax= 9.93462e+01, atom= 1129\n", - "Step= 528, Dmax= 8.0e-03 nm, Epot= -4.56540e+04 Fmax= 7.90839e+01, atom= 1129\n", - "Step= 529, Dmax= 9.6e-03 nm, Epot= -4.56553e+04 Fmax= 1.39025e+02, atom= 1129\n", - "Step= 530, Dmax= 1.2e-02 nm, Epot= -4.56568e+04 Fmax= 1.25581e+02, atom= 1129\n", - "Step= 531, Dmax= 1.4e-02 nm, Epot= -4.56576e+04 Fmax= 1.88156e+02, atom= 1129\n", - "Step= 532, Dmax= 1.7e-02 nm, Epot= -4.56589e+04 Fmax= 1.92519e+02, atom= 1129\n", - "Step= 533, Dmax= 2.0e-02 nm, Epot= -4.56589e+04 Fmax= 2.58456e+02, atom= 1129\n", - "Step= 534, Dmax= 2.4e-02 nm, Epot= -4.56596e+04 Fmax= 2.89339e+02, atom= 1129\n", - "Step= 536, Dmax= 1.4e-02 nm, Epot= -4.56646e+04 Fmax= 5.21205e+01, atom= 1287\n", - "Step= 537, Dmax= 1.7e-02 nm, Epot= -4.56658e+04 Fmax= 3.31745e+02, atom= 1287\n", - "Step= 538, Dmax= 2.1e-02 nm, Epot= -4.56694e+04 Fmax= 1.70816e+02, atom= 1129\n", - "Step= 540, Dmax= 1.2e-02 nm, Epot= -4.56715e+04 Fmax= 9.49721e+01, atom= 1129\n", - "Step= 542, Dmax= 7.5e-03 nm, Epot= -4.56730e+04 Fmax= 7.46838e+01, atom= 1129\n", - "Step= 543, Dmax= 9.0e-03 nm, Epot= -4.56743e+04 Fmax= 1.26244e+02, atom= 1129\n", - "Step= 544, Dmax= 1.1e-02 nm, Epot= -4.56757e+04 Fmax= 1.13140e+02, atom= 1129\n", - "Step= 545, Dmax= 1.3e-02 nm, Epot= -4.56765e+04 Fmax= 1.79888e+02, atom= 1129\n", - "Step= 546, Dmax= 1.5e-02 nm, Epot= -4.56780e+04 Fmax= 1.64443e+02, atom= 1129\n", - "Step= 548, Dmax= 9.3e-03 nm, Epot= -4.56802e+04 Fmax= 3.81567e+01, atom= 1129\n", - "Step= 549, Dmax= 1.1e-02 nm, Epot= -4.56819e+04 Fmax= 2.28315e+02, atom= 1129\n", - "Step= 550, Dmax= 1.3e-02 nm, Epot= -4.56853e+04 Fmax= 8.72442e+01, atom= 1129\n", - "Step= 552, Dmax= 8.0e-03 nm, Epot= -4.56866e+04 Fmax= 8.59273e+01, atom= 1129\n", - "Step= 553, Dmax= 9.6e-03 nm, Epot= -4.56878e+04 Fmax= 1.30850e+02, atom= 1129\n", - "Step= 554, Dmax= 1.2e-02 nm, Epot= -4.56892e+04 Fmax= 1.23501e+02, atom= 1129\n", - "Step= 555, Dmax= 1.4e-02 nm, Epot= -4.56898e+04 Fmax= 1.89320e+02, atom= 1129\n", - "Step= 556, Dmax= 1.7e-02 nm, Epot= -4.56912e+04 Fmax= 1.77067e+02, atom= 1129\n", - "Step= 558, Dmax= 1.0e-02 nm, Epot= -4.56938e+04 Fmax= 3.85959e+01, atom= 1129\n", - "Step= 559, Dmax= 1.2e-02 nm, Epot= -4.56948e+04 Fmax= 2.50446e+02, atom= 1129\n", - "Step= 560, Dmax= 1.4e-02 nm, Epot= -4.56990e+04 Fmax= 8.93189e+01, atom= 1129\n", - "Step= 562, Dmax= 8.6e-03 nm, Epot= -4.57003e+04 Fmax= 9.35923e+01, atom= 1129\n", - "Step= 563, Dmax= 1.0e-02 nm, Epot= -4.57014e+04 Fmax= 1.36115e+02, atom= 1129\n", - "Step= 564, Dmax= 1.2e-02 nm, Epot= -4.57026e+04 Fmax= 1.34002e+02, atom= 1129\n", - "Step= 565, Dmax= 1.5e-02 nm, Epot= -4.57029e+04 Fmax= 1.97913e+02, atom= 1129\n", - "Step= 566, Dmax= 1.8e-02 nm, Epot= -4.57041e+04 Fmax= 1.91189e+02, atom= 1129\n", - "Step= 568, Dmax= 1.1e-02 nm, Epot= -4.57075e+04 Fmax= 3.80733e+01, atom= 9499\n", - "Step= 570, Dmax= 6.4e-03 nm, Epot= -4.57090e+04 Fmax= 1.05286e+02, atom= 1129\n", - "Step= 571, Dmax= 7.7e-03 nm, Epot= -4.57107e+04 Fmax= 6.82824e+01, atom= 1129\n", - "Step= 572, Dmax= 9.3e-03 nm, Epot= -4.57111e+04 Fmax= 1.30810e+02, atom= 1129\n", - "Step= 573, Dmax= 1.1e-02 nm, Epot= -4.57126e+04 Fmax= 1.24592e+02, atom= 626\n", - "Step= 575, Dmax= 6.7e-03 nm, Epot= -4.57151e+04 Fmax= 2.88645e+01, atom= 626\n", - "Step= 576, Dmax= 8.0e-03 nm, Epot= -4.57165e+04 Fmax= 1.74019e+02, atom= 626\n", - "Step= 577, Dmax= 9.6e-03 nm, Epot= -4.57198e+04 Fmax= 5.87299e+01, atom= 626\n", - "Step= 579, Dmax= 5.8e-03 nm, Epot= -4.57210e+04 Fmax= 7.44324e+01, atom= 626\n", - "Step= 580, Dmax= 6.9e-03 nm, Epot= -4.57222e+04 Fmax= 8.57592e+01, atom= 626\n", - "Step= 581, Dmax= 8.3e-03 nm, Epot= -4.57233e+04 Fmax= 1.07498e+02, atom= 626\n", - "Step= 582, Dmax= 1.0e-02 nm, Epot= -4.57243e+04 Fmax= 1.24789e+02, atom= 626\n", - "Step= 583, Dmax= 1.2e-02 nm, Epot= -4.57251e+04 Fmax= 1.53355e+02, atom= 626\n", - "Step= 584, Dmax= 1.4e-02 nm, Epot= -4.57257e+04 Fmax= 1.83535e+02, atom= 626\n", - "Step= 585, Dmax= 1.7e-02 nm, Epot= -4.57261e+04 Fmax= 2.16522e+02, atom= 626\n", - "Step= 587, Dmax= 1.0e-02 nm, Epot= -4.57302e+04 Fmax= 3.34683e+01, atom= 111\n", - "Step= 588, Dmax= 1.2e-02 nm, Epot= -4.57319e+04 Fmax= 2.23706e+02, atom= 626\n", - "Step= 589, Dmax= 1.5e-02 nm, Epot= -4.57349e+04 Fmax= 1.57227e+02, atom= 626\n", - "Step= 591, Dmax= 8.9e-03 nm, Epot= -4.57371e+04 Fmax= 4.69325e+01, atom= 339\n", - "Step= 592, Dmax= 1.1e-02 nm, Epot= -4.57375e+04 Fmax= 2.13229e+02, atom= 626\n", - "Step= 593, Dmax= 1.3e-02 nm, Epot= -4.57408e+04 Fmax= 9.23533e+01, atom= 626\n", - "Step= 595, Dmax= 7.7e-03 nm, Epot= -4.57420e+04 Fmax= 7.89265e+01, atom= 626\n", - "Step= 596, Dmax= 9.3e-03 nm, Epot= -4.57428e+04 Fmax= 1.38552e+02, atom= 626\n", - "Step= 597, Dmax= 1.1e-02 nm, Epot= -4.57442e+04 Fmax= 1.20676e+02, atom= 626\n", - "Step= 598, Dmax= 1.3e-02 nm, Epot= -4.57443e+04 Fmax= 1.90618e+02, atom= 626\n", - "Step= 599, Dmax= 1.6e-02 nm, Epot= -4.57455e+04 Fmax= 1.85581e+02, atom= 626\n", - "Step= 601, Dmax= 9.6e-03 nm, Epot= -4.57485e+04 Fmax= 3.84797e+01, atom= 339\n", - "Step= 602, Dmax= 1.2e-02 nm, Epot= -4.57498e+04 Fmax= 2.27593e+02, atom= 626\n", - "Step= 603, Dmax= 1.4e-02 nm, Epot= -4.57530e+04 Fmax= 1.00841e+02, atom= 626\n", - "Step= 605, Dmax= 8.3e-03 nm, Epot= -4.57542e+04 Fmax= 8.62654e+01, atom= 626\n", - "Step= 606, Dmax= 1.0e-02 nm, Epot= -4.57549e+04 Fmax= 1.46401e+02, atom= 626\n", - "Step= 607, Dmax= 1.2e-02 nm, Epot= -4.57562e+04 Fmax= 1.32638e+02, atom= 626\n", - "Step= 608, Dmax= 1.4e-02 nm, Epot= -4.57563e+04 Fmax= 2.01107e+02, atom= 626\n", - "Step= 609, Dmax= 1.7e-02 nm, Epot= -4.57573e+04 Fmax= 2.04194e+02, atom= 626\n", - "Step= 611, Dmax= 1.0e-02 nm, Epot= -4.57607e+04 Fmax= 3.78875e+01, atom= 339\n", - "Step= 612, Dmax= 1.2e-02 nm, Epot= -4.57621e+04 Fmax= 2.42805e+02, atom= 626\n", - "Step= 613, Dmax= 1.5e-02 nm, Epot= -4.57653e+04 Fmax= 1.11611e+02, atom= 626\n", - "Step= 615, Dmax= 8.9e-03 nm, Epot= -4.57666e+04 Fmax= 8.98677e+01, atom= 626\n", - "Step= 616, Dmax= 1.1e-02 nm, Epot= -4.57671e+04 Fmax= 1.60285e+02, atom= 626\n", - "Step= 617, Dmax= 1.3e-02 nm, Epot= -4.57685e+04 Fmax= 1.40252e+02, atom= 626\n", - "Step= 619, Dmax= 7.7e-03 nm, Epot= -4.57705e+04 Fmax= 3.85007e+01, atom= 626\n", - "Step= 620, Dmax= 9.2e-03 nm, Epot= -4.57720e+04 Fmax= 1.75561e+02, atom= 626\n", - "Step= 621, Dmax= 1.1e-02 nm, Epot= -4.57742e+04 Fmax= 8.31898e+01, atom= 626\n", - "Step= 623, Dmax= 6.7e-03 nm, Epot= -4.57754e+04 Fmax= 6.76687e+01, atom= 626\n", - "Step= 624, Dmax= 8.0e-03 nm, Epot= -4.57764e+04 Fmax= 1.18686e+02, atom= 626\n", - "Step= 625, Dmax= 9.6e-03 nm, Epot= -4.57776e+04 Fmax= 1.04747e+02, atom= 626\n", - "Step= 626, Dmax= 1.2e-02 nm, Epot= -4.57781e+04 Fmax= 1.62329e+02, atom= 626\n", - "Step= 627, Dmax= 1.4e-02 nm, Epot= -4.57792e+04 Fmax= 1.61684e+02, atom= 626\n", - "Step= 629, Dmax= 8.3e-03 nm, Epot= -4.57815e+04 Fmax= 3.11100e+01, atom= 626\n", - "Step= 630, Dmax= 9.9e-03 nm, Epot= -4.57835e+04 Fmax= 2.00061e+02, atom= 626\n", - "Step= 631, Dmax= 1.2e-02 nm, Epot= -4.57861e+04 Fmax= 8.06966e+01, atom= 626\n", - "Step= 633, Dmax= 7.2e-03 nm, Epot= -4.57872e+04 Fmax= 8.20879e+01, atom= 626\n", - "Step= 634, Dmax= 8.6e-03 nm, Epot= -4.57881e+04 Fmax= 1.16511e+02, atom= 626\n", - "Step= 635, Dmax= 1.0e-02 nm, Epot= -4.57891e+04 Fmax= 1.23377e+02, atom= 626\n", - "Step= 636, Dmax= 1.2e-02 nm, Epot= -4.57897e+04 Fmax= 1.62122e+02, atom= 626\n", - "Step= 637, Dmax= 1.5e-02 nm, Epot= -4.57903e+04 Fmax= 1.86355e+02, atom= 626\n", - "Step= 638, Dmax= 1.8e-02 nm, Epot= -4.57905e+04 Fmax= 2.24158e+02, atom= 626\n", - "Step= 640, Dmax= 1.1e-02 nm, Epot= -4.57942e+04 Fmax= 3.34035e+01, atom= 111\n", - "Step= 641, Dmax= 1.3e-02 nm, Epot= -4.57957e+04 Fmax= 2.23691e+02, atom= 626\n", - "Step= 642, Dmax= 1.5e-02 nm, Epot= -4.57982e+04 Fmax= 1.73777e+02, atom= 626\n", - "Step= 644, Dmax= 9.2e-03 nm, Epot= -4.58004e+04 Fmax= 4.01915e+01, atom= 339\n", - "Step= 645, Dmax= 1.1e-02 nm, Epot= -4.58010e+04 Fmax= 2.16701e+02, atom= 626\n", - "Step= 646, Dmax= 1.3e-02 nm, Epot= -4.58039e+04 Fmax= 9.80511e+01, atom= 626\n", - "Step= 648, Dmax= 8.0e-03 nm, Epot= -4.58050e+04 Fmax= 7.75466e+01, atom= 626\n", - "Step= 649, Dmax= 9.6e-03 nm, Epot= -4.58056e+04 Fmax= 1.45271e+02, atom= 626\n", - "Step= 650, Dmax= 1.1e-02 nm, Epot= -4.58069e+04 Fmax= 1.21950e+02, atom= 626\n", - "Step= 652, Dmax= 6.9e-03 nm, Epot= -4.58084e+04 Fmax= 3.68743e+01, atom= 626\n", - "Step= 653, Dmax= 8.3e-03 nm, Epot= -4.58097e+04 Fmax= 1.53413e+02, atom= 626\n", - "Step= 654, Dmax= 9.9e-03 nm, Epot= -4.58115e+04 Fmax= 7.53789e+01, atom= 626\n", - "Step= 656, Dmax= 6.0e-03 nm, Epot= -4.58125e+04 Fmax= 5.92159e+01, atom= 626\n", - "Step= 657, Dmax= 7.1e-03 nm, Epot= -4.58134e+04 Fmax= 1.05945e+02, atom= 626\n", - "Step= 658, Dmax= 8.6e-03 nm, Epot= -4.58144e+04 Fmax= 9.28509e+01, atom= 626\n", - "Step= 659, Dmax= 1.0e-02 nm, Epot= -4.58149e+04 Fmax= 1.43778e+02, atom= 626\n", - "Step= 660, Dmax= 1.2e-02 nm, Epot= -4.58158e+04 Fmax= 1.44076e+02, atom= 626\n", - "Step= 661, Dmax= 1.5e-02 nm, Epot= -4.58159e+04 Fmax= 1.96017e+02, atom= 626\n", - "Step= 662, Dmax= 1.8e-02 nm, Epot= -4.58162e+04 Fmax= 2.21198e+02, atom= 626\n", - "Step= 664, Dmax= 1.1e-02 nm, Epot= -4.58197e+04 Fmax= 2.86682e+01, atom= 339\n", - "Step= 665, Dmax= 1.3e-02 nm, Epot= -4.58216e+04 Fmax= 2.46250e+02, atom= 339\n", - "Step= 666, Dmax= 1.5e-02 nm, Epot= -4.58244e+04 Fmax= 1.17483e+02, atom= 626\n", - "Step= 668, Dmax= 9.2e-03 nm, Epot= -4.58255e+04 Fmax= 9.35294e+01, atom= 626\n", - "Step= 669, Dmax= 1.1e-02 nm, Epot= -4.58257e+04 Fmax= 1.60133e+02, atom= 626\n", - "Step= 670, Dmax= 1.3e-02 nm, Epot= -4.58268e+04 Fmax= 1.47075e+02, atom= 626\n", - "Step= 672, Dmax= 8.0e-03 nm, Epot= -4.58286e+04 Fmax= 3.48702e+01, atom= 626\n", - "Step= 673, Dmax= 9.6e-03 nm, Epot= -4.58296e+04 Fmax= 1.84975e+02, atom= 626\n", - "Step= 674, Dmax= 1.1e-02 nm, Epot= -4.58317e+04 Fmax= 7.91715e+01, atom= 626\n", - "Step= 676, Dmax= 6.9e-03 nm, Epot= -4.58326e+04 Fmax= 7.54126e+01, atom= 626\n", - "Step= 677, Dmax= 8.3e-03 nm, Epot= -4.58332e+04 Fmax= 1.13053e+02, atom= 626\n", - "Step= 678, Dmax= 9.9e-03 nm, Epot= -4.58341e+04 Fmax= 1.13923e+02, atom= 626\n", - "Step= 679, Dmax= 1.2e-02 nm, Epot= -4.58344e+04 Fmax= 1.56866e+02, atom= 626\n", - "Step= 680, Dmax= 1.4e-02 nm, Epot= -4.58349e+04 Fmax= 1.73781e+02, atom= 626\n", - "Step= 682, Dmax= 8.6e-03 nm, Epot= -4.58373e+04 Fmax= 2.43104e+01, atom= 339\n", - "Step= 683, Dmax= 1.0e-02 nm, Epot= -4.58392e+04 Fmax= 1.98552e+02, atom= 626\n", - "Step= 684, Dmax= 1.2e-02 nm, Epot= -4.58414e+04 Fmax= 8.76776e+01, atom= 626\n", - "Step= 686, Dmax= 7.4e-03 nm, Epot= -4.58423e+04 Fmax= 7.96636e+01, atom= 626\n", - "Step= 687, Dmax= 8.9e-03 nm, Epot= -4.58428e+04 Fmax= 1.22100e+02, atom= 626\n", - "Step= 688, Dmax= 1.1e-02 nm, Epot= -4.58436e+04 Fmax= 1.22873e+02, atom= 626\n", - "Step= 689, Dmax= 1.3e-02 nm, Epot= -4.58437e+04 Fmax= 1.67119e+02, atom= 626\n", - "Step= 690, Dmax= 1.5e-02 nm, Epot= -4.58441e+04 Fmax= 1.88465e+02, atom= 626\n", - "Step= 692, Dmax= 9.2e-03 nm, Epot= -4.58468e+04 Fmax= 2.43464e+01, atom= 339\n", - "Step= 693, Dmax= 1.1e-02 nm, Epot= -4.58485e+04 Fmax= 2.13060e+02, atom= 626\n", - "Step= 694, Dmax= 1.3e-02 nm, Epot= -4.58508e+04 Fmax= 9.51410e+01, atom= 626\n", - "Step= 696, Dmax= 7.9e-03 nm, Epot= -4.58517e+04 Fmax= 8.46092e+01, atom= 626\n", - "Step= 697, Dmax= 9.5e-03 nm, Epot= -4.58520e+04 Fmax= 1.31069e+02, atom= 626\n", - "Step= 698, Dmax= 1.1e-02 nm, Epot= -4.58527e+04 Fmax= 1.31274e+02, atom= 626\n", - "Step= 700, Dmax= 6.9e-03 nm, Epot= -4.58543e+04 Fmax= 2.45783e+01, atom= 626\n", - "Step= 701, Dmax= 8.2e-03 nm, Epot= -4.58556e+04 Fmax= 1.62084e+02, atom= 626\n", - "Step= 702, Dmax= 9.9e-03 nm, Epot= -4.58574e+04 Fmax= 6.35204e+01, atom= 626\n", - "Step= 704, Dmax= 5.9e-03 nm, Epot= -4.58581e+04 Fmax= 6.93124e+01, atom= 626\n", - "Step= 705, Dmax= 7.1e-03 nm, Epot= -4.58587e+04 Fmax= 9.09135e+01, atom= 626\n", - "Step= 706, Dmax= 8.5e-03 nm, Epot= -4.58593e+04 Fmax= 1.03836e+02, atom= 626\n", - "Step= 707, Dmax= 1.0e-02 nm, Epot= -4.58597e+04 Fmax= 1.26700e+02, atom= 626\n", - "Step= 708, Dmax= 1.2e-02 nm, Epot= -4.58600e+04 Fmax= 1.55535e+02, atom= 626\n", - "Step= 709, Dmax= 1.5e-02 nm, Epot= -4.58602e+04 Fmax= 1.76519e+02, atom= 626\n", - "Step= 711, Dmax= 8.9e-03 nm, Epot= -4.58627e+04 Fmax= 2.80137e+01, atom= 111\n", - "Step= 713, Dmax= 5.3e-03 nm, Epot= -4.58637e+04 Fmax= 8.28236e+01, atom= 626\n", - "Step= 714, Dmax= 6.4e-03 nm, Epot= -4.58646e+04 Fmax= 6.59385e+01, atom= 626\n", - "Step= 715, Dmax= 7.7e-03 nm, Epot= -4.58648e+04 Fmax= 1.04491e+02, atom= 626\n", - "Step= 716, Dmax= 9.2e-03 nm, Epot= -4.58654e+04 Fmax= 1.04483e+02, atom= 626\n", - "Step= 718, Dmax= 5.5e-03 nm, Epot= -4.58669e+04 Fmax= 2.96837e+01, atom= 696\n", - "Step= 719, Dmax= 6.6e-03 nm, Epot= -4.58676e+04 Fmax= 1.36893e+02, atom= 696\n", - "Step= 720, Dmax= 7.9e-03 nm, Epot= -4.58690e+04 Fmax= 5.98559e+01, atom= 696\n", - "Step= 722, Dmax= 4.8e-03 nm, Epot= -4.58696e+04 Fmax= 5.55559e+01, atom= 696\n", - "Step= 723, Dmax= 5.7e-03 nm, Epot= -4.58703e+04 Fmax= 8.28382e+01, atom= 696\n", - "Step= 724, Dmax= 6.9e-03 nm, Epot= -4.58709e+04 Fmax= 8.51594e+01, atom= 696\n", - "Step= 725, Dmax= 8.2e-03 nm, Epot= -4.58714e+04 Fmax= 1.14127e+02, atom= 696\n", - "Step= 726, Dmax= 9.9e-03 nm, Epot= -4.58719e+04 Fmax= 1.27865e+02, atom= 696\n", - "Step= 727, Dmax= 1.2e-02 nm, Epot= -4.58722e+04 Fmax= 1.58770e+02, atom= 696\n", - "Step= 728, Dmax= 1.4e-02 nm, Epot= -4.58725e+04 Fmax= 1.91316e+02, atom= 696\n", - "Step= 730, Dmax= 8.5e-03 nm, Epot= -4.58743e+04 Fmax= 2.53731e+01, atom= 191\n", - "Step= 731, Dmax= 1.0e-02 nm, Epot= -4.58754e+04 Fmax= 2.27614e+02, atom= 696\n", - "Step= 732, Dmax= 1.2e-02 nm, Epot= -4.58774e+04 Fmax= 9.43082e+01, atom= 696\n", - "Step= 734, Dmax= 7.4e-03 nm, Epot= -4.58781e+04 Fmax= 8.37465e+01, atom= 696\n", - "Step= 735, Dmax= 8.8e-03 nm, Epot= -4.58784e+04 Fmax= 1.30938e+02, atom= 696\n", - "Step= 736, Dmax= 1.1e-02 nm, Epot= -4.58791e+04 Fmax= 1.29128e+02, atom= 696\n", - "Step= 737, Dmax= 1.3e-02 nm, Epot= -4.58791e+04 Fmax= 1.79510e+02, atom= 696\n", - "Step= 738, Dmax= 1.5e-02 nm, Epot= -4.58796e+04 Fmax= 1.96587e+02, atom= 696\n", - "Step= 740, Dmax= 9.2e-03 nm, Epot= -4.58815e+04 Fmax= 3.34952e+01, atom= 696\n", - "Step= 741, Dmax= 1.1e-02 nm, Epot= -4.58815e+04 Fmax= 2.61026e+02, atom= 696\n", - "Step= 742, Dmax= 1.3e-02 nm, Epot= -4.58840e+04 Fmax= 8.84561e+01, atom= 696\n", - "Step= 744, Dmax= 7.9e-03 nm, Epot= -4.58846e+04 Fmax= 1.03517e+02, atom= 696\n", - "Step= 745, Dmax= 9.5e-03 nm, Epot= -4.58850e+04 Fmax= 1.27714e+02, atom= 696\n", - "Step= 746, Dmax= 1.1e-02 nm, Epot= -4.58855e+04 Fmax= 1.53982e+02, atom= 696\n", - "Step= 747, Dmax= 1.4e-02 nm, Epot= -4.58857e+04 Fmax= 1.79021e+02, atom= 696\n", - "Step= 749, Dmax= 8.2e-03 nm, Epot= -4.58875e+04 Fmax= 1.68681e+01, atom= 696\n", - "Step= 750, Dmax= 9.9e-03 nm, Epot= -4.58890e+04 Fmax= 2.55762e+02, atom= 696\n", - "Step= 751, Dmax= 1.2e-02 nm, Epot= -4.58921e+04 Fmax= 6.30489e+01, atom= 696\n", - "Step= 753, Dmax= 7.1e-03 nm, Epot= -4.58928e+04 Fmax= 9.88373e+01, atom= 696\n", - "Step= 754, Dmax= 8.5e-03 nm, Epot= -4.58934e+04 Fmax= 1.09249e+02, atom= 696\n", - "Step= 755, Dmax= 1.0e-02 nm, Epot= -4.58937e+04 Fmax= 1.39228e+02, atom= 696\n", - "Step= 756, Dmax= 1.2e-02 nm, Epot= -4.58941e+04 Fmax= 1.64990e+02, atom= 696\n", - "Step= 757, Dmax= 1.5e-02 nm, Epot= -4.58942e+04 Fmax= 1.93183e+02, atom= 696\n", - "Step= 759, Dmax= 8.8e-03 nm, Epot= -4.58963e+04 Fmax= 1.79444e+01, atom= 1511\n", - "Step= 760, Dmax= 1.1e-02 nm, Epot= -4.58975e+04 Fmax= 2.75260e+02, atom= 696\n", - "Step= 761, Dmax= 1.3e-02 nm, Epot= -4.59011e+04 Fmax= 7.16349e+01, atom= 696\n", - "Step= 763, Dmax= 7.6e-03 nm, Epot= -4.59017e+04 Fmax= 1.01123e+02, atom= 696\n", - "Step= 764, Dmax= 9.2e-03 nm, Epot= -4.59022e+04 Fmax= 1.24428e+02, atom= 696\n", - "Step= 765, Dmax= 1.1e-02 nm, Epot= -4.59026e+04 Fmax= 1.42586e+02, atom= 696\n", - "Step= 766, Dmax= 1.3e-02 nm, Epot= -4.59029e+04 Fmax= 1.86544e+02, atom= 696\n", - "Step= 767, Dmax= 1.6e-02 nm, Epot= -4.59032e+04 Fmax= 1.98758e+02, atom= 696\n", - "Step= 769, Dmax= 9.5e-03 nm, Epot= -4.59053e+04 Fmax= 2.60362e+01, atom= 696\n", - "Step= 771, Dmax= 5.7e-03 nm, Epot= -4.59065e+04 Fmax= 1.21331e+02, atom= 696\n", - "Step= 772, Dmax= 6.8e-03 nm, Epot= -4.59075e+04 Fmax= 5.12257e+01, atom= 696\n", - "Step= 773, Dmax= 8.2e-03 nm, Epot= -4.59081e+04 Fmax= 1.43502e+02, atom= 696\n", - "Step= 774, Dmax= 9.8e-03 nm, Epot= -4.59091e+04 Fmax= 9.64388e+01, atom= 696\n", - "Step= 776, Dmax= 5.9e-03 nm, Epot= -4.59100e+04 Fmax= 4.93222e+01, atom= 696\n", - "Step= 777, Dmax= 7.1e-03 nm, Epot= -4.59106e+04 Fmax= 1.27857e+02, atom= 696\n", - "Step= 778, Dmax= 8.5e-03 nm, Epot= -4.59115e+04 Fmax= 8.28113e+01, atom= 696\n", - "Step= 779, Dmax= 1.0e-02 nm, Epot= -4.59117e+04 Fmax= 1.74407e+02, atom= 696\n", - "Step= 780, Dmax= 1.2e-02 nm, Epot= -4.59127e+04 Fmax= 1.28255e+02, atom= 696\n", - "Step= 782, Dmax= 7.3e-03 nm, Epot= -4.59139e+04 Fmax= 4.71149e+01, atom= 696\n", - "Step= 783, Dmax= 8.8e-03 nm, Epot= -4.59143e+04 Fmax= 1.70745e+02, atom= 696\n", - "Step= 784, Dmax= 1.1e-02 nm, Epot= -4.59159e+04 Fmax= 9.03932e+01, atom= 696\n", - "Step= 786, Dmax= 6.3e-03 nm, Epot= -4.59167e+04 Fmax= 6.52017e+01, atom= 696\n", - "Step= 787, Dmax= 7.6e-03 nm, Epot= -4.59173e+04 Fmax= 1.24195e+02, atom= 696\n", - "Step= 788, Dmax= 9.1e-03 nm, Epot= -4.59182e+04 Fmax= 1.00740e+02, atom= 696\n", - "Step= 789, Dmax= 1.1e-02 nm, Epot= -4.59184e+04 Fmax= 1.73851e+02, atom= 696\n", - "Step= 790, Dmax= 1.3e-02 nm, Epot= -4.59193e+04 Fmax= 1.49320e+02, atom= 696\n", - "Step= 792, Dmax= 7.9e-03 nm, Epot= -4.59208e+04 Fmax= 3.80837e+01, atom= 696\n", - "Step= 793, Dmax= 9.5e-03 nm, Epot= -4.59213e+04 Fmax= 2.01673e+02, atom= 696\n", - "Step= 794, Dmax= 1.1e-02 nm, Epot= -4.59235e+04 Fmax= 8.16628e+01, atom= 696\n", - "Step= 796, Dmax= 6.8e-03 nm, Epot= -4.59242e+04 Fmax= 8.32237e+01, atom= 696\n", - "Step= 797, Dmax= 8.2e-03 nm, Epot= -4.59249e+04 Fmax= 1.18894e+02, atom= 696\n", - "Step= 798, Dmax= 9.8e-03 nm, Epot= -4.59257e+04 Fmax= 1.20546e+02, atom= 696\n", - "Step= 799, Dmax= 1.2e-02 nm, Epot= -4.59261e+04 Fmax= 1.73150e+02, atom= 696\n", - "Step= 800, Dmax= 1.4e-02 nm, Epot= -4.59267e+04 Fmax= 1.71757e+02, atom= 696\n", - "Step= 802, Dmax= 8.5e-03 nm, Epot= -4.59286e+04 Fmax= 2.88038e+01, atom= 696\n", - "Step= 803, Dmax= 1.0e-02 nm, Epot= -4.59295e+04 Fmax= 2.37911e+02, atom= 696\n", - "Step= 804, Dmax= 1.2e-02 nm, Epot= -4.59325e+04 Fmax= 7.37178e+01, atom= 696\n", - "Step= 806, Dmax= 7.3e-03 nm, Epot= -4.59333e+04 Fmax= 9.95469e+01, atom= 696\n", - "Step= 807, Dmax= 8.8e-03 nm, Epot= -4.59341e+04 Fmax= 1.16390e+02, atom= 696\n", - "Step= 808, Dmax= 1.1e-02 nm, Epot= -4.59347e+04 Fmax= 1.39321e+02, atom= 696\n", - "Step= 809, Dmax= 1.3e-02 nm, Epot= -4.59353e+04 Fmax= 1.74346e+02, atom= 696\n", - "Step= 810, Dmax= 1.5e-02 nm, Epot= -4.59357e+04 Fmax= 1.93123e+02, atom= 696\n", - "Step= 812, Dmax= 9.1e-03 nm, Epot= -4.59379e+04 Fmax= 2.10786e+01, atom= 696\n", - "Step= 813, Dmax= 1.1e-02 nm, Epot= -4.59394e+04 Fmax= 2.86557e+02, atom= 696\n", - "Step= 814, Dmax= 1.3e-02 nm, Epot= -4.59437e+04 Fmax= 6.38750e+01, atom= 696\n", - "Step= 816, Dmax= 7.9e-03 nm, Epot= -4.59446e+04 Fmax= 1.11839e+02, atom= 696\n", - "Step= 817, Dmax= 9.5e-03 nm, Epot= -4.59454e+04 Fmax= 1.15613e+02, atom= 696\n", - "Step= 818, Dmax= 1.1e-02 nm, Epot= -4.59458e+04 Fmax= 1.56136e+02, atom= 696\n", - "Step= 819, Dmax= 1.4e-02 nm, Epot= -4.59465e+04 Fmax= 1.78894e+02, atom= 696\n", - "Step= 820, Dmax= 1.6e-02 nm, Epot= -4.59465e+04 Fmax= 2.12800e+02, atom= 696\n", - "Step= 822, Dmax= 9.8e-03 nm, Epot= -4.59492e+04 Fmax= 2.06677e+01, atom= 1511\n", - "Step= 823, Dmax= 1.2e-02 nm, Epot= -4.59516e+04 Fmax= 2.51790e+02, atom= 696\n", - "Step= 824, Dmax= 1.4e-02 nm, Epot= -4.59549e+04 Fmax= 1.31246e+02, atom= 696\n", - "Step= 826, Dmax= 8.5e-03 nm, Epot= -4.59559e+04 Fmax= 6.92900e+01, atom= 696\n", - "Step= 827, Dmax= 1.0e-02 nm, Epot= -4.59560e+04 Fmax= 1.96379e+02, atom= 696\n", - "Step= 828, Dmax= 1.2e-02 nm, Epot= -4.59576e+04 Fmax= 1.05095e+02, atom= 696\n", - "Step= 830, Dmax= 7.3e-03 nm, Epot= -4.59586e+04 Fmax= 6.67046e+01, atom= 696\n", - "Step= 831, Dmax= 8.8e-03 nm, Epot= -4.59591e+04 Fmax= 1.44450e+02, atom= 696\n", - "Step= 832, Dmax= 1.1e-02 nm, Epot= -4.59603e+04 Fmax= 1.10789e+02, atom= 696\n", - "Step= 834, Dmax= 6.3e-03 nm, Epot= -4.59613e+04 Fmax= 4.47419e+01, atom= 696\n", - "Step= 835, Dmax= 7.6e-03 nm, Epot= -4.59622e+04 Fmax= 1.41817e+02, atom= 696\n", - "Step= 836, Dmax= 9.1e-03 nm, Epot= -4.59633e+04 Fmax= 7.99906e+01, atom= 696\n", - "Step= 837, Dmax= 1.1e-02 nm, Epot= -4.59634e+04 Fmax= 1.94667e+02, atom= 696\n", - "Step= 838, Dmax= 1.3e-02 nm, Epot= -4.59648e+04 Fmax= 1.25324e+02, atom= 696\n", - "Step= 840, Dmax= 7.9e-03 nm, Epot= -4.59660e+04 Fmax= 5.69470e+01, atom= 696\n", - "Step= 841, Dmax= 9.4e-03 nm, Epot= -4.59663e+04 Fmax= 1.70257e+02, atom= 696\n", - "Step= 842, Dmax= 1.1e-02 nm, Epot= -4.59679e+04 Fmax= 1.02786e+02, atom= 696\n", - "Step= 844, Dmax= 6.8e-03 nm, Epot= -4.59688e+04 Fmax= 6.11445e+01, atom= 696\n", - "Step= 845, Dmax= 8.2e-03 nm, Epot= -4.59694e+04 Fmax= 1.37869e+02, atom= 696\n", - "Step= 846, Dmax= 9.8e-03 nm, Epot= -4.59704e+04 Fmax= 9.83886e+01, atom= 696\n", - "Step= 848, Dmax= 5.9e-03 nm, Epot= -4.59714e+04 Fmax= 3.85417e+01, atom= 696\n", - "Step= 849, Dmax= 7.1e-03 nm, Epot= -4.59723e+04 Fmax= 1.29147e+02, atom= 696\n", - "Step= 850, Dmax= 8.5e-03 nm, Epot= -4.59735e+04 Fmax= 7.34971e+01, atom= 696\n", - "Step= 851, Dmax= 1.0e-02 nm, Epot= -4.59736e+04 Fmax= 1.64444e+02, atom= 696\n", - "Step= 852, Dmax= 1.2e-02 nm, Epot= -4.59749e+04 Fmax= 1.26935e+02, atom= 696\n", - "Step= 854, Dmax= 7.3e-03 nm, Epot= -4.59761e+04 Fmax= 5.01021e+01, atom= 696\n", - "Step= 855, Dmax= 8.8e-03 nm, Epot= -4.59766e+04 Fmax= 1.64919e+02, atom= 696\n", - "Step= 856, Dmax= 1.1e-02 nm, Epot= -4.59779e+04 Fmax= 8.98120e+01, atom= 696\n", - "Step= 858, Dmax= 6.3e-03 nm, Epot= -4.59788e+04 Fmax= 5.65161e+01, atom= 696\n", - "Step= 859, Dmax= 7.6e-03 nm, Epot= -4.59794e+04 Fmax= 1.22357e+02, atom= 696\n", - "Step= 860, Dmax= 9.1e-03 nm, Epot= -4.59804e+04 Fmax= 9.39430e+01, atom= 696\n", - "Step= 861, Dmax= 1.1e-02 nm, Epot= -4.59805e+04 Fmax= 1.61725e+02, atom= 696\n", - "Step= 862, Dmax= 1.3e-02 nm, Epot= -4.59814e+04 Fmax= 1.51142e+02, atom= 696\n", - "Step= 864, Dmax= 7.9e-03 nm, Epot= -4.59829e+04 Fmax= 3.98937e+01, atom= 696\n", - "Step= 865, Dmax= 9.4e-03 nm, Epot= -4.59835e+04 Fmax= 1.92098e+02, atom= 696\n", - "Step= 866, Dmax= 1.1e-02 nm, Epot= -4.59852e+04 Fmax= 8.41308e+01, atom= 696\n", - "Step= 868, Dmax= 6.8e-03 nm, Epot= -4.59860e+04 Fmax= 7.31203e+01, atom= 696\n", - "Step= 869, Dmax= 8.1e-03 nm, Epot= -4.59865e+04 Fmax= 1.17310e+02, atom= 696\n", - "Step= 870, Dmax= 9.8e-03 nm, Epot= -4.59873e+04 Fmax= 1.13644e+02, atom= 696\n", - "Step= 871, Dmax= 1.2e-02 nm, Epot= -4.59874e+04 Fmax= 1.59660e+02, atom= 696\n", - "Step= 872, Dmax= 1.4e-02 nm, Epot= -4.59880e+04 Fmax= 1.75921e+02, atom= 696\n", - "Step= 874, Dmax= 8.4e-03 nm, Epot= -4.59899e+04 Fmax= 2.95566e+01, atom= 191\n", - "Step= 875, Dmax= 1.0e-02 nm, Epot= -4.59908e+04 Fmax= 2.21059e+02, atom= 696\n", - "Step= 876, Dmax= 1.2e-02 nm, Epot= -4.59930e+04 Fmax= 8.19043e+01, atom= 696\n", - "Step= 878, Dmax= 7.3e-03 nm, Epot= -4.59937e+04 Fmax= 8.62007e+01, atom= 696\n", - "Step= 879, Dmax= 8.8e-03 nm, Epot= -4.59942e+04 Fmax= 1.16754e+02, atom= 696\n", - "Step= 880, Dmax= 1.1e-02 nm, Epot= -4.59948e+04 Fmax= 1.30602e+02, atom= 696\n", - "Step= 881, Dmax= 1.3e-02 nm, Epot= -4.59950e+04 Fmax= 1.60549e+02, atom= 696\n", - "Step= 882, Dmax= 1.5e-02 nm, Epot= -4.59953e+04 Fmax= 1.99084e+02, atom= 696\n", - "Step= 883, Dmax= 1.8e-02 nm, Epot= -4.59953e+04 Fmax= 2.19377e+02, atom= 696\n", - "Step= 885, Dmax= 1.1e-02 nm, Epot= -4.59983e+04 Fmax= 2.72405e+01, atom= 1511\n", - "Step= 887, Dmax= 6.5e-03 nm, Epot= -4.59995e+04 Fmax= 1.16456e+02, atom= 696\n", - "Step= 888, Dmax= 7.8e-03 nm, Epot= -4.60006e+04 Fmax= 7.52595e+01, atom= 696\n", - "Step= 889, Dmax= 9.4e-03 nm, Epot= -4.60009e+04 Fmax= 1.36825e+02, atom= 696\n", - "Step= 890, Dmax= 1.1e-02 nm, Epot= -4.60018e+04 Fmax= 1.23755e+02, atom= 696\n", - "Step= 892, Dmax= 6.8e-03 nm, Epot= -4.60029e+04 Fmax= 3.58911e+01, atom= 696\n", - "Step= 893, Dmax= 8.1e-03 nm, Epot= -4.60037e+04 Fmax= 1.59753e+02, atom= 696\n", - "Step= 894, Dmax= 9.8e-03 nm, Epot= -4.60051e+04 Fmax= 7.26474e+01, atom= 696\n", - "Step= 896, Dmax= 5.9e-03 nm, Epot= -4.60058e+04 Fmax= 6.05773e+01, atom= 696\n", - "Step= 897, Dmax= 7.0e-03 nm, Epot= -4.60064e+04 Fmax= 9.97408e+01, atom= 696\n", - "Step= 898, Dmax= 8.4e-03 nm, Epot= -4.60071e+04 Fmax= 9.56890e+01, atom= 696\n", - "Step= 899, Dmax= 1.0e-02 nm, Epot= -4.60074e+04 Fmax= 1.34885e+02, atom= 696\n", - "Step= 900, Dmax= 1.2e-02 nm, Epot= -4.60080e+04 Fmax= 1.47724e+02, atom= 696\n", - "Step= 902, Dmax= 7.3e-03 nm, Epot= -4.60095e+04 Fmax= 2.60782e+01, atom= 696\n", - "Step= 903, Dmax= 8.7e-03 nm, Epot= -4.60107e+04 Fmax= 1.81071e+02, atom= 696\n", - "Step= 904, Dmax= 1.0e-02 nm, Epot= -4.60123e+04 Fmax= 6.99609e+01, atom= 696\n", - "Step= 906, Dmax= 6.3e-03 nm, Epot= -4.60130e+04 Fmax= 7.39022e+01, atom= 696\n", - "Step= 907, Dmax= 7.6e-03 nm, Epot= -4.60136e+04 Fmax= 9.79917e+01, atom= 696\n", - "Step= 908, Dmax= 9.1e-03 nm, Epot= -4.60142e+04 Fmax= 1.10863e+02, atom= 696\n", - "Step= 909, Dmax= 1.1e-02 nm, Epot= -4.60145e+04 Fmax= 1.35643e+02, atom= 696\n", - "Step= 910, Dmax= 1.3e-02 nm, Epot= -4.60149e+04 Fmax= 1.66970e+02, atom= 696\n", - "Step= 911, Dmax= 1.6e-02 nm, Epot= -4.60150e+04 Fmax= 1.86074e+02, atom= 696\n", - "Step= 913, Dmax= 9.4e-03 nm, Epot= -4.60173e+04 Fmax= 2.15397e+01, atom= 1511\n", - "Step= 914, Dmax= 1.1e-02 nm, Epot= -4.60175e+04 Fmax= 2.43080e+02, atom= 696\n", - "Step= 915, Dmax= 1.4e-02 nm, Epot= -4.60212e+04 Fmax= 9.64143e+01, atom= 696\n", - "Step= 917, Dmax= 8.1e-03 nm, Epot= -4.60219e+04 Fmax= 8.13839e+01, atom= 696\n", - "Step= 918, Dmax= 9.7e-03 nm, Epot= -4.60221e+04 Fmax= 1.46521e+02, atom= 696\n", - "Step= 919, Dmax= 1.2e-02 nm, Epot= -4.60229e+04 Fmax= 1.17913e+02, atom= 696\n", - "Step= 921, Dmax= 7.0e-03 nm, Epot= -4.60241e+04 Fmax= 3.54228e+01, atom= 696\n", - "Step= 922, Dmax= 8.4e-03 nm, Epot= -4.60244e+04 Fmax= 1.56269e+02, atom= 696\n", - "Step= 923, Dmax= 1.0e-02 nm, Epot= -4.60260e+04 Fmax= 7.40305e+01, atom= 696\n", - "Step= 925, Dmax= 6.1e-03 nm, Epot= -4.60267e+04 Fmax= 6.27464e+01, atom= 696\n", - "Step= 926, Dmax= 7.3e-03 nm, Epot= -4.60271e+04 Fmax= 1.02365e+02, atom= 696\n", - "Step= 927, Dmax= 8.7e-03 nm, Epot= -4.60278e+04 Fmax= 9.37348e+01, atom= 696\n", - "Step= 928, Dmax= 1.0e-02 nm, Epot= -4.60279e+04 Fmax= 1.46106e+02, atom= 696\n", - "Step= 929, Dmax= 1.3e-02 nm, Epot= -4.60286e+04 Fmax= 1.35090e+02, atom= 696\n", - "Step= 931, Dmax= 7.5e-03 nm, Epot= -4.60300e+04 Fmax= 2.75206e+01, atom= 696\n", - "Step= 932, Dmax= 9.1e-03 nm, Epot= -4.60302e+04 Fmax= 1.83359e+02, atom= 696\n", - "Step= 933, Dmax= 1.1e-02 nm, Epot= -4.60325e+04 Fmax= 6.64250e+01, atom= 696\n", - "Step= 935, Dmax= 6.5e-03 nm, Epot= -4.60331e+04 Fmax= 7.74249e+01, atom= 696\n", - "Step= 936, Dmax= 7.8e-03 nm, Epot= -4.60336e+04 Fmax= 9.81062e+01, atom= 696\n", - "Step= 937, Dmax= 9.4e-03 nm, Epot= -4.60340e+04 Fmax= 1.09572e+02, atom= 696\n", - "Step= 938, Dmax= 1.1e-02 nm, Epot= -4.60343e+04 Fmax= 1.45081e+02, atom= 696\n", - "Step= 939, Dmax= 1.4e-02 nm, Epot= -4.60347e+04 Fmax= 1.52938e+02, atom= 696\n", - "Step= 941, Dmax= 8.1e-03 nm, Epot= -4.60364e+04 Fmax= 2.02457e+01, atom= 696\n", - "Step= 942, Dmax= 9.7e-03 nm, Epot= -4.60365e+04 Fmax= 2.16684e+02, atom= 696\n", - "Step= 943, Dmax= 1.2e-02 nm, Epot= -4.60399e+04 Fmax= 5.84330e+01, atom= 696\n", - "Step= 945, Dmax= 7.0e-03 nm, Epot= -4.60404e+04 Fmax= 9.02180e+01, atom= 696\n", - "Step= 946, Dmax= 8.4e-03 nm, Epot= -4.60410e+04 Fmax= 9.50576e+01, atom= 696\n", - "Step= 947, Dmax= 1.0e-02 nm, Epot= -4.60413e+04 Fmax= 1.24530e+02, atom= 696\n", - "Step= 948, Dmax= 1.2e-02 nm, Epot= -4.60417e+04 Fmax= 1.44572e+02, atom= 696\n", - "Step= 950, Dmax= 7.3e-03 nm, Epot= -4.60432e+04 Fmax= 2.13276e+01, atom= 696\n", - "Step= 951, Dmax= 8.7e-03 nm, Epot= -4.60445e+04 Fmax= 1.70152e+02, atom= 191\n", - "Step= 952, Dmax= 1.0e-02 nm, Epot= -4.60461e+04 Fmax= 6.71149e+01, atom= 696\n", - "Step= 954, Dmax= 6.3e-03 nm, Epot= -4.60467e+04 Fmax= 6.99240e+01, atom= 696\n", - "Step= 955, Dmax= 7.5e-03 nm, Epot= -4.60472e+04 Fmax= 9.29654e+01, atom= 696\n", - "Step= 956, Dmax= 9.0e-03 nm, Epot= -4.60477e+04 Fmax= 1.06140e+02, atom= 696\n", - "Step= 957, Dmax= 1.1e-02 nm, Epot= -4.60480e+04 Fmax= 1.27478e+02, atom= 696\n", - "Step= 958, Dmax= 1.3e-02 nm, Epot= -4.60482e+04 Fmax= 1.60675e+02, atom= 696\n", - "Step= 959, Dmax= 1.6e-02 nm, Epot= -4.60483e+04 Fmax= 1.74802e+02, atom= 696\n", - "Step= 961, Dmax= 9.4e-03 nm, Epot= -4.60506e+04 Fmax= 2.13263e+01, atom= 1511\n", - "Step= 963, Dmax= 5.6e-03 nm, Epot= -4.60515e+04 Fmax= 1.06058e+02, atom= 696\n", - "Step= 964, Dmax= 6.7e-03 nm, Epot= -4.60527e+04 Fmax= 4.72374e+01, atom= 696\n", - "Step= 965, Dmax= 8.1e-03 nm, Epot= -4.60529e+04 Fmax= 1.22496e+02, atom= 696\n", - "Step= 966, Dmax= 9.7e-03 nm, Epot= -4.60540e+04 Fmax= 8.66934e+01, atom= 696\n", - "Step= 968, Dmax= 5.8e-03 nm, Epot= -4.60548e+04 Fmax= 4.15966e+01, atom= 696\n", - "Step= 969, Dmax= 7.0e-03 nm, Epot= -4.60552e+04 Fmax= 1.09255e+02, atom= 696\n", - "Step= 970, Dmax= 8.4e-03 nm, Epot= -4.60561e+04 Fmax= 7.27999e+01, atom= 696\n", - "Step= 972, Dmax= 5.0e-03 nm, Epot= -4.60568e+04 Fmax= 3.34387e+01, atom= 696\n", - "Step= 973, Dmax= 6.0e-03 nm, Epot= -4.60574e+04 Fmax= 9.65631e+01, atom= 696\n", - "Step= 974, Dmax= 7.3e-03 nm, Epot= -4.60583e+04 Fmax= 5.99155e+01, atom= 696\n", - "Step= 975, Dmax= 8.7e-03 nm, Epot= -4.60583e+04 Fmax= 1.24573e+02, atom= 696\n", - "Step= 976, Dmax= 1.0e-02 nm, Epot= -4.60592e+04 Fmax= 1.00296e+02, atom= 696\n", - "Step= 978, Dmax= 6.3e-03 nm, Epot= -4.60602e+04 Fmax= 3.68558e+01, atom= 696\n", - "Step= 979, Dmax= 7.5e-03 nm, Epot= -4.60606e+04 Fmax= 1.24790e+02, atom= 696\n", - "Step= 980, Dmax= 9.0e-03 nm, Epot= -4.60617e+04 Fmax= 6.99728e+01, atom= 696\n", - "Step= 982, Dmax= 5.4e-03 nm, Epot= -4.60624e+04 Fmax= 4.32977e+01, atom= 696\n", - "Step= 983, Dmax= 6.5e-03 nm, Epot= -4.60627e+04 Fmax= 9.44745e+01, atom= 696\n", - "Step= 984, Dmax= 7.8e-03 nm, Epot= -4.60635e+04 Fmax= 7.23624e+01, atom= 191\n", - "Step= 986, Dmax= 4.7e-03 nm, Epot= -4.60642e+04 Fmax= 2.87493e+01, atom= 696\n", - "Step= 987, Dmax= 5.6e-03 nm, Epot= -4.60649e+04 Fmax= 9.08944e+01, atom= 191\n", - "Step= 988, Dmax= 6.7e-03 nm, Epot= -4.60657e+04 Fmax= 5.25537e+01, atom= 696\n", - "Step= 989, Dmax= 8.1e-03 nm, Epot= -4.60658e+04 Fmax= 1.24282e+02, atom= 191\n", - "Step= 990, Dmax= 9.7e-03 nm, Epot= -4.60667e+04 Fmax= 8.18549e+01, atom= 696\n", - "Step= 992, Dmax= 5.8e-03 nm, Epot= -4.60675e+04 Fmax= 3.90673e+01, atom= 191\n", - "Step= 993, Dmax= 7.0e-03 nm, Epot= -4.60678e+04 Fmax= 1.05917e+02, atom= 191\n", - "Step= 994, Dmax= 8.4e-03 nm, Epot= -4.60687e+04 Fmax= 7.41061e+01, atom= 191\n", - "Step= 996, Dmax= 5.0e-03 nm, Epot= -4.60694e+04 Fmax= 3.27753e+01, atom= 696\n", - "Step= 997, Dmax= 6.0e-03 nm, Epot= -4.60699e+04 Fmax= 9.71702e+01, atom= 191\n", - "Step= 998, Dmax= 7.2e-03 nm, Epot= -4.60707e+04 Fmax= 5.52218e+01, atom= 191\n", - "Step= 1000, Dmax= 4.3e-03 nm, Epot= -4.60713e+04 Fmax= 3.61445e+01, atom= 191\n", - "\n", + "Step= 43, Dmax= 1.1e-01 nm, Epot= -3.73994e+04 Fmax= 2.71563e+03, atom= 1090\n", + "Step= 44, Dmax= 1.3e-01 nm, Epot= -3.78345e+04 Fmax= 2.32957e+03, atom= 1200\n", + "Step= 45, Dmax= 1.6e-01 nm, Epot= -3.80154e+04 Fmax= 6.23576e+03, atom= 1363\n", + "Step= 47, Dmax= 9.6e-02 nm, Epot= -3.85620e+04 Fmax= 2.23182e+03, atom= 867\n", + "Step= 48, Dmax= 1.1e-01 nm, Epot= -3.89186e+04 Fmax= 1.51575e+03, atom= 666\n", + "Step= 50, Dmax= 6.9e-02 nm, Epot= -3.92438e+04 Fmax= 1.20553e+03, atom= 1190\n", + "Step= 52, Dmax= 4.1e-02 nm, Epot= -3.94255e+04 Fmax= 1.81611e+03, atom= 1190\n", + "Step= 53, Dmax= 5.0e-02 nm, Epot= -3.95620e+04 Fmax= 1.81494e+03, atom= 1190\n", + "Step= 54, Dmax= 6.0e-02 nm, Epot= -3.96129e+04 Fmax= 3.54853e+03, atom= 1190\n", + "Step= 55, Dmax= 7.1e-02 nm, Epot= -3.97853e+04 Fmax= 1.91470e+03, atom= 652\n", + "Step= 57, Dmax= 4.3e-02 nm, Epot= -3.99181e+04 Fmax= 1.12190e+03, atom= 1469\n", + "Step= 58, Dmax= 5.1e-02 nm, Epot= -4.00826e+04 Fmax= 1.67277e+03, atom= 652\n", + "Step= 59, Dmax= 6.2e-02 nm, Epot= -4.01534e+04 Fmax= 2.68809e+03, atom= 652\n", + "Step= 60, Dmax= 7.4e-02 nm, Epot= -4.02825e+04 Fmax= 2.17815e+03, atom= 1190\n", + "Step= 61, Dmax= 8.9e-02 nm, Epot= -4.03034e+04 Fmax= 2.91113e+03, atom= 1190\n", + "Step= 63, Dmax= 5.3e-02 nm, Epot= -4.05242e+04 Fmax= 7.06199e+02, atom= 5920\n", + "Step= 64, Dmax= 6.4e-02 nm, Epot= -4.07516e+04 Fmax= 1.27266e+03, atom= 620\n", + "Step= 66, Dmax= 3.8e-02 nm, Epot= -4.08794e+04 Fmax= 1.06149e+03, atom= 620\n", + "Step= 67, Dmax= 4.6e-02 nm, Epot= -4.09733e+04 Fmax= 1.25278e+03, atom= 1190\n", + "Step= 68, Dmax= 5.5e-02 nm, Epot= -4.10696e+04 Fmax= 1.23272e+03, atom= 652\n", + "Step= 69, Dmax= 6.6e-02 nm, Epot= -4.10937e+04 Fmax= 2.04367e+03, atom= 652\n", + "Step= 70, Dmax= 8.0e-02 nm, Epot= -4.11796e+04 Fmax= 2.15705e+03, atom= 652\n", + "Step= 72, Dmax= 4.8e-02 nm, Epot= -4.13411e+04 Fmax= 5.25685e+02, atom= 1469\n", + "Step= 73, Dmax= 5.7e-02 nm, Epot= -4.14434e+04 Fmax= 4.45001e+03, atom= 113\n", + "Step= 74, Dmax= 6.9e-02 nm, Epot= -4.15758e+04 Fmax= 1.05509e+03, atom= 170\n", + "Step= 75, Dmax= 8.3e-02 nm, Epot= -4.16118e+04 Fmax= 4.05136e+03, atom= 170\n", + "Step= 76, Dmax= 9.9e-02 nm, Epot= -4.17121e+04 Fmax= 1.42697e+03, atom= 113\n", + "Step= 78, Dmax= 5.9e-02 nm, Epot= -4.18215e+04 Fmax= 6.13638e+02, atom= 1281\n", + "Step= 79, Dmax= 7.1e-02 nm, Epot= -4.19450e+04 Fmax= 1.31910e+03, atom= 1281\n", + "Step= 81, Dmax= 4.3e-02 nm, Epot= -4.20505e+04 Fmax= 6.91802e+02, atom= 170\n", + "Step= 82, Dmax= 5.1e-02 nm, Epot= -4.21356e+04 Fmax= 8.32550e+02, atom= 170\n", + "Step= 83, Dmax= 6.2e-02 nm, Epot= -4.22091e+04 Fmax= 1.12090e+03, atom= 170\n", + "Step= 84, Dmax= 7.4e-02 nm, Epot= -4.22628e+04 Fmax= 1.29047e+03, atom= 170\n", + "Step= 85, Dmax= 8.9e-02 nm, Epot= -4.22998e+04 Fmax= 1.20931e+03, atom= 1281\n", + "Step= 87, Dmax= 5.3e-02 nm, Epot= -4.24262e+04 Fmax= 6.06238e+02, atom= 240\n", + "Step= 88, Dmax= 6.4e-02 nm, Epot= -4.24605e+04 Fmax= 1.74500e+03, atom= 850\n", + "Step= 89, Dmax= 7.7e-02 nm, Epot= -4.25572e+04 Fmax= 1.22862e+03, atom= 850\n", + "Step= 91, Dmax= 4.6e-02 nm, Epot= -4.26389e+04 Fmax= 4.53331e+02, atom= 70\n", + "Step= 92, Dmax= 5.5e-02 nm, Epot= -4.27303e+04 Fmax= 7.46617e+02, atom= 70\n", + "Step= 94, Dmax= 3.3e-02 nm, Epot= -4.27945e+04 Fmax= 3.51139e+02, atom= 1589\n", + "Step= 95, Dmax= 4.0e-02 nm, Epot= -4.28458e+04 Fmax= 1.50975e+03, atom= 1589\n", + "Step= 96, Dmax= 4.8e-02 nm, Epot= -4.29169e+04 Fmax= 4.34395e+02, atom= 434\n", + "Step= 97, Dmax= 5.7e-02 nm, Epot= -4.29790e+04 Fmax= 1.84347e+03, atom= 434\n", + "Step= 98, Dmax= 6.9e-02 nm, Epot= -4.30295e+04 Fmax= 6.99437e+02, atom= 1589\n", + "Step= 100, Dmax= 4.1e-02 nm, Epot= -4.30858e+04 Fmax= 3.84717e+02, atom= 3179\n", + "Step= 101, Dmax= 4.9e-02 nm, Epot= -4.31399e+04 Fmax= 1.11457e+03, atom= 1589\n", + "Step= 102, Dmax= 5.9e-02 nm, Epot= -4.31821e+04 Fmax= 1.23817e+03, atom= 1589\n", + "Step= 103, Dmax= 7.1e-02 nm, Epot= -4.32218e+04 Fmax= 9.44305e+02, atom= 434\n", + "Step= 104, Dmax= 8.5e-02 nm, Epot= -4.32496e+04 Fmax= 1.23802e+03, atom= 317\n", + "Step= 106, Dmax= 5.1e-02 nm, Epot= -4.33232e+04 Fmax= 2.80499e+02, atom= 421\n", + "Step= 107, Dmax= 6.2e-02 nm, Epot= -4.33684e+04 Fmax= 1.22256e+03, atom= 317\n", + "Step= 109, Dmax= 3.7e-02 nm, Epot= -4.34593e+04 Fmax= 3.28381e+02, atom= 434\n", + "Step= 110, Dmax= 4.4e-02 nm, Epot= -4.35167e+04 Fmax= 5.77616e+02, atom= 434\n", + "Step= 111, Dmax= 5.3e-02 nm, Epot= -4.35590e+04 Fmax= 4.92084e+02, atom= 434\n", + "Step= 112, Dmax= 6.4e-02 nm, Epot= -4.35752e+04 Fmax= 1.25946e+03, atom= 434\n", + "Step= 113, Dmax= 7.7e-02 nm, Epot= -4.36228e+04 Fmax= 6.72230e+02, atom= 434\n", + "Step= 115, Dmax= 4.6e-02 nm, Epot= -4.36728e+04 Fmax= 4.09361e+02, atom= 317\n", + "Step= 116, Dmax= 5.5e-02 nm, Epot= -4.37177e+04 Fmax= 4.93751e+02, atom= 317\n", + "Step= 118, Dmax= 3.3e-02 nm, Epot= -4.37555e+04 Fmax= 1.90875e+02, atom= 317\n", + "Step= 119, Dmax= 4.0e-02 nm, Epot= -4.37799e+04 Fmax= 8.72544e+02, atom= 317\n", + "Step= 120, Dmax= 4.8e-02 nm, Epot= -4.38416e+04 Fmax= 3.21396e+02, atom= 317\n", + "Step= 122, Dmax= 2.9e-02 nm, Epot= -4.38683e+04 Fmax= 3.75706e+02, atom= 983\n", + "Step= 123, Dmax= 3.4e-02 nm, Epot= -4.38805e+04 Fmax= 6.54084e+02, atom= 983\n", + "Step= 124, Dmax= 4.1e-02 nm, Epot= -4.39104e+04 Fmax= 6.00286e+02, atom= 983\n", + "Step= 125, Dmax= 4.9e-02 nm, Epot= -4.39152e+04 Fmax= 8.68779e+02, atom= 983\n", + "Step= 126, Dmax= 5.9e-02 nm, Epot= -4.39302e+04 Fmax= 1.08168e+03, atom= 983\n", + "Step= 127, Dmax= 7.1e-02 nm, Epot= -4.39395e+04 Fmax= 9.88661e+02, atom= 983\n", + "Step= 129, Dmax= 4.3e-02 nm, Epot= -4.39979e+04 Fmax= 3.41137e+02, atom= 939\n", + "Step= 130, Dmax= 5.1e-02 nm, Epot= -4.40179e+04 Fmax= 6.91514e+02, atom= 939\n", + "Step= 132, Dmax= 3.1e-02 nm, Epot= -4.40575e+04 Fmax= 3.17552e+02, atom= 983\n", + "Step= 133, Dmax= 3.7e-02 nm, Epot= -4.40739e+04 Fmax= 6.66329e+02, atom= 983\n", + "Step= 134, Dmax= 4.4e-02 nm, Epot= -4.40973e+04 Fmax= 4.71807e+02, atom= 983\n", + "Step= 136, Dmax= 2.7e-02 nm, Epot= -4.41213e+04 Fmax= 2.13679e+02, atom= 983\n", + "Step= 137, Dmax= 3.2e-02 nm, Epot= -4.41340e+04 Fmax= 8.04992e+02, atom= 983\n", + "Step= 138, Dmax= 3.8e-02 nm, Epot= -4.41653e+04 Fmax= 4.08978e+02, atom= 983\n", + "Step= 139, Dmax= 4.6e-02 nm, Epot= -4.41654e+04 Fmax= 9.12027e+02, atom= 983\n", + "Step= 140, Dmax= 5.5e-02 nm, Epot= -4.41841e+04 Fmax= 6.40748e+02, atom= 983\n", + "Step= 142, Dmax= 3.3e-02 nm, Epot= -4.42228e+04 Fmax= 1.94678e+02, atom= 1550\n", + "Step= 143, Dmax= 4.0e-02 nm, Epot= -4.42232e+04 Fmax= 9.91222e+02, atom= 983\n", + "Step= 144, Dmax= 4.8e-02 nm, Epot= -4.42676e+04 Fmax= 5.88017e+02, atom= 983\n", + "Step= 146, Dmax= 2.9e-02 nm, Epot= -4.42914e+04 Fmax= 2.00081e+02, atom= 292\n", + "Step= 147, Dmax= 3.4e-02 nm, Epot= -4.43066e+04 Fmax= 6.57932e+02, atom= 983\n", + "Step= 148, Dmax= 4.1e-02 nm, Epot= -4.43211e+04 Fmax= 6.61051e+02, atom= 983\n", + "Step= 149, Dmax= 4.9e-02 nm, Epot= -4.43348e+04 Fmax= 5.51796e+02, atom= 1550\n", + "Step= 151, Dmax= 3.0e-02 nm, Epot= -4.43616e+04 Fmax= 2.86698e+02, atom= 681\n", + "Step= 152, Dmax= 3.5e-02 nm, Epot= -4.43737e+04 Fmax= 6.52987e+02, atom= 681\n", + "Step= 153, Dmax= 4.3e-02 nm, Epot= -4.43882e+04 Fmax= 4.78678e+02, atom= 681\n", + "Step= 155, Dmax= 2.6e-02 nm, Epot= -4.44101e+04 Fmax= 1.28188e+02, atom= 983\n", + "Step= 156, Dmax= 3.1e-02 nm, Epot= -4.44202e+04 Fmax= 7.33390e+02, atom= 983\n", + "Step= 157, Dmax= 3.7e-02 nm, Epot= -4.44518e+04 Fmax= 3.99576e+02, atom= 681\n", + "Step= 159, Dmax= 2.2e-02 nm, Epot= -4.44669e+04 Fmax= 2.09813e+02, atom= 681\n", + "Step= 160, Dmax= 2.6e-02 nm, Epot= -4.44788e+04 Fmax= 5.11277e+02, atom= 681\n", + "Step= 161, Dmax= 3.2e-02 nm, Epot= -4.44914e+04 Fmax= 3.36731e+02, atom= 681\n", + "Step= 162, Dmax= 3.8e-02 nm, Epot= -4.44938e+04 Fmax= 7.53557e+02, atom= 681\n", + "Step= 163, Dmax= 4.6e-02 nm, Epot= -4.45092e+04 Fmax= 4.64951e+02, atom= 681\n", + "Step= 165, Dmax= 2.7e-02 nm, Epot= -4.45278e+04 Fmax= 1.18372e+02, atom= 983\n", + "Step= 167, Dmax= 1.6e-02 nm, Epot= -4.45403e+04 Fmax= 3.23636e+02, atom= 681\n", + "Step= 168, Dmax= 2.0e-02 nm, Epot= -4.45534e+04 Fmax= 1.92375e+02, atom= 681\n", + "Step= 169, Dmax= 2.4e-02 nm, Epot= -4.45599e+04 Fmax= 4.12217e+02, atom= 681\n", + "Step= 170, Dmax= 2.8e-02 nm, Epot= -4.45729e+04 Fmax= 3.01949e+02, atom= 681\n", + "Step= 172, Dmax= 1.7e-02 nm, Epot= -4.45842e+04 Fmax= 1.46158e+02, atom= 681\n", + "Step= 173, Dmax= 2.1e-02 nm, Epot= -4.45943e+04 Fmax= 3.90585e+02, atom= 681\n", + "Step= 174, Dmax= 2.5e-02 nm, Epot= -4.46044e+04 Fmax= 2.59083e+02, atom= 681\n", + "Step= 175, Dmax= 3.0e-02 nm, Epot= -4.46081e+04 Fmax= 5.38443e+02, atom= 681\n", + "Step= 176, Dmax= 3.5e-02 nm, Epot= -4.46187e+04 Fmax= 3.74000e+02, atom= 681\n", + "Step= 178, Dmax= 2.1e-02 nm, Epot= -4.46318e+04 Fmax= 9.02203e+01, atom= 983\n", + "Step= 179, Dmax= 2.6e-02 nm, Epot= -4.46325e+04 Fmax= 6.66137e+02, atom= 681\n", + "Step= 180, Dmax= 3.1e-02 nm, Epot= -4.46619e+04 Fmax= 1.99727e+02, atom= 681\n", + "Step= 182, Dmax= 1.8e-02 nm, Epot= -4.46696e+04 Fmax= 2.44846e+02, atom= 6810\n", + "Step= 183, Dmax= 2.2e-02 nm, Epot= -4.46765e+04 Fmax= 2.94585e+02, atom= 681\n", + "Step= 184, Dmax= 2.6e-02 nm, Epot= -4.46816e+04 Fmax= 3.47376e+02, atom= 681\n", + "Step= 185, Dmax= 3.2e-02 nm, Epot= -4.46868e+04 Fmax= 4.39946e+02, atom= 681\n", + "Step= 186, Dmax= 3.8e-02 nm, Epot= -4.46898e+04 Fmax= 4.71115e+02, atom= 681\n", + "Step= 187, Dmax= 4.6e-02 nm, Epot= -4.46898e+04 Fmax= 6.77977e+02, atom= 681\n", + "Step= 188, Dmax= 5.5e-02 nm, Epot= -4.46925e+04 Fmax= 6.10074e+02, atom= 681\n", + "Step= 190, Dmax= 3.3e-02 nm, Epot= -4.47210e+04 Fmax= 1.01508e+02, atom= 983\n", + "Step= 192, Dmax= 2.0e-02 nm, Epot= -4.47298e+04 Fmax= 2.69819e+02, atom= 681\n", + "Step= 193, Dmax= 2.4e-02 nm, Epot= -4.47359e+04 Fmax= 3.46552e+02, atom= 681\n", + "Step= 194, Dmax= 2.8e-02 nm, Epot= -4.47430e+04 Fmax= 3.27692e+02, atom= 681\n", + "Step= 196, Dmax= 1.7e-02 nm, Epot= -4.47558e+04 Fmax= 5.07418e+01, atom= 642\n", + "Step= 197, Dmax= 2.0e-02 nm, Epot= -4.47571e+04 Fmax= 6.92420e+02, atom= 642\n", + "Step= 198, Dmax= 2.5e-02 nm, Epot= -4.47880e+04 Fmax= 1.27053e+02, atom= 1455\n", + "Step= 200, Dmax= 1.5e-02 nm, Epot= -4.47949e+04 Fmax= 2.45018e+02, atom= 642\n", + "Step= 201, Dmax= 1.8e-02 nm, Epot= -4.48003e+04 Fmax= 1.99268e+02, atom= 642\n", + "Step= 202, Dmax= 2.1e-02 nm, Epot= -4.48046e+04 Fmax= 3.81867e+02, atom= 642\n", + "Step= 203, Dmax= 2.5e-02 nm, Epot= -4.48107e+04 Fmax= 2.66375e+02, atom= 642\n", + "Step= 204, Dmax= 3.1e-02 nm, Epot= -4.48110e+04 Fmax= 6.07559e+02, atom= 642\n", + "Step= 205, Dmax= 3.7e-02 nm, Epot= -4.48195e+04 Fmax= 3.41567e+02, atom= 642\n", + "Step= 207, Dmax= 2.2e-02 nm, Epot= -4.48299e+04 Fmax= 1.05062e+02, atom= 642\n", + "Step= 209, Dmax= 1.3e-02 nm, Epot= -4.48363e+04 Fmax= 2.31245e+02, atom= 642\n", + "Step= 210, Dmax= 1.6e-02 nm, Epot= -4.48430e+04 Fmax= 1.63280e+02, atom= 642\n", + "Step= 211, Dmax= 1.9e-02 nm, Epot= -4.48474e+04 Fmax= 2.83732e+02, atom= 642\n", + "Step= 212, Dmax= 2.3e-02 nm, Epot= -4.48535e+04 Fmax= 2.78904e+02, atom= 642\n", + "Step= 213, Dmax= 2.7e-02 nm, Epot= -4.48555e+04 Fmax= 3.67479e+02, atom= 642\n", + "Step= 214, Dmax= 3.3e-02 nm, Epot= -4.48593e+04 Fmax= 4.58425e+02, atom= 642\n", + "Step= 215, Dmax= 3.9e-02 nm, Epot= -4.48603e+04 Fmax= 4.68145e+02, atom= 642\n", + "Step= 217, Dmax= 2.4e-02 nm, Epot= -4.48776e+04 Fmax= 8.09518e+01, atom= 566\n", + "Step= 219, Dmax= 1.4e-02 nm, Epot= -4.48858e+04 Fmax= 2.02442e+02, atom= 809\n", + "Step= 220, Dmax= 1.7e-02 nm, Epot= -4.48911e+04 Fmax= 2.16388e+02, atom= 809\n", + "Step= 221, Dmax= 2.0e-02 nm, Epot= -4.48947e+04 Fmax= 2.72316e+02, atom= 809\n", + "Step= 222, Dmax= 2.5e-02 nm, Epot= -4.48976e+04 Fmax= 3.23222e+02, atom= 809\n", + "Step= 223, Dmax= 2.9e-02 nm, Epot= -4.48989e+04 Fmax= 3.85369e+02, atom= 809\n", + "Step= 225, Dmax= 1.8e-02 nm, Epot= -4.49146e+04 Fmax= 7.07322e+01, atom= 1517\n", + "Step= 226, Dmax= 2.1e-02 nm, Epot= -4.49244e+04 Fmax= 4.20600e+02, atom= 1517\n", + "Step= 227, Dmax= 2.5e-02 nm, Epot= -4.49333e+04 Fmax= 2.49944e+02, atom= 809\n", + "Step= 229, Dmax= 1.5e-02 nm, Epot= -4.49396e+04 Fmax= 9.11969e+01, atom= 809\n", + "Step= 230, Dmax= 1.8e-02 nm, Epot= -4.49417e+04 Fmax= 4.04562e+02, atom= 809\n", + "Step= 231, Dmax= 2.2e-02 nm, Epot= -4.49536e+04 Fmax= 1.37484e+02, atom= 809\n", + "Step= 233, Dmax= 1.3e-02 nm, Epot= -4.49582e+04 Fmax= 1.63833e+02, atom= 809\n", + "Step= 234, Dmax= 1.6e-02 nm, Epot= -4.49617e+04 Fmax= 2.04513e+02, atom= 809\n", + "Step= 235, Dmax= 1.9e-02 nm, Epot= -4.49640e+04 Fmax= 2.56307e+02, atom= 401\n", + "Step= 236, Dmax= 2.3e-02 nm, Epot= -4.49657e+04 Fmax= 3.34286e+02, atom= 401\n", + "Step= 237, Dmax= 2.7e-02 nm, Epot= -4.49688e+04 Fmax= 3.87506e+02, atom= 401\n", + "Step= 238, Dmax= 3.3e-02 nm, Epot= -4.49703e+04 Fmax= 4.62960e+02, atom= 401\n", + "Step= 240, Dmax= 2.0e-02 nm, Epot= -4.49872e+04 Fmax= 6.32842e+01, atom= 732\n", + "Step= 241, Dmax= 2.4e-02 nm, Epot= -4.49890e+04 Fmax= 6.36481e+02, atom= 401\n", + "Step= 242, Dmax= 2.8e-02 nm, Epot= -4.50072e+04 Fmax= 2.93148e+02, atom= 401\n", + "Step= 244, Dmax= 1.7e-02 nm, Epot= -4.50125e+04 Fmax= 1.27292e+02, atom= 401\n", + "Step= 245, Dmax= 2.0e-02 nm, Epot= -4.50138e+04 Fmax= 4.35828e+02, atom= 401\n", + "Step= 246, Dmax= 2.4e-02 nm, Epot= -4.50225e+04 Fmax= 2.00383e+02, atom= 401\n", + "Step= 248, Dmax= 1.5e-02 nm, Epot= -4.50270e+04 Fmax= 1.44593e+02, atom= 401\n", + "Step= 249, Dmax= 1.8e-02 nm, Epot= -4.50292e+04 Fmax= 3.14123e+02, atom= 401\n", + "Step= 250, Dmax= 2.1e-02 nm, Epot= -4.50349e+04 Fmax= 2.31536e+02, atom= 401\n", + "Step= 252, Dmax= 1.3e-02 nm, Epot= -4.50402e+04 Fmax= 8.56108e+01, atom= 401\n", + "Step= 253, Dmax= 1.5e-02 nm, Epot= -4.50449e+04 Fmax= 3.04497e+02, atom= 401\n", + "Step= 254, Dmax= 1.8e-02 nm, Epot= -4.50510e+04 Fmax= 1.61504e+02, atom= 401\n", + "Step= 256, Dmax= 1.1e-02 nm, Epot= -4.50551e+04 Fmax= 1.01147e+02, atom= 401\n", + "Step= 257, Dmax= 1.3e-02 nm, Epot= -4.50588e+04 Fmax= 2.37717e+02, atom= 401\n", + "Step= 258, Dmax= 1.6e-02 nm, Epot= -4.50637e+04 Fmax= 1.64128e+02, atom= 401\n", + "Step= 259, Dmax= 1.9e-02 nm, Epot= -4.50650e+04 Fmax= 3.18171e+02, atom= 401\n", + "Step= 260, Dmax= 2.3e-02 nm, Epot= -4.50699e+04 Fmax= 2.68223e+02, atom= 401\n", + "Step= 262, Dmax= 1.4e-02 nm, Epot= -4.50763e+04 Fmax= 7.52588e+01, atom= 401\n", + "Step= 263, Dmax= 1.6e-02 nm, Epot= -4.50810e+04 Fmax= 3.45060e+02, atom= 401\n", + "Step= 264, Dmax= 2.0e-02 nm, Epot= -4.50880e+04 Fmax= 1.59837e+02, atom= 401\n", + "Step= 266, Dmax= 1.2e-02 nm, Epot= -4.50918e+04 Fmax= 1.20073e+02, atom= 401\n", + "Step= 267, Dmax= 1.4e-02 nm, Epot= -4.50946e+04 Fmax= 2.39634e+02, atom= 401\n", + "Step= 268, Dmax= 1.7e-02 nm, Epot= -4.50990e+04 Fmax= 1.90055e+02, atom= 401\n", + "Step= 269, Dmax= 2.0e-02 nm, Epot= -4.50997e+04 Fmax= 3.24806e+02, atom= 401\n", + "Step= 270, Dmax= 2.4e-02 nm, Epot= -4.51036e+04 Fmax= 3.05721e+02, atom= 401\n", + "Step= 272, Dmax= 1.5e-02 nm, Epot= -4.51111e+04 Fmax= 6.60527e+01, atom= 401\n", + "Step= 273, Dmax= 1.8e-02 nm, Epot= -4.51161e+04 Fmax= 3.82814e+02, atom= 401\n", + "Step= 274, Dmax= 2.1e-02 nm, Epot= -4.51237e+04 Fmax= 1.63521e+02, atom= 401\n", + "Step= 276, Dmax= 1.3e-02 nm, Epot= -4.51273e+04 Fmax= 1.36521e+02, atom= 401\n", + "Step= 277, Dmax= 1.5e-02 nm, Epot= -4.51294e+04 Fmax= 2.45335e+02, atom= 401\n", + "Step= 278, Dmax= 1.8e-02 nm, Epot= -4.51333e+04 Fmax= 2.14659e+02, atom= 401\n", + "Step= 279, Dmax= 2.2e-02 nm, Epot= -4.51336e+04 Fmax= 3.34622e+02, atom= 401\n", + "Step= 280, Dmax= 2.6e-02 nm, Epot= -4.51364e+04 Fmax= 3.46212e+02, atom= 401\n", + "Step= 282, Dmax= 1.6e-02 nm, Epot= -4.51453e+04 Fmax= 5.70057e+01, atom= 401\n", + "Step= 283, Dmax= 1.9e-02 nm, Epot= -4.51516e+04 Fmax= 4.16424e+02, atom= 401\n", + "Step= 284, Dmax= 2.3e-02 nm, Epot= -4.51593e+04 Fmax= 1.73258e+02, atom= 401\n", + "Step= 286, Dmax= 1.4e-02 nm, Epot= -4.51626e+04 Fmax= 1.52974e+02, atom= 401\n", + "Step= 287, Dmax= 1.6e-02 nm, Epot= -4.51643e+04 Fmax= 2.52309e+02, atom= 401\n", + "Step= 288, Dmax= 2.0e-02 nm, Epot= -4.51675e+04 Fmax= 2.42247e+02, atom= 401\n", + "Step= 290, Dmax= 1.2e-02 nm, Epot= -4.51730e+04 Fmax= 5.38744e+01, atom= 401\n", + "Step= 291, Dmax= 1.4e-02 nm, Epot= -4.51789e+04 Fmax= 2.88017e+02, atom= 401\n", + "Step= 292, Dmax= 1.7e-02 nm, Epot= -4.51843e+04 Fmax= 1.35095e+02, atom= 401\n", + "Step= 294, Dmax= 1.0e-02 nm, Epot= -4.51874e+04 Fmax= 1.07492e+02, atom= 401\n", + "Step= 295, Dmax= 1.2e-02 nm, Epot= -4.51899e+04 Fmax= 1.94901e+02, atom= 401\n", + "Step= 296, Dmax= 1.5e-02 nm, Epot= -4.51932e+04 Fmax= 1.70760e+02, atom= 401\n", + "Step= 297, Dmax= 1.8e-02 nm, Epot= -4.51944e+04 Fmax= 2.63306e+02, atom= 401\n", + "Step= 298, Dmax= 2.1e-02 nm, Epot= -4.51971e+04 Fmax= 2.73339e+02, atom= 401\n", + "Step= 299, Dmax= 2.5e-02 nm, Epot= -4.51971e+04 Fmax= 3.51506e+02, atom= 401\n", + "Step= 301, Dmax= 1.5e-02 nm, Epot= -4.52067e+04 Fmax= 5.00179e+01, atom= 732\n", + "Step= 302, Dmax= 1.8e-02 nm, Epot= -4.52134e+04 Fmax= 3.31663e+02, atom= 732\n", + "Step= 303, Dmax= 2.2e-02 nm, Epot= -4.52186e+04 Fmax= 2.61202e+02, atom= 1356\n", + "Step= 305, Dmax= 1.3e-02 nm, Epot= -4.52239e+04 Fmax= 7.50971e+01, atom= 401\n", + "Step= 306, Dmax= 1.6e-02 nm, Epot= -4.52271e+04 Fmax= 3.02770e+02, atom= 401\n", + "Step= 307, Dmax= 1.9e-02 nm, Epot= -4.52323e+04 Fmax= 1.51597e+02, atom= 401\n", + "Step= 309, Dmax= 1.1e-02 nm, Epot= -4.52355e+04 Fmax= 1.13761e+02, atom= 401\n", + "Step= 310, Dmax= 1.4e-02 nm, Epot= -4.52372e+04 Fmax= 2.18595e+02, atom= 401\n", + "Step= 311, Dmax= 1.6e-02 nm, Epot= -4.52407e+04 Fmax= 1.88675e+02, atom= 401\n", + "Step= 312, Dmax= 2.0e-02 nm, Epot= -4.52410e+04 Fmax= 2.86985e+02, atom= 401\n", + "Step= 313, Dmax= 2.3e-02 nm, Epot= -4.52431e+04 Fmax= 3.11899e+02, atom= 401\n", + "Step= 315, Dmax= 1.4e-02 nm, Epot= -4.52510e+04 Fmax= 4.49427e+01, atom= 401\n", + "Step= 316, Dmax= 1.7e-02 nm, Epot= -4.52589e+04 Fmax= 3.31565e+02, atom= 401\n", + "Step= 317, Dmax= 2.0e-02 nm, Epot= -4.52642e+04 Fmax= 1.64041e+02, atom= 1356\n", + "Step= 319, Dmax= 1.2e-02 nm, Epot= -4.52673e+04 Fmax= 1.24027e+02, atom= 401\n", + "Step= 320, Dmax= 1.5e-02 nm, Epot= -4.52684e+04 Fmax= 2.30370e+02, atom= 1356\n", + "Step= 321, Dmax= 1.8e-02 nm, Epot= -4.52718e+04 Fmax= 2.02402e+02, atom= 401\n", + "Step= 323, Dmax= 1.1e-02 nm, Epot= -4.52763e+04 Fmax= 5.69089e+01, atom= 4016\n", + "Step= 324, Dmax= 1.3e-02 nm, Epot= -4.52803e+04 Fmax= 2.35743e+02, atom= 401\n", + "Step= 325, Dmax= 1.5e-02 nm, Epot= -4.52845e+04 Fmax= 1.23375e+02, atom= 1356\n", + "Step= 327, Dmax= 9.1e-03 nm, Epot= -4.52873e+04 Fmax= 8.89979e+01, atom= 401\n", + "Step= 328, Dmax= 1.1e-02 nm, Epot= -4.52894e+04 Fmax= 1.75425e+02, atom= 1356\n", + "Step= 329, Dmax= 1.3e-02 nm, Epot= -4.52925e+04 Fmax= 1.40784e+02, atom= 1356\n", + "Step= 330, Dmax= 1.6e-02 nm, Epot= -4.52932e+04 Fmax= 2.40298e+02, atom= 1356\n", + "Step= 331, Dmax= 1.9e-02 nm, Epot= -4.52962e+04 Fmax= 2.16653e+02, atom= 1356\n", + "Step= 333, Dmax= 1.1e-02 nm, Epot= -4.53011e+04 Fmax= 5.95828e+01, atom= 4016\n", + "Step= 334, Dmax= 1.4e-02 nm, Epot= -4.53043e+04 Fmax= 2.50744e+02, atom= 401\n", + "Step= 335, Dmax= 1.6e-02 nm, Epot= -4.53087e+04 Fmax= 1.33888e+02, atom= 1356\n", + "Step= 337, Dmax= 9.8e-03 nm, Epot= -4.53114e+04 Fmax= 9.00042e+01, atom= 1356\n", + "Step= 338, Dmax= 1.2e-02 nm, Epot= -4.53128e+04 Fmax= 1.95609e+02, atom= 1356\n", + "Step= 339, Dmax= 1.4e-02 nm, Epot= -4.53162e+04 Fmax= 1.40319e+02, atom= 1356\n", + "Step= 341, Dmax= 8.4e-03 nm, Epot= -4.53191e+04 Fmax= 5.90424e+01, atom= 4016\n", + "Step= 342, Dmax= 1.0e-02 nm, Epot= -4.53217e+04 Fmax= 1.77152e+02, atom= 401\n", + "Step= 343, Dmax= 1.2e-02 nm, Epot= -4.53249e+04 Fmax= 1.07718e+02, atom= 1356\n", + "Step= 344, Dmax= 1.5e-02 nm, Epot= -4.53251e+04 Fmax= 2.43520e+02, atom= 401\n", + "Step= 345, Dmax= 1.8e-02 nm, Epot= -4.53290e+04 Fmax= 1.67318e+02, atom= 1356\n", + "Step= 347, Dmax= 1.1e-02 nm, Epot= -4.53323e+04 Fmax= 7.74304e+01, atom= 732\n", + "Step= 348, Dmax= 1.3e-02 nm, Epot= -4.53333e+04 Fmax= 2.19156e+02, atom= 1356\n", + "Step= 349, Dmax= 1.5e-02 nm, Epot= -4.53371e+04 Fmax= 1.41075e+02, atom= 1356\n", + "Step= 351, Dmax= 9.1e-03 nm, Epot= -4.53399e+04 Fmax= 6.69161e+01, atom= 4016\n", + "Step= 352, Dmax= 1.1e-02 nm, Epot= -4.53415e+04 Fmax= 1.85721e+02, atom= 401\n", + "Step= 353, Dmax= 1.3e-02 nm, Epot= -4.53448e+04 Fmax= 1.18214e+02, atom= 1356\n", + "Step= 355, Dmax= 7.8e-03 nm, Epot= -4.53472e+04 Fmax= 6.13028e+01, atom= 732\n", + "Step= 356, Dmax= 9.4e-03 nm, Epot= -4.53491e+04 Fmax= 1.58820e+02, atom= 1356\n", + "Step= 357, Dmax= 1.1e-02 nm, Epot= -4.53519e+04 Fmax= 1.03229e+02, atom= 1356\n", + "Step= 358, Dmax= 1.4e-02 nm, Epot= -4.53522e+04 Fmax= 2.17340e+02, atom= 1356\n", + "Step= 359, Dmax= 1.6e-02 nm, Epot= -4.53554e+04 Fmax= 1.58522e+02, atom= 1356\n", + "Step= 361, Dmax= 9.8e-03 nm, Epot= -4.53585e+04 Fmax= 6.23680e+01, atom= 401\n", + "Step= 362, Dmax= 1.2e-02 nm, Epot= -4.53596e+04 Fmax= 2.04066e+02, atom= 401\n", + "Step= 363, Dmax= 1.4e-02 nm, Epot= -4.53633e+04 Fmax= 1.21447e+02, atom= 1356\n", + "Step= 365, Dmax= 8.4e-03 nm, Epot= -4.53657e+04 Fmax= 6.97432e+01, atom= 7326\n", + "Step= 366, Dmax= 1.0e-02 nm, Epot= -4.53672e+04 Fmax= 1.61126e+02, atom= 732\n", + "Step= 367, Dmax= 1.2e-02 nm, Epot= -4.53698e+04 Fmax= 1.12871e+02, atom= 1356\n", + "Step= 369, Dmax= 7.3e-03 nm, Epot= -4.53721e+04 Fmax= 4.85567e+01, atom= 1356\n", + "Step= 370, Dmax= 8.7e-03 nm, Epot= -4.53740e+04 Fmax= 1.49619e+02, atom= 1356\n", + "Step= 371, Dmax= 1.0e-02 nm, Epot= -4.53769e+04 Fmax= 9.05348e+01, atom= 1356\n", + "Step= 372, Dmax= 1.3e-02 nm, Epot= -4.53771e+04 Fmax= 1.91229e+02, atom= 1356\n", + "Step= 373, Dmax= 1.5e-02 nm, Epot= -4.53800e+04 Fmax= 1.54674e+02, atom= 732\n", + "Step= 375, Dmax= 9.1e-03 nm, Epot= -4.53832e+04 Fmax= 5.34967e+01, atom= 7326\n", + "Step= 376, Dmax= 1.1e-02 nm, Epot= -4.53848e+04 Fmax= 1.88271e+02, atom= 732\n", + "Step= 377, Dmax= 1.3e-02 nm, Epot= -4.53881e+04 Fmax= 1.03203e+02, atom= 732\n", + "Step= 379, Dmax= 7.8e-03 nm, Epot= -4.53902e+04 Fmax= 6.70056e+01, atom= 732\n", + "Step= 380, Dmax= 9.4e-03 nm, Epot= -4.53914e+04 Fmax= 1.40503e+02, atom= 732\n", + "Step= 381, Dmax= 1.1e-02 nm, Epot= -4.53938e+04 Fmax= 1.13925e+02, atom= 732\n", + "Step= 382, Dmax= 1.4e-02 nm, Epot= -4.53938e+04 Fmax= 1.82442e+02, atom= 732\n", + "Step= 383, Dmax= 1.6e-02 nm, Epot= -4.53956e+04 Fmax= 1.86432e+02, atom= 732\n", + "Step= 385, Dmax= 9.7e-03 nm, Epot= -4.54002e+04 Fmax= 3.45548e+01, atom= 732\n", + "Step= 386, Dmax= 1.2e-02 nm, Epot= -4.54021e+04 Fmax= 2.22666e+02, atom= 732\n", + "Step= 387, Dmax= 1.4e-02 nm, Epot= -4.54072e+04 Fmax= 9.98106e+01, atom= 1264\n", + "Step= 389, Dmax= 8.4e-03 nm, Epot= -4.54092e+04 Fmax= 8.52490e+01, atom= 1264\n", + "Step= 390, Dmax= 1.0e-02 nm, Epot= -4.54101e+04 Fmax= 1.42023e+02, atom= 1264\n", + "Step= 391, Dmax= 1.2e-02 nm, Epot= -4.54122e+04 Fmax= 1.32120e+02, atom= 1264\n", + "Step= 392, Dmax= 1.5e-02 nm, Epot= -4.54123e+04 Fmax= 1.95726e+02, atom= 1264\n", + "Step= 393, Dmax= 1.7e-02 nm, Epot= -4.54141e+04 Fmax= 2.01007e+02, atom= 1264\n", + "Step= 395, Dmax= 1.0e-02 nm, Epot= -4.54190e+04 Fmax= 4.75607e+01, atom= 5824\n", + "Step= 396, Dmax= 1.3e-02 nm, Epot= -4.54211e+04 Fmax= 2.24722e+02, atom= 582\n", + "Step= 397, Dmax= 1.5e-02 nm, Epot= -4.54246e+04 Fmax= 1.24923e+02, atom= 1264\n", + "Step= 399, Dmax= 9.0e-03 nm, Epot= -4.54267e+04 Fmax= 6.83893e+01, atom= 1264\n", + "Step= 400, Dmax= 1.1e-02 nm, Epot= -4.54277e+04 Fmax= 1.77135e+02, atom= 1264\n", + "Step= 401, Dmax= 1.3e-02 nm, Epot= -4.54306e+04 Fmax= 1.16403e+02, atom= 1264\n", + "Step= 403, Dmax= 7.8e-03 nm, Epot= -4.54327e+04 Fmax= 5.91627e+01, atom= 1264\n", + "Step= 404, Dmax= 9.4e-03 nm, Epot= -4.54344e+04 Fmax= 1.60136e+02, atom= 1264\n", + "Step= 405, Dmax= 1.1e-02 nm, Epot= -4.54369e+04 Fmax= 9.59752e+01, atom= 1264\n", + "Step= 406, Dmax= 1.4e-02 nm, Epot= -4.54372e+04 Fmax= 2.22145e+02, atom= 1264\n", + "Step= 407, Dmax= 1.6e-02 nm, Epot= -4.54403e+04 Fmax= 1.46206e+02, atom= 1264\n", + "Step= 409, Dmax= 9.7e-03 nm, Epot= -4.54429e+04 Fmax= 6.10649e+01, atom= 1264\n", + "Step= 410, Dmax= 1.2e-02 nm, Epot= -4.54435e+04 Fmax= 2.10118e+02, atom= 1264\n", + "Step= 411, Dmax= 1.4e-02 nm, Epot= -4.54476e+04 Fmax= 1.10080e+02, atom= 1264\n", + "Step= 413, Dmax= 8.4e-03 nm, Epot= -4.54496e+04 Fmax= 7.58745e+01, atom= 1264\n", + "Step= 414, Dmax= 1.0e-02 nm, Epot= -4.54509e+04 Fmax= 1.59076e+02, atom= 1264\n", + "Step= 415, Dmax= 1.2e-02 nm, Epot= -4.54533e+04 Fmax= 1.14893e+02, atom= 1264\n", + "Step= 416, Dmax= 1.5e-02 nm, Epot= -4.54533e+04 Fmax= 2.25622e+02, atom= 1264\n", + "Step= 417, Dmax= 1.7e-02 nm, Epot= -4.54562e+04 Fmax= 1.69988e+02, atom= 1264\n", + "Step= 419, Dmax= 1.0e-02 nm, Epot= -4.54596e+04 Fmax= 5.53755e+01, atom= 7184\n", + "Step= 420, Dmax= 1.3e-02 nm, Epot= -4.54597e+04 Fmax= 2.36358e+02, atom= 1264\n", + "Step= 421, Dmax= 1.5e-02 nm, Epot= -4.54650e+04 Fmax= 1.14802e+02, atom= 1264\n", + "Step= 423, Dmax= 9.0e-03 nm, Epot= -4.54671e+04 Fmax= 8.30082e+01, atom= 1264\n", + "Step= 424, Dmax= 1.1e-02 nm, Epot= -4.54682e+04 Fmax= 1.71070e+02, atom= 1264\n", + "Step= 425, Dmax= 1.3e-02 nm, Epot= -4.54709e+04 Fmax= 1.23981e+02, atom= 1264\n", + "Step= 427, Dmax= 7.8e-03 nm, Epot= -4.54735e+04 Fmax= 4.69152e+01, atom= 1264\n", + "Step= 428, Dmax= 9.4e-03 nm, Epot= -4.54754e+04 Fmax= 1.66723e+02, atom= 1264\n", + "Step= 429, Dmax= 1.1e-02 nm, Epot= -4.54789e+04 Fmax= 9.07986e+01, atom= 1264\n", + "Step= 431, Dmax= 6.7e-03 nm, Epot= -4.54810e+04 Fmax= 5.99520e+01, atom= 1264\n", + "Step= 432, Dmax= 8.1e-03 nm, Epot= -4.54829e+04 Fmax= 1.29197e+02, atom= 1264\n", + "Step= 433, Dmax= 9.7e-03 nm, Epot= -4.54854e+04 Fmax= 9.15278e+01, atom= 1264\n", + "Step= 434, Dmax= 1.2e-02 nm, Epot= -4.54863e+04 Fmax= 1.81738e+02, atom= 1264\n", + "Step= 435, Dmax= 1.4e-02 nm, Epot= -4.54892e+04 Fmax= 1.37133e+02, atom= 1264\n", + "Step= 437, Dmax= 8.4e-03 nm, Epot= -4.54922e+04 Fmax= 4.61792e+01, atom= 1264\n", + "Step= 438, Dmax= 1.0e-02 nm, Epot= -4.54938e+04 Fmax= 1.91067e+02, atom= 1264\n", + "Step= 439, Dmax= 1.2e-02 nm, Epot= -4.54983e+04 Fmax= 8.91475e+01, atom= 1264\n", + "Step= 441, Dmax= 7.2e-03 nm, Epot= -4.55005e+04 Fmax= 7.20804e+01, atom= 1264\n", + "Step= 442, Dmax= 8.7e-03 nm, Epot= -4.55023e+04 Fmax= 1.30895e+02, atom= 1264\n", + "Step= 443, Dmax= 1.0e-02 nm, Epot= -4.55048e+04 Fmax= 1.06668e+02, atom= 1264\n", + "Step= 444, Dmax= 1.3e-02 nm, Epot= -4.55056e+04 Fmax= 1.86899e+02, atom= 1264\n", + "Step= 445, Dmax= 1.5e-02 nm, Epot= -4.55084e+04 Fmax= 1.56771e+02, atom= 1264\n", + "Step= 447, Dmax= 9.0e-03 nm, Epot= -4.55121e+04 Fmax= 4.47535e+01, atom= 7184\n", + "Step= 448, Dmax= 1.1e-02 nm, Epot= -4.55141e+04 Fmax= 1.99787e+02, atom= 1264\n", + "Step= 449, Dmax= 1.3e-02 nm, Epot= -4.55189e+04 Fmax= 1.06720e+02, atom= 1264\n", + "Step= 451, Dmax= 7.8e-03 nm, Epot= -4.55214e+04 Fmax= 6.72726e+01, atom= 1264\n", + "Step= 452, Dmax= 9.4e-03 nm, Epot= -4.55231e+04 Fmax= 1.55689e+02, atom= 1264\n", + "Step= 453, Dmax= 1.1e-02 nm, Epot= -4.55262e+04 Fmax= 1.03024e+02, atom= 1264\n", + "Step= 454, Dmax= 1.3e-02 nm, Epot= -4.55267e+04 Fmax= 2.17718e+02, atom= 1264\n", + "Step= 455, Dmax= 1.6e-02 nm, Epot= -4.55304e+04 Fmax= 1.55432e+02, atom= 1264\n", + "Step= 457, Dmax= 9.7e-03 nm, Epot= -4.55338e+04 Fmax= 5.67265e+01, atom= 7184\n", + "Step= 458, Dmax= 1.2e-02 nm, Epot= -4.55349e+04 Fmax= 2.21905e+02, atom= 1264\n", + "Step= 459, Dmax= 1.4e-02 nm, Epot= -4.55402e+04 Fmax= 1.05630e+02, atom= 1264\n", + "Step= 461, Dmax= 8.4e-03 nm, Epot= -4.55426e+04 Fmax= 8.11209e+01, atom= 1264\n", + "Step= 462, Dmax= 1.0e-02 nm, Epot= -4.55444e+04 Fmax= 1.56235e+02, atom= 1264\n", + "Step= 463, Dmax= 1.2e-02 nm, Epot= -4.55473e+04 Fmax= 1.20712e+02, atom= 1264\n", + "Step= 464, Dmax= 1.4e-02 nm, Epot= -4.55478e+04 Fmax= 2.22606e+02, atom= 1264\n", + "Step= 465, Dmax= 1.7e-02 nm, Epot= -4.55511e+04 Fmax= 1.77102e+02, atom= 1264\n", + "Step= 467, Dmax= 1.0e-02 nm, Epot= -4.55550e+04 Fmax= 5.61709e+01, atom= 7184\n", + "Step= 468, Dmax= 1.3e-02 nm, Epot= -4.55566e+04 Fmax= 2.26963e+02, atom= 1264\n", + "Step= 469, Dmax= 1.5e-02 nm, Epot= -4.55615e+04 Fmax= 1.29722e+02, atom= 1264\n", + "Step= 471, Dmax= 9.0e-03 nm, Epot= -4.55642e+04 Fmax= 7.08086e+01, atom= 1264\n", + "Step= 472, Dmax= 1.1e-02 nm, Epot= -4.55658e+04 Fmax= 1.92649e+02, atom= 1264\n", + "Step= 473, Dmax= 1.3e-02 nm, Epot= -4.55694e+04 Fmax= 1.08901e+02, atom= 1264\n", + "Step= 475, Dmax= 7.8e-03 nm, Epot= -4.55718e+04 Fmax= 6.45256e+01, atom= 1264\n", + "Step= 476, Dmax= 9.3e-03 nm, Epot= -4.55739e+04 Fmax= 1.48044e+02, atom= 1264\n", + "Step= 477, Dmax= 1.1e-02 nm, Epot= -4.55767e+04 Fmax= 1.10633e+02, atom= 1264\n", + "Step= 478, Dmax= 1.3e-02 nm, Epot= -4.55776e+04 Fmax= 1.95536e+02, atom= 1264\n", + "Step= 479, Dmax= 1.6e-02 nm, Epot= -4.55803e+04 Fmax= 1.76651e+02, atom= 1264\n", + "Step= 481, Dmax= 9.7e-03 nm, Epot= -4.55839e+04 Fmax= 5.26737e+01, atom= 5824\n", + "Step= 482, Dmax= 1.2e-02 nm, Epot= -4.55866e+04 Fmax= 2.10209e+02, atom= 1264\n", + "Step= 483, Dmax= 1.4e-02 nm, Epot= -4.55900e+04 Fmax= 1.18189e+02, atom= 1264\n", + "Step= 485, Dmax= 8.4e-03 nm, Epot= -4.55924e+04 Fmax= 6.57998e+01, atom= 1264\n", + "Step= 486, Dmax= 1.0e-02 nm, Epot= -4.55942e+04 Fmax= 1.63159e+02, atom= 1264\n", + "Step= 487, Dmax= 1.2e-02 nm, Epot= -4.55971e+04 Fmax= 1.14192e+02, atom= 1264\n", + "Step= 488, Dmax= 1.4e-02 nm, Epot= -4.55974e+04 Fmax= 2.13428e+02, atom= 1264\n", + "Step= 489, Dmax= 1.7e-02 nm, Epot= -4.56001e+04 Fmax= 1.85925e+02, atom= 1264\n", + "Step= 491, Dmax= 1.0e-02 nm, Epot= -4.56038e+04 Fmax= 5.90512e+01, atom= 5824\n", + "Step= 492, Dmax= 1.2e-02 nm, Epot= -4.56054e+04 Fmax= 2.24859e+02, atom= 1264\n", + "Step= 493, Dmax= 1.5e-02 nm, Epot= -4.56090e+04 Fmax= 1.26452e+02, atom= 1264\n", + "Step= 495, Dmax= 9.0e-03 nm, Epot= -4.56113e+04 Fmax= 6.98403e+01, atom= 1264\n", + "Step= 496, Dmax= 1.1e-02 nm, Epot= -4.56125e+04 Fmax= 1.74811e+02, atom= 1264\n", + "Step= 497, Dmax= 1.3e-02 nm, Epot= -4.56154e+04 Fmax= 1.22608e+02, atom= 1264\n", + "Step= 499, Dmax= 7.8e-03 nm, Epot= -4.56176e+04 Fmax= 5.37046e+01, atom= 5824\n", + "Step= 500, Dmax= 9.3e-03 nm, Epot= -4.56195e+04 Fmax= 1.67245e+02, atom= 1264\n", + "Step= 501, Dmax= 1.1e-02 nm, Epot= -4.56222e+04 Fmax= 8.98307e+01, atom= 1264\n", + "Step= 502, Dmax= 1.3e-02 nm, Epot= -4.56222e+04 Fmax= 2.34486e+02, atom= 1264\n", + "Step= 503, Dmax= 1.6e-02 nm, Epot= -4.56258e+04 Fmax= 1.36234e+02, atom= 1264\n", + "Step= 505, Dmax= 9.7e-03 nm, Epot= -4.56282e+04 Fmax= 7.40982e+01, atom= 1264\n", + "Step= 506, Dmax= 1.2e-02 nm, Epot= -4.56287e+04 Fmax= 1.89739e+02, atom= 1264\n", + "Step= 507, Dmax= 1.4e-02 nm, Epot= -4.56318e+04 Fmax= 1.30278e+02, atom= 1264\n", + "Step= 509, Dmax= 8.3e-03 nm, Epot= -4.56342e+04 Fmax= 5.96627e+01, atom= 5824\n", + "Step= 510, Dmax= 1.0e-02 nm, Epot= -4.56353e+04 Fmax= 1.74925e+02, atom= 1264\n", + "Step= 511, Dmax= 1.2e-02 nm, Epot= -4.56382e+04 Fmax= 1.00090e+02, atom= 1264\n", + "Step= 513, Dmax= 7.2e-03 nm, Epot= -4.56402e+04 Fmax= 5.99708e+01, atom= 1264\n", + "Step= 514, Dmax= 8.7e-03 nm, Epot= -4.56414e+04 Fmax= 1.32142e+02, atom= 1264\n", + "Step= 515, Dmax= 1.0e-02 nm, Epot= -4.56435e+04 Fmax= 1.06018e+02, atom= 1264\n", + "Step= 517, Dmax= 6.2e-03 nm, Epot= -4.56457e+04 Fmax= 3.76699e+01, atom= 5824\n", + "Step= 518, Dmax= 7.5e-03 nm, Epot= -4.56476e+04 Fmax= 1.31954e+02, atom= 1264\n", + "Step= 519, Dmax= 9.0e-03 nm, Epot= -4.56502e+04 Fmax= 7.45799e+01, atom= 626\n", + "Step= 521, Dmax= 5.4e-03 nm, Epot= -4.56519e+04 Fmax= 5.08350e+01, atom= 626\n", + "Step= 522, Dmax= 6.5e-03 nm, Epot= -4.56533e+04 Fmax= 1.04445e+02, atom= 626\n", + "Step= 523, Dmax= 7.8e-03 nm, Epot= -4.56552e+04 Fmax= 7.94883e+01, atom= 626\n", + "Step= 524, Dmax= 9.3e-03 nm, Epot= -4.56561e+04 Fmax= 1.42802e+02, atom= 626\n", + "Step= 525, Dmax= 1.1e-02 nm, Epot= -4.56581e+04 Fmax= 1.23094e+02, atom= 626\n", + "Step= 526, Dmax= 1.3e-02 nm, Epot= -4.56583e+04 Fmax= 1.96708e+02, atom= 626\n", + "Step= 527, Dmax= 1.6e-02 nm, Epot= -4.56600e+04 Fmax= 1.88176e+02, atom= 626\n", + "Step= 529, Dmax= 9.6e-03 nm, Epot= -4.56635e+04 Fmax= 4.08446e+01, atom= 339\n", + "Step= 530, Dmax= 1.2e-02 nm, Epot= -4.56653e+04 Fmax= 2.31817e+02, atom= 626\n", + "Step= 531, Dmax= 1.4e-02 nm, Epot= -4.56688e+04 Fmax= 1.05576e+02, atom= 626\n", + "Step= 533, Dmax= 8.3e-03 nm, Epot= -4.56704e+04 Fmax= 8.48921e+01, atom= 626\n", + "Step= 534, Dmax= 1.0e-02 nm, Epot= -4.56713e+04 Fmax= 1.55737e+02, atom= 626\n", + "Step= 535, Dmax= 1.2e-02 nm, Epot= -4.56730e+04 Fmax= 1.29263e+02, atom= 626\n", + "Step= 536, Dmax= 1.4e-02 nm, Epot= -4.56731e+04 Fmax= 2.15519e+02, atom= 626\n", + "Step= 537, Dmax= 1.7e-02 nm, Epot= -4.56747e+04 Fmax= 1.98912e+02, atom= 626\n", + "Step= 539, Dmax= 1.0e-02 nm, Epot= -4.56779e+04 Fmax= 4.67466e+01, atom= 339\n", + "Step= 540, Dmax= 1.2e-02 nm, Epot= -4.56791e+04 Fmax= 2.47455e+02, atom= 626\n", + "Step= 541, Dmax= 1.5e-02 nm, Epot= -4.56825e+04 Fmax= 1.15021e+02, atom= 626\n", + "Step= 543, Dmax= 9.0e-03 nm, Epot= -4.56840e+04 Fmax= 8.88231e+01, atom= 626\n", + "Step= 544, Dmax= 1.1e-02 nm, Epot= -4.56847e+04 Fmax= 1.70270e+02, atom= 626\n", + "Step= 545, Dmax= 1.3e-02 nm, Epot= -4.56864e+04 Fmax= 1.37225e+02, atom= 626\n", + "Step= 547, Dmax= 7.7e-03 nm, Epot= -4.56883e+04 Fmax= 4.60359e+01, atom= 626\n", + "Step= 548, Dmax= 9.3e-03 nm, Epot= -4.56899e+04 Fmax= 1.71175e+02, atom= 626\n", + "Step= 549, Dmax= 1.1e-02 nm, Epot= -4.56920e+04 Fmax= 9.40015e+01, atom= 626\n", + "Step= 551, Dmax= 6.7e-03 nm, Epot= -4.56934e+04 Fmax= 5.98856e+01, atom= 626\n", + "Step= 552, Dmax= 8.0e-03 nm, Epot= -4.56945e+04 Fmax= 1.34785e+02, atom= 626\n", + "Step= 553, Dmax= 9.6e-03 nm, Epot= -4.56961e+04 Fmax= 9.46899e+01, atom= 626\n", + "Step= 554, Dmax= 1.2e-02 nm, Epot= -4.56965e+04 Fmax= 1.82785e+02, atom= 626\n", + "Step= 555, Dmax= 1.4e-02 nm, Epot= -4.56982e+04 Fmax= 1.49079e+02, atom= 626\n", + "Step= 557, Dmax= 8.3e-03 nm, Epot= -4.57002e+04 Fmax= 4.78267e+01, atom= 626\n", + "Step= 558, Dmax= 1.0e-02 nm, Epot= -4.57014e+04 Fmax= 1.88086e+02, atom= 626\n", + "Step= 559, Dmax= 1.2e-02 nm, Epot= -4.57037e+04 Fmax= 9.81260e+01, atom= 626\n", + "Step= 561, Dmax= 7.2e-03 nm, Epot= -4.57050e+04 Fmax= 6.65660e+01, atom= 626\n", + "Step= 562, Dmax= 8.6e-03 nm, Epot= -4.57059e+04 Fmax= 1.42578e+02, atom= 626\n", + "Step= 563, Dmax= 1.0e-02 nm, Epot= -4.57075e+04 Fmax= 1.04330e+02, atom= 626\n", + "Step= 564, Dmax= 1.2e-02 nm, Epot= -4.57075e+04 Fmax= 1.93645e+02, atom= 626\n", + "Step= 565, Dmax= 1.5e-02 nm, Epot= -4.57092e+04 Fmax= 1.64932e+02, atom= 626\n", + "Step= 567, Dmax= 8.9e-03 nm, Epot= -4.57115e+04 Fmax= 4.80302e+01, atom= 626\n", + "Step= 568, Dmax= 1.1e-02 nm, Epot= -4.57123e+04 Fmax= 2.05861e+02, atom= 626\n", + "Step= 569, Dmax= 1.3e-02 nm, Epot= -4.57149e+04 Fmax= 1.02901e+02, atom= 626\n", + "Step= 571, Dmax= 7.7e-03 nm, Epot= -4.57162e+04 Fmax= 7.43972e+01, atom= 626\n", + "Step= 572, Dmax= 9.3e-03 nm, Epot= -4.57168e+04 Fmax= 1.49815e+02, atom= 626\n", + "Step= 573, Dmax= 1.1e-02 nm, Epot= -4.57183e+04 Fmax= 1.16146e+02, atom= 626\n", + "Step= 575, Dmax= 6.7e-03 nm, Epot= -4.57198e+04 Fmax= 4.34834e+01, atom= 626\n", + "Step= 576, Dmax= 8.0e-03 nm, Epot= -4.57211e+04 Fmax= 1.43232e+02, atom= 626\n", + "Step= 577, Dmax= 9.6e-03 nm, Epot= -4.57228e+04 Fmax= 8.55387e+01, atom= 626\n", + "Step= 578, Dmax= 1.2e-02 nm, Epot= -4.57228e+04 Fmax= 1.92399e+02, atom= 626\n", + "Step= 579, Dmax= 1.4e-02 nm, Epot= -4.57247e+04 Fmax= 1.36339e+02, atom= 626\n", + "Step= 581, Dmax= 8.3e-03 nm, Epot= -4.57264e+04 Fmax= 5.45353e+01, atom= 626\n", + "Step= 582, Dmax= 1.0e-02 nm, Epot= -4.57265e+04 Fmax= 1.96394e+02, atom= 626\n", + "Step= 583, Dmax= 1.2e-02 nm, Epot= -4.57291e+04 Fmax= 9.64268e+01, atom= 626\n", + "Step= 585, Dmax= 7.2e-03 nm, Epot= -4.57303e+04 Fmax= 7.41450e+01, atom= 626\n", + "Step= 586, Dmax= 8.6e-03 nm, Epot= -4.57311e+04 Fmax= 1.29012e+02, atom= 626\n", + "Step= 587, Dmax= 1.0e-02 nm, Epot= -4.57323e+04 Fmax= 1.15697e+02, atom= 626\n", + "Step= 588, Dmax= 1.2e-02 nm, Epot= -4.57324e+04 Fmax= 1.82031e+02, atom= 626\n", + "Step= 589, Dmax= 1.5e-02 nm, Epot= -4.57336e+04 Fmax= 1.69834e+02, atom= 626\n", + "Step= 591, Dmax= 8.9e-03 nm, Epot= -4.57359e+04 Fmax= 3.83471e+01, atom= 111\n", + "Step= 593, Dmax= 5.4e-03 nm, Epot= -4.57372e+04 Fmax= 9.56553e+01, atom= 626\n", + "Step= 594, Dmax= 6.4e-03 nm, Epot= -4.57383e+04 Fmax= 5.84311e+01, atom= 626\n", + "Step= 595, Dmax= 7.7e-03 nm, Epot= -4.57391e+04 Fmax= 1.26123e+02, atom= 626\n", + "Step= 596, Dmax= 9.3e-03 nm, Epot= -4.57405e+04 Fmax= 9.46619e+01, atom= 626\n", + "Step= 597, Dmax= 1.1e-02 nm, Epot= -4.57406e+04 Fmax= 1.70938e+02, atom= 626\n", + "Step= 598, Dmax= 1.3e-02 nm, Epot= -4.57419e+04 Fmax= 1.50439e+02, atom= 626\n", + "Step= 600, Dmax= 8.0e-03 nm, Epot= -4.57439e+04 Fmax= 4.12865e+01, atom= 626\n", + "Step= 601, Dmax= 9.6e-03 nm, Epot= -4.57448e+04 Fmax= 1.85942e+02, atom= 339\n", + "Step= 602, Dmax= 1.2e-02 nm, Epot= -4.57469e+04 Fmax= 8.88933e+01, atom= 626\n", + "Step= 604, Dmax= 6.9e-03 nm, Epot= -4.57480e+04 Fmax= 7.14680e+01, atom= 339\n", + "Step= 605, Dmax= 8.3e-03 nm, Epot= -4.57486e+04 Fmax= 1.26724e+02, atom= 626\n", + "Step= 606, Dmax= 1.0e-02 nm, Epot= -4.57497e+04 Fmax= 1.11488e+02, atom= 626\n", + "Step= 607, Dmax= 1.2e-02 nm, Epot= -4.57498e+04 Fmax= 1.73017e+02, atom= 626\n", + "Step= 608, Dmax= 1.4e-02 nm, Epot= -4.57507e+04 Fmax= 1.73464e+02, atom= 626\n", + "Step= 610, Dmax= 8.6e-03 nm, Epot= -4.57532e+04 Fmax= 3.38567e+01, atom= 626\n", + "Step= 611, Dmax= 1.0e-02 nm, Epot= -4.57544e+04 Fmax= 2.09504e+02, atom= 339\n", + "Step= 612, Dmax= 1.2e-02 nm, Epot= -4.57568e+04 Fmax= 8.74946e+01, atom= 626\n", + "Step= 614, Dmax= 7.4e-03 nm, Epot= -4.57577e+04 Fmax= 8.69064e+01, atom= 339\n", + "Step= 615, Dmax= 8.9e-03 nm, Epot= -4.57583e+04 Fmax= 1.23988e+02, atom= 626\n", + "Step= 616, Dmax= 1.1e-02 nm, Epot= -4.57591e+04 Fmax= 1.31773e+02, atom= 626\n", + "Step= 617, Dmax= 1.3e-02 nm, Epot= -4.57594e+04 Fmax= 1.72500e+02, atom= 626\n", + "Step= 618, Dmax= 1.5e-02 nm, Epot= -4.57597e+04 Fmax= 2.00409e+02, atom= 626\n", + "Step= 620, Dmax= 9.2e-03 nm, Epot= -4.57627e+04 Fmax= 2.39675e+01, atom= 339\n", + "Step= 621, Dmax= 1.1e-02 nm, Epot= -4.57653e+04 Fmax= 2.31660e+02, atom= 339\n", + "Step= 622, Dmax= 1.3e-02 nm, Epot= -4.57678e+04 Fmax= 8.94231e+01, atom= 626\n", + "Step= 624, Dmax= 8.0e-03 nm, Epot= -4.57686e+04 Fmax= 1.03530e+02, atom= 339\n", + "Step= 625, Dmax= 9.6e-03 nm, Epot= -4.57693e+04 Fmax= 1.21607e+02, atom= 626\n", + "Step= 626, Dmax= 1.2e-02 nm, Epot= -4.57698e+04 Fmax= 1.55201e+02, atom= 339\n", + "Step= 627, Dmax= 1.4e-02 nm, Epot= -4.57704e+04 Fmax= 1.70058e+02, atom= 626\n", + "Step= 629, Dmax= 8.3e-03 nm, Epot= -4.57727e+04 Fmax= 2.72581e+01, atom= 111\n", + "Step= 630, Dmax= 9.9e-03 nm, Epot= -4.57733e+04 Fmax= 2.16085e+02, atom= 339\n", + "Step= 631, Dmax= 1.2e-02 nm, Epot= -4.57766e+04 Fmax= 9.24663e+01, atom= 626\n", + "Step= 633, Dmax= 7.2e-03 nm, Epot= -4.57776e+04 Fmax= 7.42935e+01, atom= 626\n", + "Step= 634, Dmax= 8.6e-03 nm, Epot= -4.57781e+04 Fmax= 1.31618e+02, atom= 339\n", + "Step= 635, Dmax= 1.0e-02 nm, Epot= -4.57792e+04 Fmax= 1.10678e+02, atom= 339\n", + "Step= 637, Dmax= 6.2e-03 nm, Epot= -4.57805e+04 Fmax= 3.43018e+01, atom= 339\n", + "Step= 638, Dmax= 7.4e-03 nm, Epot= -4.57814e+04 Fmax= 1.47363e+02, atom= 339\n", + "Step= 639, Dmax= 8.9e-03 nm, Epot= -4.57831e+04 Fmax= 6.95464e+01, atom= 339\n", + "Step= 641, Dmax= 5.3e-03 nm, Epot= -4.57840e+04 Fmax= 5.67596e+01, atom= 339\n", + "Step= 642, Dmax= 6.4e-03 nm, Epot= -4.57848e+04 Fmax= 9.61592e+01, atom= 339\n", + "Step= 643, Dmax= 7.7e-03 nm, Epot= -4.57857e+04 Fmax= 8.50610e+01, atom= 339\n", + "Step= 644, Dmax= 9.2e-03 nm, Epot= -4.57862e+04 Fmax= 1.37083e+02, atom= 339\n", + "Step= 645, Dmax= 1.1e-02 nm, Epot= -4.57872e+04 Fmax= 1.23699e+02, atom= 339\n", + "Step= 647, Dmax= 6.6e-03 nm, Epot= -4.57886e+04 Fmax= 3.11872e+01, atom= 339\n", + "Step= 648, Dmax= 8.0e-03 nm, Epot= -4.57894e+04 Fmax= 1.69219e+02, atom= 339\n", + "Step= 649, Dmax= 9.6e-03 nm, Epot= -4.57916e+04 Fmax= 6.72612e+01, atom= 339\n", + "Step= 651, Dmax= 5.7e-03 nm, Epot= -4.57924e+04 Fmax= 6.75795e+01, atom= 339\n", + "Step= 652, Dmax= 6.9e-03 nm, Epot= -4.57932e+04 Fmax= 9.69829e+01, atom= 339\n", + "Step= 653, Dmax= 8.3e-03 nm, Epot= -4.57940e+04 Fmax= 9.75978e+01, atom= 339\n", + "Step= 654, Dmax= 9.9e-03 nm, Epot= -4.57944e+04 Fmax= 1.40862e+02, atom= 339\n", + "Step= 655, Dmax= 1.2e-02 nm, Epot= -4.57953e+04 Fmax= 1.39190e+02, atom= 339\n", + "Step= 657, Dmax= 7.1e-03 nm, Epot= -4.57969e+04 Fmax= 2.73913e+01, atom= 339\n", + "Step= 658, Dmax= 8.6e-03 nm, Epot= -4.57976e+04 Fmax= 1.95066e+02, atom= 339\n", + "Step= 659, Dmax= 1.0e-02 nm, Epot= -4.58004e+04 Fmax= 6.36849e+01, atom= 339\n", + "Step= 661, Dmax= 6.2e-03 nm, Epot= -4.58013e+04 Fmax= 8.04211e+01, atom= 339\n", + "Step= 662, Dmax= 7.4e-03 nm, Epot= -4.58020e+04 Fmax= 9.60683e+01, atom= 339\n", + "Step= 663, Dmax= 8.9e-03 nm, Epot= -4.58027e+04 Fmax= 1.13041e+02, atom= 339\n", + "Step= 664, Dmax= 1.1e-02 nm, Epot= -4.58032e+04 Fmax= 1.42921e+02, atom= 339\n", + "Step= 665, Dmax= 1.3e-02 nm, Epot= -4.58038e+04 Fmax= 1.57267e+02, atom= 339\n", + "Step= 667, Dmax= 7.7e-03 nm, Epot= -4.58057e+04 Fmax= 2.35192e+01, atom= 373\n", + "Step= 668, Dmax= 9.2e-03 nm, Epot= -4.58066e+04 Fmax= 2.15002e+02, atom= 339\n", + "Step= 669, Dmax= 1.1e-02 nm, Epot= -4.58099e+04 Fmax= 6.96320e+01, atom= 339\n", + "Step= 671, Dmax= 6.6e-03 nm, Epot= -4.58107e+04 Fmax= 8.30808e+01, atom= 339\n", + "Step= 672, Dmax= 8.0e-03 nm, Epot= -4.58113e+04 Fmax= 1.06300e+02, atom= 339\n", + "Step= 673, Dmax= 9.6e-03 nm, Epot= -4.58120e+04 Fmax= 1.17744e+02, atom= 339\n", + "Step= 674, Dmax= 1.1e-02 nm, Epot= -4.58123e+04 Fmax= 1.57048e+02, atom= 339\n", + "Step= 675, Dmax= 1.4e-02 nm, Epot= -4.58130e+04 Fmax= 1.65546e+02, atom= 339\n", + "Step= 677, Dmax= 8.3e-03 nm, Epot= -4.58151e+04 Fmax= 2.78218e+01, atom= 373\n", + "Step= 678, Dmax= 9.9e-03 nm, Epot= -4.58151e+04 Fmax= 2.34164e+02, atom= 339\n", + "Step= 679, Dmax= 1.2e-02 nm, Epot= -4.58188e+04 Fmax= 7.10347e+01, atom= 339\n", + "Step= 681, Dmax= 7.1e-03 nm, Epot= -4.58195e+04 Fmax= 9.26905e+01, atom= 339\n", + "Step= 682, Dmax= 8.6e-03 nm, Epot= -4.58202e+04 Fmax= 1.09829e+02, atom= 339\n", + "Step= 683, Dmax= 1.0e-02 nm, Epot= -4.58208e+04 Fmax= 1.30072e+02, atom= 339\n", + "Step= 684, Dmax= 1.2e-02 nm, Epot= -4.58211e+04 Fmax= 1.64335e+02, atom= 339\n", + "Step= 685, Dmax= 1.5e-02 nm, Epot= -4.58216e+04 Fmax= 1.80792e+02, atom= 339\n", + "Step= 687, Dmax= 8.9e-03 nm, Epot= -4.58240e+04 Fmax= 2.92893e+01, atom= 373\n", + "Step= 689, Dmax= 5.3e-03 nm, Epot= -4.58251e+04 Fmax= 9.78425e+01, atom= 339\n", + "Step= 690, Dmax= 6.4e-03 nm, Epot= -4.58262e+04 Fmax= 5.70152e+01, atom= 339\n", + "Step= 691, Dmax= 7.7e-03 nm, Epot= -4.58267e+04 Fmax= 1.22595e+02, atom= 339\n", + "Step= 692, Dmax= 9.2e-03 nm, Epot= -4.58278e+04 Fmax= 9.57025e+01, atom= 339\n", + "Step= 693, Dmax= 1.1e-02 nm, Epot= -4.58278e+04 Fmax= 1.63069e+02, atom= 339\n", + "Step= 694, Dmax= 1.3e-02 nm, Epot= -4.58288e+04 Fmax= 1.53822e+02, atom= 339\n", + "Step= 696, Dmax= 7.9e-03 nm, Epot= -4.58307e+04 Fmax= 3.37759e+01, atom= 626\n", + "Step= 697, Dmax= 9.5e-03 nm, Epot= -4.58315e+04 Fmax= 1.89961e+02, atom= 339\n", + "Step= 698, Dmax= 1.1e-02 nm, Epot= -4.58336e+04 Fmax= 8.22114e+01, atom= 339\n", + "Step= 700, Dmax= 6.9e-03 nm, Epot= -4.58345e+04 Fmax= 7.66694e+01, atom= 339\n", + "Step= 701, Dmax= 8.2e-03 nm, Epot= -4.58350e+04 Fmax= 1.16153e+02, atom= 339\n", + "Step= 702, Dmax= 9.9e-03 nm, Epot= -4.58358e+04 Fmax= 1.17988e+02, atom= 339\n", + "Step= 703, Dmax= 1.2e-02 nm, Epot= -4.58361e+04 Fmax= 1.59671e+02, atom= 339\n", + "Step= 704, Dmax= 1.4e-02 nm, Epot= -4.58365e+04 Fmax= 1.80375e+02, atom= 339\n", + "Step= 706, Dmax= 8.5e-03 nm, Epot= -4.58389e+04 Fmax= 2.33530e+01, atom= 626\n", + "Step= 707, Dmax= 1.0e-02 nm, Epot= -4.58411e+04 Fmax= 2.03565e+02, atom= 626\n", + "Step= 708, Dmax= 1.2e-02 nm, Epot= -4.58433e+04 Fmax= 9.12305e+01, atom= 339\n", + "Step= 710, Dmax= 7.4e-03 nm, Epot= -4.58441e+04 Fmax= 8.27932e+01, atom= 339\n", + "Step= 711, Dmax= 8.9e-03 nm, Epot= -4.58447e+04 Fmax= 1.23413e+02, atom= 339\n", + "Step= 712, Dmax= 1.1e-02 nm, Epot= -4.58454e+04 Fmax= 1.28785e+02, atom= 339\n", + "Step= 713, Dmax= 1.3e-02 nm, Epot= -4.58456e+04 Fmax= 1.69024e+02, atom= 339\n", + "Step= 714, Dmax= 1.5e-02 nm, Epot= -4.58459e+04 Fmax= 1.96916e+02, atom= 339\n", + "Step= 716, Dmax= 9.2e-03 nm, Epot= -4.58487e+04 Fmax= 2.28121e+01, atom= 626\n", + "Step= 717, Dmax= 1.1e-02 nm, Epot= -4.58512e+04 Fmax= 2.16066e+02, atom= 626\n", + "Step= 718, Dmax= 1.3e-02 nm, Epot= -4.58535e+04 Fmax= 1.00925e+02, atom= 339\n", + "Step= 720, Dmax= 7.9e-03 nm, Epot= -4.58544e+04 Fmax= 8.63834e+01, atom= 339\n", + "Step= 721, Dmax= 9.5e-03 nm, Epot= -4.58548e+04 Fmax= 1.35204e+02, atom= 339\n", + "Step= 722, Dmax= 1.1e-02 nm, Epot= -4.58557e+04 Fmax= 1.35654e+02, atom= 339\n", + "Step= 723, Dmax= 1.4e-02 nm, Epot= -4.58557e+04 Fmax= 1.84251e+02, atom= 339\n", + "Step= 724, Dmax= 1.6e-02 nm, Epot= -4.58561e+04 Fmax= 2.08713e+02, atom= 339\n", + "Step= 726, Dmax= 9.9e-03 nm, Epot= -4.58591e+04 Fmax= 2.69558e+01, atom= 626\n", + "Step= 727, Dmax= 1.2e-02 nm, Epot= -4.58610e+04 Fmax= 2.30049e+02, atom= 626\n", + "Step= 728, Dmax= 1.4e-02 nm, Epot= -4.58635e+04 Fmax= 1.11443e+02, atom= 339\n", + "Step= 730, Dmax= 8.5e-03 nm, Epot= -4.58645e+04 Fmax= 8.79935e+01, atom= 339\n", + "Step= 731, Dmax= 1.0e-02 nm, Epot= -4.58648e+04 Fmax= 1.50752e+02, atom= 339\n", + "Step= 732, Dmax= 1.2e-02 nm, Epot= -4.58658e+04 Fmax= 1.39305e+02, atom= 339\n", + "Step= 734, Dmax= 7.4e-03 nm, Epot= -4.58675e+04 Fmax= 3.31729e+01, atom= 626\n", + "Step= 735, Dmax= 8.8e-03 nm, Epot= -4.58687e+04 Fmax= 1.72629e+02, atom= 339\n", + "Step= 736, Dmax= 1.1e-02 nm, Epot= -4.58706e+04 Fmax= 7.76954e+01, atom= 339\n", + "Step= 738, Dmax= 6.4e-03 nm, Epot= -4.58715e+04 Fmax= 6.80183e+01, atom= 339\n", + "Step= 739, Dmax= 7.6e-03 nm, Epot= -4.58723e+04 Fmax= 1.10730e+02, atom= 339\n", + "Step= 740, Dmax= 9.2e-03 nm, Epot= -4.58732e+04 Fmax= 1.04167e+02, atom= 339\n", + "Step= 741, Dmax= 1.1e-02 nm, Epot= -4.58737e+04 Fmax= 1.52042e+02, atom= 339\n", + "Step= 742, Dmax= 1.3e-02 nm, Epot= -4.58744e+04 Fmax= 1.59245e+02, atom= 339\n", + "Step= 744, Dmax= 7.9e-03 nm, Epot= -4.58764e+04 Fmax= 2.68021e+01, atom= 626\n", + "Step= 745, Dmax= 9.5e-03 nm, Epot= -4.58785e+04 Fmax= 1.86342e+02, atom= 339\n", + "Step= 746, Dmax= 1.1e-02 nm, Epot= -4.58805e+04 Fmax= 8.42300e+01, atom= 339\n", + "Step= 748, Dmax= 6.8e-03 nm, Epot= -4.58815e+04 Fmax= 7.29713e+01, atom= 339\n", + "Step= 749, Dmax= 8.2e-03 nm, Epot= -4.58822e+04 Fmax= 1.18122e+02, atom= 339\n", + "Step= 750, Dmax= 9.9e-03 nm, Epot= -4.58832e+04 Fmax= 1.12316e+02, atom= 339\n", + "Step= 751, Dmax= 1.2e-02 nm, Epot= -4.58836e+04 Fmax= 1.61764e+02, atom= 339\n", + "Step= 752, Dmax= 1.4e-02 nm, Epot= -4.58844e+04 Fmax= 1.71788e+02, atom= 339\n", + "Step= 754, Dmax= 8.5e-03 nm, Epot= -4.58866e+04 Fmax= 2.84467e+01, atom= 626\n", + "Step= 755, Dmax= 1.0e-02 nm, Epot= -4.58887e+04 Fmax= 1.95087e+02, atom= 626\n", + "Step= 756, Dmax= 1.2e-02 nm, Epot= -4.58909e+04 Fmax= 9.54889e+01, atom= 339\n", + "Step= 758, Dmax= 7.4e-03 nm, Epot= -4.58919e+04 Fmax= 7.29046e+01, atom= 339\n", + "Step= 759, Dmax= 8.8e-03 nm, Epot= -4.58927e+04 Fmax= 1.31941e+02, atom= 339\n", + "Step= 760, Dmax= 1.1e-02 nm, Epot= -4.58938e+04 Fmax= 1.15030e+02, atom= 339\n", + "Step= 761, Dmax= 1.3e-02 nm, Epot= -4.58940e+04 Fmax= 1.79516e+02, atom= 339\n", + "Step= 762, Dmax= 1.5e-02 nm, Epot= -4.58950e+04 Fmax= 1.78274e+02, atom= 339\n", + "Step= 764, Dmax= 9.2e-03 nm, Epot= -4.58975e+04 Fmax= 3.50347e+01, atom= 626\n", + "Step= 765, Dmax= 1.1e-02 nm, Epot= -4.58989e+04 Fmax= 2.10127e+02, atom= 339\n", + "Step= 766, Dmax= 1.3e-02 nm, Epot= -4.59014e+04 Fmax= 1.00796e+02, atom= 339\n", + "Step= 768, Dmax= 7.9e-03 nm, Epot= -4.59025e+04 Fmax= 7.79165e+01, atom= 339\n", + "Step= 769, Dmax= 9.5e-03 nm, Epot= -4.59031e+04 Fmax= 1.42516e+02, atom= 339\n", + "Step= 770, Dmax= 1.1e-02 nm, Epot= -4.59044e+04 Fmax= 1.22166e+02, atom= 339\n", + "Step= 771, Dmax= 1.4e-02 nm, Epot= -4.59044e+04 Fmax= 1.93761e+02, atom= 339\n", + "Step= 772, Dmax= 1.6e-02 nm, Epot= -4.59055e+04 Fmax= 1.90051e+02, atom= 339\n", + "Step= 774, Dmax= 9.8e-03 nm, Epot= -4.59082e+04 Fmax= 3.91080e+01, atom= 626\n", + "Step= 775, Dmax= 1.2e-02 nm, Epot= -4.59094e+04 Fmax= 2.19922e+02, atom= 626\n", + "Step= 776, Dmax= 1.4e-02 nm, Epot= -4.59120e+04 Fmax= 1.13231e+02, atom= 339\n", + "Step= 778, Dmax= 8.5e-03 nm, Epot= -4.59133e+04 Fmax= 7.78003e+01, atom= 339\n", + "Step= 779, Dmax= 1.0e-02 nm, Epot= -4.59137e+04 Fmax= 1.60113e+02, atom= 339\n", + "Step= 780, Dmax= 1.2e-02 nm, Epot= -4.59153e+04 Fmax= 1.23893e+02, atom= 339\n", + "Step= 782, Dmax= 7.3e-03 nm, Epot= -4.59169e+04 Fmax= 4.34073e+01, atom= 339\n", + "Step= 783, Dmax= 8.8e-03 nm, Epot= -4.59180e+04 Fmax= 1.60361e+02, atom= 339\n", + "Step= 784, Dmax= 1.1e-02 nm, Epot= -4.59199e+04 Fmax= 8.34727e+01, atom= 339\n", + "Step= 786, Dmax= 6.3e-03 nm, Epot= -4.59210e+04 Fmax= 5.90294e+01, atom= 339\n", + "Step= 787, Dmax= 7.6e-03 nm, Epot= -4.59220e+04 Fmax= 1.17917e+02, atom= 339\n", + "Step= 788, Dmax= 9.1e-03 nm, Epot= -4.59233e+04 Fmax= 9.33944e+01, atom= 339\n", + "Step= 789, Dmax= 1.1e-02 nm, Epot= -4.59238e+04 Fmax= 1.59164e+02, atom= 339\n", + "Step= 790, Dmax= 1.3e-02 nm, Epot= -4.59251e+04 Fmax= 1.45658e+02, atom= 339\n", + "Step= 792, Dmax= 7.9e-03 nm, Epot= -4.59270e+04 Fmax= 3.54126e+01, atom= 626\n", + "Step= 793, Dmax= 9.5e-03 nm, Epot= -4.59287e+04 Fmax= 1.77841e+02, atom= 339\n", + "Step= 794, Dmax= 1.1e-02 nm, Epot= -4.59309e+04 Fmax= 8.54512e+01, atom= 339\n", + "Step= 796, Dmax= 6.8e-03 nm, Epot= -4.59321e+04 Fmax= 6.73159e+01, atom= 339\n", + "Step= 797, Dmax= 8.2e-03 nm, Epot= -4.59331e+04 Fmax= 1.21367e+02, atom= 339\n", + "Step= 798, Dmax= 9.8e-03 nm, Epot= -4.59343e+04 Fmax= 1.04717e+02, atom= 339\n", + "Step= 799, Dmax= 1.2e-02 nm, Epot= -4.59348e+04 Fmax= 1.65276e+02, atom= 339\n", + "Step= 800, Dmax= 1.4e-02 nm, Epot= -4.59360e+04 Fmax= 1.61438e+02, atom= 339\n", + "Step= 802, Dmax= 8.5e-03 nm, Epot= -4.59382e+04 Fmax= 3.35367e+01, atom= 626\n", + "Step= 803, Dmax= 1.0e-02 nm, Epot= -4.59403e+04 Fmax= 1.88881e+02, atom= 626\n", + "Step= 804, Dmax= 1.2e-02 nm, Epot= -4.59427e+04 Fmax= 9.43843e+01, atom= 339\n", + "Step= 806, Dmax= 7.3e-03 nm, Epot= -4.59439e+04 Fmax= 6.94536e+01, atom= 339\n", + "Step= 807, Dmax= 8.8e-03 nm, Epot= -4.59449e+04 Fmax= 1.32682e+02, atom= 339\n", + "Step= 808, Dmax= 1.1e-02 nm, Epot= -4.59463e+04 Fmax= 1.09795e+02, atom= 339\n", + "Step= 809, Dmax= 1.3e-02 nm, Epot= -4.59467e+04 Fmax= 1.79183e+02, atom= 339\n", + "Step= 810, Dmax= 1.5e-02 nm, Epot= -4.59480e+04 Fmax= 1.70905e+02, atom= 339\n", + "Step= 812, Dmax= 9.1e-03 nm, Epot= -4.59505e+04 Fmax= 3.74880e+01, atom= 626\n", + "Step= 813, Dmax= 1.1e-02 nm, Epot= -4.59524e+04 Fmax= 2.00786e+02, atom= 626\n", + "Step= 814, Dmax= 1.3e-02 nm, Epot= -4.59550e+04 Fmax= 1.02289e+02, atom= 339\n", + "Step= 816, Dmax= 7.9e-03 nm, Epot= -4.59563e+04 Fmax= 7.28154e+01, atom= 339\n", + "Step= 817, Dmax= 9.5e-03 nm, Epot= -4.59573e+04 Fmax= 1.43715e+02, atom= 339\n", + "Step= 818, Dmax= 1.1e-02 nm, Epot= -4.59588e+04 Fmax= 1.15034e+02, atom= 339\n", + "Step= 819, Dmax= 1.4e-02 nm, Epot= -4.59590e+04 Fmax= 1.94107e+02, atom= 339\n", + "Step= 820, Dmax= 1.6e-02 nm, Epot= -4.59605e+04 Fmax= 1.80866e+02, atom= 339\n", + "Step= 822, Dmax= 9.8e-03 nm, Epot= -4.59633e+04 Fmax= 4.16821e+01, atom= 626\n", + "Step= 823, Dmax= 1.2e-02 nm, Epot= -4.59649e+04 Fmax= 2.13495e+02, atom= 626\n", + "Step= 824, Dmax= 1.4e-02 nm, Epot= -4.59677e+04 Fmax= 1.10673e+02, atom= 339\n", + "Step= 826, Dmax= 8.5e-03 nm, Epot= -4.59692e+04 Fmax= 7.58230e+01, atom= 339\n", + "Step= 827, Dmax= 1.0e-02 nm, Epot= -4.59700e+04 Fmax= 1.56275e+02, atom= 339\n", + "Step= 828, Dmax= 1.2e-02 nm, Epot= -4.59718e+04 Fmax= 1.20715e+02, atom= 339\n", + "Step= 830, Dmax= 7.3e-03 nm, Epot= -4.59735e+04 Fmax= 4.24621e+01, atom= 339\n", + "Step= 831, Dmax= 8.8e-03 nm, Epot= -4.59752e+04 Fmax= 1.55357e+02, atom= 339\n", + "Step= 832, Dmax= 1.1e-02 nm, Epot= -4.59773e+04 Fmax= 8.19048e+01, atom= 339\n", + "Step= 833, Dmax= 1.3e-02 nm, Epot= -4.59774e+04 Fmax= 2.07308e+02, atom= 339\n", + "Step= 834, Dmax= 1.5e-02 nm, Epot= -4.59799e+04 Fmax= 1.31297e+02, atom= 339\n", + "Step= 836, Dmax= 9.1e-03 nm, Epot= -4.59817e+04 Fmax= 6.74730e+01, atom= 339\n", + "Step= 837, Dmax= 1.1e-02 nm, Epot= -4.59823e+04 Fmax= 1.86538e+02, atom= 339\n", + "Step= 838, Dmax= 1.3e-02 nm, Epot= -4.59847e+04 Fmax= 1.14235e+02, atom= 339\n", + "Step= 840, Dmax= 7.9e-03 nm, Epot= -4.59863e+04 Fmax= 5.96225e+01, atom= 339\n", + "Step= 841, Dmax= 9.4e-03 nm, Epot= -4.59874e+04 Fmax= 1.50472e+02, atom= 339\n", + "Step= 842, Dmax= 1.1e-02 nm, Epot= -4.59892e+04 Fmax= 1.00988e+02, atom= 339\n", + "Step= 844, Dmax= 6.8e-03 nm, Epot= -4.59907e+04 Fmax= 4.82523e+01, atom= 339\n", + "Step= 845, Dmax= 8.2e-03 nm, Epot= -4.59921e+04 Fmax= 1.38474e+02, atom= 339\n", + "Step= 846, Dmax= 9.8e-03 nm, Epot= -4.59939e+04 Fmax= 8.34365e+01, atom= 339\n", + "Step= 847, Dmax= 1.2e-02 nm, Epot= -4.59942e+04 Fmax= 1.80634e+02, atom= 339\n", + "Step= 848, Dmax= 1.4e-02 nm, Epot= -4.59962e+04 Fmax= 1.37406e+02, atom= 339\n", + "Step= 850, Dmax= 8.5e-03 nm, Epot= -4.59981e+04 Fmax= 4.80834e+01, atom= 626\n", + "Step= 851, Dmax= 1.0e-02 nm, Epot= -4.59992e+04 Fmax= 1.79239e+02, atom= 339\n", + "Step= 852, Dmax= 1.2e-02 nm, Epot= -4.60015e+04 Fmax= 9.23964e+01, atom= 339\n", + "Step= 854, Dmax= 7.3e-03 nm, Epot= -4.60028e+04 Fmax= 6.56046e+01, atom= 339\n", + "Step= 855, Dmax= 8.8e-03 nm, Epot= -4.60038e+04 Fmax= 1.30952e+02, atom= 339\n", + "Step= 856, Dmax= 1.1e-02 nm, Epot= -4.60053e+04 Fmax= 1.03950e+02, atom= 339\n", + "Step= 857, Dmax= 1.3e-02 nm, Epot= -4.60056e+04 Fmax= 1.76467e+02, atom= 339\n", + "Step= 858, Dmax= 1.5e-02 nm, Epot= -4.60069e+04 Fmax= 1.63622e+02, atom= 339\n", + "Step= 860, Dmax= 9.1e-03 nm, Epot= -4.60093e+04 Fmax= 3.73812e+01, atom= 626\n", + "Step= 861, Dmax= 1.1e-02 nm, Epot= -4.60108e+04 Fmax= 1.95469e+02, atom= 339\n", + "Step= 862, Dmax= 1.3e-02 nm, Epot= -4.60133e+04 Fmax= 9.79406e+01, atom= 339\n", + "Step= 864, Dmax= 7.9e-03 nm, Epot= -4.60145e+04 Fmax= 7.10330e+01, atom= 339\n", + "Step= 865, Dmax= 9.4e-03 nm, Epot= -4.60152e+04 Fmax= 1.38319e+02, atom= 339\n", + "Step= 866, Dmax= 1.1e-02 nm, Epot= -4.60166e+04 Fmax= 1.12971e+02, atom= 339\n", + "Step= 867, Dmax= 1.4e-02 nm, Epot= -4.60166e+04 Fmax= 1.86197e+02, atom= 339\n", + "Step= 868, Dmax= 1.6e-02 nm, Epot= -4.60178e+04 Fmax= 1.77816e+02, atom= 339\n", + "Step= 870, Dmax= 9.8e-03 nm, Epot= -4.60204e+04 Fmax= 3.77205e+01, atom= 626\n", + "Step= 871, Dmax= 1.2e-02 nm, Epot= -4.60216e+04 Fmax= 2.07593e+02, atom= 626\n", + "Step= 872, Dmax= 1.4e-02 nm, Epot= -4.60241e+04 Fmax= 1.06280e+02, atom= 339\n", + "Step= 874, Dmax= 8.4e-03 nm, Epot= -4.60253e+04 Fmax= 7.44738e+01, atom= 339\n", + "Step= 875, Dmax= 1.0e-02 nm, Epot= -4.60257e+04 Fmax= 1.50066e+02, atom= 339\n", + "Step= 876, Dmax= 1.2e-02 nm, Epot= -4.60271e+04 Fmax= 1.18824e+02, atom= 339\n", + "Step= 878, Dmax= 7.3e-03 nm, Epot= -4.60286e+04 Fmax= 3.98415e+01, atom= 339\n", + "Step= 879, Dmax= 8.8e-03 nm, Epot= -4.60296e+04 Fmax= 1.51006e+02, atom= 339\n", + "Step= 880, Dmax= 1.1e-02 nm, Epot= -4.60314e+04 Fmax= 7.89362e+01, atom= 339\n", + "Step= 882, Dmax= 6.3e-03 nm, Epot= -4.60324e+04 Fmax= 5.61341e+01, atom= 339\n", + "Step= 883, Dmax= 7.6e-03 nm, Epot= -4.60332e+04 Fmax= 1.10035e+02, atom= 339\n", + "Step= 884, Dmax= 9.1e-03 nm, Epot= -4.60343e+04 Fmax= 8.91024e+01, atom= 339\n", + "Step= 885, Dmax= 1.1e-02 nm, Epot= -4.60346e+04 Fmax= 1.48725e+02, atom= 339\n", + "Step= 886, Dmax= 1.3e-02 nm, Epot= -4.60357e+04 Fmax= 1.39380e+02, atom= 339\n", + "Step= 888, Dmax= 7.8e-03 nm, Epot= -4.60375e+04 Fmax= 3.12563e+01, atom= 626\n", + "Step= 889, Dmax= 9.4e-03 nm, Epot= -4.60387e+04 Fmax= 1.71736e+02, atom= 339\n", + "Step= 890, Dmax= 1.1e-02 nm, Epot= -4.60408e+04 Fmax= 7.72520e+01, atom= 339\n", + "Step= 892, Dmax= 6.8e-03 nm, Epot= -4.60417e+04 Fmax= 6.74849e+01, atom= 339\n", + "Step= 893, Dmax= 8.1e-03 nm, Epot= -4.60423e+04 Fmax= 1.09795e+02, atom= 339\n", + "Step= 894, Dmax= 9.8e-03 nm, Epot= -4.60432e+04 Fmax= 1.03174e+02, atom= 339\n", + "Step= 895, Dmax= 1.2e-02 nm, Epot= -4.60435e+04 Fmax= 1.50259e+02, atom= 339\n", + "Step= 896, Dmax= 1.4e-02 nm, Epot= -4.60442e+04 Fmax= 1.58043e+02, atom= 339\n", + "Step= 898, Dmax= 8.4e-03 nm, Epot= -4.60463e+04 Fmax= 2.61751e+01, atom= 626\n", + "Step= 899, Dmax= 1.0e-02 nm, Epot= -4.60478e+04 Fmax= 1.81278e+02, atom= 626\n", + "Step= 900, Dmax= 1.2e-02 nm, Epot= -4.60499e+04 Fmax= 8.68027e+01, atom= 339\n", + "Step= 902, Dmax= 7.3e-03 nm, Epot= -4.60508e+04 Fmax= 6.90929e+01, atom= 339\n", + "Step= 903, Dmax= 8.7e-03 nm, Epot= -4.60512e+04 Fmax= 1.20307e+02, atom= 339\n", + "Step= 904, Dmax= 1.0e-02 nm, Epot= -4.60522e+04 Fmax= 1.07849e+02, atom= 339\n", + "Step= 906, Dmax= 6.3e-03 nm, Epot= -4.60535e+04 Fmax= 2.74008e+01, atom= 339\n", + "Step= 907, Dmax= 7.6e-03 nm, Epot= -4.60546e+04 Fmax= 1.35223e+02, atom= 339\n", + "Step= 908, Dmax= 9.1e-03 nm, Epot= -4.60562e+04 Fmax= 6.11478e+01, atom= 339\n", + "Step= 910, Dmax= 5.4e-03 nm, Epot= -4.60570e+04 Fmax= 5.44143e+01, atom= 339\n", + "Step= 911, Dmax= 6.5e-03 nm, Epot= -4.60576e+04 Fmax= 8.66402e+01, atom= 339\n", + "Step= 912, Dmax= 7.8e-03 nm, Epot= -4.60583e+04 Fmax= 8.25002e+01, atom= 339\n", + "Step= 913, Dmax= 9.4e-03 nm, Epot= -4.60586e+04 Fmax= 1.19756e+02, atom= 339\n", + "Step= 914, Dmax= 1.1e-02 nm, Epot= -4.60592e+04 Fmax= 1.24849e+02, atom= 339\n", + "Step= 916, Dmax= 6.8e-03 nm, Epot= -4.60610e+04 Fmax= 2.10007e+01, atom= 626\n", + "Step= 917, Dmax= 8.1e-03 nm, Epot= -4.60619e+04 Fmax= 1.48160e+02, atom= 339\n", + "Step= 918, Dmax= 9.7e-03 nm, Epot= -4.60642e+04 Fmax= 6.43929e+01, atom= 339\n", + "Step= 920, Dmax= 5.8e-03 nm, Epot= -4.60650e+04 Fmax= 5.98242e+01, atom= 339\n", + "Step= 921, Dmax= 7.0e-03 nm, Epot= -4.60652e+04 Fmax= 9.92604e+01, atom= 1368\n", + "Step= 922, Dmax= 8.4e-03 nm, Epot= -4.60661e+04 Fmax= 8.97723e+01, atom= 1368\n", + "Step= 924, Dmax= 5.1e-03 nm, Epot= -4.60675e+04 Fmax= 2.15263e+01, atom= 1368\n", + "Step= 925, Dmax= 6.1e-03 nm, Epot= -4.60684e+04 Fmax= 1.15788e+02, atom= 1368\n", + "Step= 926, Dmax= 7.3e-03 nm, Epot= -4.60700e+04 Fmax= 4.81783e+01, atom= 1368\n", + "Step= 928, Dmax= 4.4e-03 nm, Epot= -4.60707e+04 Fmax= 4.94505e+01, atom= 1368\n", + "Step= 929, Dmax= 5.2e-03 nm, Epot= -4.60713e+04 Fmax= 6.82019e+01, atom= 1368\n", + "Step= 930, Dmax= 6.3e-03 nm, Epot= -4.60720e+04 Fmax= 7.24909e+01, atom= 1368\n", + "Step= 931, Dmax= 7.5e-03 nm, Epot= -4.60724e+04 Fmax= 9.72356e+01, atom= 1368\n", + "Step= 932, Dmax= 9.1e-03 nm, Epot= -4.60730e+04 Fmax= 1.04855e+02, atom= 1368\n", + "Step= 933, Dmax= 1.1e-02 nm, Epot= -4.60731e+04 Fmax= 1.41015e+02, atom= 1368\n", + "Step= 934, Dmax= 1.3e-02 nm, Epot= -4.60735e+04 Fmax= 1.49464e+02, atom= 1368\n", + "Step= 936, Dmax= 7.8e-03 nm, Epot= -4.60758e+04 Fmax= 1.99619e+01, atom= 1368\n", + "Step= 938, Dmax= 4.7e-03 nm, Epot= -4.60768e+04 Fmax= 8.99570e+01, atom= 1368\n", + "Step= 939, Dmax= 5.6e-03 nm, Epot= -4.60779e+04 Fmax= 3.81441e+01, atom= 1368\n", + "Step= 940, Dmax= 6.8e-03 nm, Epot= -4.60781e+04 Fmax= 1.09635e+02, atom= 1368\n", + "Step= 941, Dmax= 8.1e-03 nm, Epot= -4.60794e+04 Fmax= 6.98445e+01, atom= 1368\n", + "Step= 943, Dmax= 4.9e-03 nm, Epot= -4.60803e+04 Fmax= 3.94161e+01, atom= 1368\n", + "Step= 944, Dmax= 5.8e-03 nm, Epot= -4.60807e+04 Fmax= 9.22727e+01, atom= 1368\n", + "Step= 945, Dmax= 7.0e-03 nm, Epot= -4.60817e+04 Fmax= 6.52531e+01, atom= 1368\n", + "Step= 947, Dmax= 4.2e-03 nm, Epot= -4.60826e+04 Fmax= 2.73306e+01, atom= 1368\n", + "Step= 948, Dmax= 5.0e-03 nm, Epot= -4.60831e+04 Fmax= 8.60369e+01, atom= 1026\n", + "Step= 949, Dmax= 6.1e-03 nm, Epot= -4.60843e+04 Fmax= 5.11679e+01, atom= 1026\n", + "Step= 951, Dmax= 3.6e-03 nm, Epot= -4.60850e+04 Fmax= 3.00145e+01, atom= 1026\n", + "Step= 952, Dmax= 4.4e-03 nm, Epot= -4.60856e+04 Fmax= 6.71428e+01, atom= 1026\n", + "Step= 953, Dmax= 5.2e-03 nm, Epot= -4.60865e+04 Fmax= 5.07159e+01, atom= 1026\n", + "Step= 954, Dmax= 6.3e-03 nm, Epot= -4.60867e+04 Fmax= 8.89054e+01, atom= 1026\n", + "Step= 955, Dmax= 7.5e-03 nm, Epot= -4.60875e+04 Fmax= 8.11168e+01, atom= 1026\n", + "Step= 957, Dmax= 4.5e-03 nm, Epot= -4.60886e+04 Fmax= 2.18573e+01, atom= 1026\n", + "Step= 958, Dmax= 5.4e-03 nm, Epot= -4.60895e+04 Fmax= 1.04464e+02, atom= 1026\n", + "Step= 959, Dmax= 6.5e-03 nm, Epot= -4.60908e+04 Fmax= 4.48000e+01, atom= 1026\n", + "Step= 961, Dmax= 3.9e-03 nm, Epot= -4.60914e+04 Fmax= 4.28859e+01, atom= 1026\n", + "Step= 962, Dmax= 4.7e-03 nm, Epot= -4.60920e+04 Fmax= 6.15801e+01, atom= 1026\n", + "Step= 963, Dmax= 5.6e-03 nm, Epot= -4.60926e+04 Fmax= 6.56971e+01, atom= 1026\n", + "Step= 964, Dmax= 6.7e-03 nm, Epot= -4.60931e+04 Fmax= 8.46946e+01, atom= 1026\n", + "Step= 965, Dmax= 8.1e-03 nm, Epot= -4.60936e+04 Fmax= 9.90914e+01, atom= 1026\n", + "Step= 966, Dmax= 9.7e-03 nm, Epot= -4.60939e+04 Fmax= 1.17320e+02, atom= 1026\n", + "Step= 967, Dmax= 1.2e-02 nm, Epot= -4.60941e+04 Fmax= 1.46918e+02, atom= 1026\n", + "Step= 968, Dmax= 1.4e-02 nm, Epot= -4.60942e+04 Fmax= 1.63409e+02, atom= 1026\n", + "Step= 970, Dmax= 8.4e-03 nm, Epot= -4.60967e+04 Fmax= 1.96308e+01, atom= 4826\n", + "Step= 972, Dmax= 5.0e-03 nm, Epot= -4.60977e+04 Fmax= 8.77423e+01, atom= 1026\n", + "Step= 973, Dmax= 6.0e-03 nm, Epot= -4.60987e+04 Fmax= 5.22804e+01, atom= 1026\n", + "Step= 974, Dmax= 7.3e-03 nm, Epot= -4.60988e+04 Fmax= 1.06596e+02, atom= 1026\n", + "Step= 975, Dmax= 8.7e-03 nm, Epot= -4.60997e+04 Fmax= 8.86450e+01, atom= 1026\n", + "Step= 977, Dmax= 5.2e-03 nm, Epot= -4.61008e+04 Fmax= 2.98101e+01, atom= 1026\n", + "Step= 978, Dmax= 6.3e-03 nm, Epot= -4.61012e+04 Fmax= 1.15733e+02, atom= 1026\n", + "Step= 979, Dmax= 7.5e-03 nm, Epot= -4.61025e+04 Fmax= 5.60872e+01, atom= 1026\n", + "Step= 981, Dmax= 4.5e-03 nm, Epot= -4.61031e+04 Fmax= 4.45764e+01, atom= 1026\n", + "Step= 982, Dmax= 5.4e-03 nm, Epot= -4.61036e+04 Fmax= 7.54621e+01, atom= 1026\n", + "Step= 983, Dmax= 6.5e-03 nm, Epot= -4.61042e+04 Fmax= 7.08865e+01, atom= 1026\n", + "Step= 984, Dmax= 7.8e-03 nm, Epot= -4.61046e+04 Fmax= 1.01943e+02, atom= 1026\n", + "Step= 985, Dmax= 9.4e-03 nm, Epot= -4.61051e+04 Fmax= 1.09669e+02, atom= 1026\n", + "Step= 986, Dmax= 1.1e-02 nm, Epot= -4.61051e+04 Fmax= 1.39034e+02, atom= 1026\n", + "Step= 987, Dmax= 1.3e-02 nm, Epot= -4.61053e+04 Fmax= 1.66041e+02, atom= 1026\n", + "Step= 989, Dmax= 8.1e-03 nm, Epot= -4.61075e+04 Fmax= 2.46161e+01, atom= 4336\n", + "Step= 990, Dmax= 9.7e-03 nm, Epot= -4.61084e+04 Fmax= 1.87621e+02, atom= 1026\n", + "Step= 991, Dmax= 1.2e-02 nm, Epot= -4.61101e+04 Fmax= 8.92817e+01, atom= 1026\n", + "Step= 993, Dmax= 7.0e-03 nm, Epot= -4.61108e+04 Fmax= 6.53803e+01, atom= 1026\n", + "Step= 994, Dmax= 8.4e-03 nm, Epot= -4.61110e+04 Fmax= 1.19211e+02, atom= 1026\n", + "Step= 995, Dmax= 1.0e-02 nm, Epot= -4.61118e+04 Fmax= 1.05027e+02, atom= 1026\n", + "Step= 997, Dmax= 6.0e-03 nm, Epot= -4.61127e+04 Fmax= 3.14732e+01, atom= 1026\n", + "Step= 998, Dmax= 7.2e-03 nm, Epot= -4.61132e+04 Fmax= 1.38389e+02, atom= 1026\n", + "Step= 999, Dmax= 8.7e-03 nm, Epot= -4.61144e+04 Fmax= 6.15178e+01, atom= 1026\n", + "Step= 1000, Dmax= 1.0e-02 nm, Epot= -4.61141e+04 Fmax= 1.83454e+02, atom= 1026\n", "Energy minimization reached the maximum number of steps before the forces\n", "reached the requested precision Fmax < 10.\n", "\n", "writing lowest energy coordinates.\n", "\n", - "Back Off! I just backed up em.pdb to ./#em.pdb.11#\n", - "\n", "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n", - "Potential Energy = -4.6071258e+04\n", - "Maximum force = 3.6144512e+01 on atom 191\n", - "Norm of force = 2.4094036e+00\n", + "Potential Energy = -4.6114367e+04\n", + "Maximum force = 6.1517822e+01 on atom 1026\n", + "Norm of force = 3.0288026e+00\n", "\n", - "GROMACS reminds you: \"You see it through a charmed medium: you can not discern that the gilding is slime and the silk draperies cobwebs; that the marble is sordid slate, and the polished woods mere refuse chips and scale bark.\" (Mr. Rochester in Jane Eyre by Charlotte Bronte)\n", + "GROMACS reminds you: \"In the End Science Comes Down to Praying\" (P. v.d. Berg)\n", "\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -1525,13 +1520,9 @@ "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top\n", "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.11#\n", "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.11#\n", - "\n", - "GROMACS reminds you: \"You see it through a charmed medium: you can not discern that the gilding is slime and the silk draperies cobwebs; that the marble is sordid slate, and the polished woods mere refuse chips and scale bark.\" (Mr. Rochester in Jane Eyre by Charlotte Bronte)\n", + "GROMACS reminds you: \"In the End Science Comes Down to Praying\" (P. v.d. Berg)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -1547,7 +1538,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1881604097\n", + "Setting the LD random seed to -2343429\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -1623,7 +1614,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 10 to 50, rlist from 1.107 to 1.268\n", + "Changing nstlist from 10 to 50, rlist from 1.108 to 1.274\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -1634,21 +1625,22 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "100000 steps, 1000.0 ps (continuing from step 100000, 1000.0 ps).\n", + "100000 steps, 1000.0 ps.\n", "\n", + "Step 0 Warning: pressure scaling more than 1%, mu: 0.98589 0.98589 0.98589\n", + "step 0\n", + "Step 50 Warning: pressure scaling more than 1%, mu: 1.02318 1.02318 1.02318\n", + "step 100, remaining wall clock time: 39 s \n", + "Step 150 Warning: pressure scaling more than 1%, mu: 1.0125 1.0125 1.0125\n", + "step 99900, remaining wall clock time: 0 s 700, remaining wall clock time: 38 s \n", "Writing final coordinates.\n", - "\n", - "Back Off! I just backed up md.pdb to ./#md.pdb.11#\n", "step 100000, remaining wall clock time: 0 s \n", - "NOTE: 42 % of the run time was spent in pair search,\n", - " you might want to increase nstlist (this has no effect on accuracy)\n", - "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 0.100 0.025 398.4\n", + " Time: 127.012 31.753 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 34.436 0.697\n", + "Performance: 2721.028 0.009\n", "\n", - "GROMACS reminds you: \"I originally implemented PME to prove that you didn't need it...\" (Erik Lindahl)\n", + "GROMACS reminds you: \"The Path Of the Righteous Man is Beset On All Sides With the Iniquities Of the Selfish and the Tyranny Of Evil Men.\" (Pulp Fiction)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n" ] @@ -1689,6 +1681,7 @@ "mdpow.equil : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.gro').\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 't']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -1704,14 +1697,10 @@ "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -t /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt\n", "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.10#\n", "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "Last frame -1 time 1000.000 \n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.9#\n", - "\n", - "GROMACS reminds you: \"I originally implemented PME to prove that you didn't need it...\" (Erik Lindahl)\n", + "GROMACS reminds you: \"The Path Of the Righteous Man is Beset On All Sides With the Iniquities Of the Selfish and the Tyranny Of Evil Men.\" (Pulp Fiction)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -1736,7 +1725,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -269549605\n", + "Setting the LD random seed to -100958209\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -1779,21 +1768,16 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "500000 steps, 10000.0 ps (continuing from step 500000, 10000.0 ps).\n", - "\n", + "500000 steps, 10000.0 ps.\n", + "step 499900, remaining wall clock time: 0 s 443700, remaining wall clock time: 26 s 493000, remaining wall clock time: 3 s \n", "Writing final coordinates.\n", - "\n", - "Back Off! I just backed up md.pdb to ./#md.pdb.9#\n", "step 500000, remaining wall clock time: 0 s \n", - "NOTE: 11 % of the run time was spent in pair search,\n", - " you might want to increase nstlist (this has no effect on accuracy)\n", - "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 0.054 0.014 397.1\n", + " Time: 942.251 235.563 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 126.362 0.190\n", + "Performance: 3667.817 0.007\n", "\n", - "GROMACS reminds you: \"Philosophy of science is about as useful to scientists as ornithology is to birds.\" (Richard Feynman)\n", + "GROMACS reminds you: \"Inventions have long since reached their limit, and I see no hope for further development.\" (Julius Sextus Frontinus, 1st century A.D.)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n" ] @@ -1811,7 +1795,7 @@ ], "source": [ "sim.MD(\n", - " runtime=10e3, qscript=[\"local.sh\"], dt=0.02\n", + " runtime=1e4, qscript=[\"local.sh\"], dt=0.02\n", ")\n", "\n", "r = gromacs.run.MDrunner(\n", @@ -1822,26 +1806,13 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "Warning on use of the timeseries module: If the inherent timescales of the system are long compared to those being analyzed, this statistical inefficiency may be an underestimate. The estimate presumes the use of many statistically independent samples. Tests should be performed to assess whether this condition is satisfied. Be cautious in the interpretation of the data.\n", - "\n", - "****** PyMBAR will use 64-bit JAX! *******\n", - "* JAX is currently set to 32-bit bitsize *\n", - "* which is its default. *\n", - "* *\n", - "* PyMBAR requires 64-bit mode and WILL *\n", - "* enable JAX's 64-bit mode when called. *\n", - "* *\n", - "* This MAY cause problems with other *\n", - "* Uses of JAX in the same code. *\n", - "******************************************\n", - "\n", "mdpow.fep : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.gro').\n", "/home/awsm/MDPOW/mdpow/fep.py:596: UserWarning: Directory 'FEP/water' already exists --- will overwrite existing files.\n", " warnings.warn(wmsg)\n", @@ -1851,7 +1822,7 @@ "mdpow.fep : INFO Using setup directories under 'FEP/water': {'coulomb': 'FEP/water/Coulomb', 'vdw': 'FEP/water/VDW'}\n", "mdpow.fep : INFO Default checkpoint file is '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep'\n", "mdpow.fep : INFO Preparing coulomb for lambda=0\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", @@ -1883,10 +1854,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -1894,17 +1861,13 @@ " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n", "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"Pain is inevitable. Suffering is optional.\" (Haruki Murakami)\n", + "GROMACS reminds you: \"What If None Of Your Dreams Come True ?\" (E. Costello)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -1913,11 +1876,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing coulomb for lambda=0.25\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -1947,26 +1911,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -30909756\n", + "Setting the LD random seed to -1276686385\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -1986,7 +1944,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 15 Mb of data\n" + "This run will generate roughly 2 Mb of data\n" ] }, { @@ -1995,13 +1953,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"Pain is inevitable. Suffering is optional.\" (Haruki Murakami)\n", + "GROMACS reminds you: \"Not to get technical... but according to chemistry, alcohol is a solution.\" (Anonymous)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2010,11 +1966,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing coulomb for lambda=0.5\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2044,26 +2001,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -154140945\n", + "Setting the LD random seed to -313278573\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -2083,7 +2034,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 15 Mb of data\n" + "This run will generate roughly 2 Mb of data\n" ] }, { @@ -2092,13 +2043,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"Wait a Minute, aren't You.... ? (gunshots) Yeah.\" (Bodycount)\n", + "GROMACS reminds you: \"Not to get technical... but according to chemistry, alcohol is a solution.\" (Anonymous)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2107,11 +2056,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing coulomb for lambda=0.75\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2141,26 +2091,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1612087323\n", + "Setting the LD random seed to -18777225\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -2180,7 +2124,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 15 Mb of data\n" + "This run will generate roughly 2 Mb of data\n" ] }, { @@ -2189,13 +2133,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"Wait a Minute, aren't You.... ? (gunshots) Yeah.\" (Bodycount)\n", + "GROMACS reminds you: \"In science, truth always wins.\" (Max Perutz)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2204,11 +2146,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing coulomb for lambda=1\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2238,26 +2181,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -20971547\n", + "Setting the LD random seed to -1187233801\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -2277,7 +2214,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 15 Mb of data\n" + "This run will generate roughly 2 Mb of data\n" ] }, { @@ -2286,13 +2223,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"I Quit My Job Blowing Leaves\" (Beck)\n", + "GROMACS reminds you: \"Your Bones Got a Little Machine\" (Pixies)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2301,13 +2236,14 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", "mdpow.fep : INFO [coulomb] Wrote array job scripts [None]\n", "mdpow.fep : INFO Preparing vdw for lambda=0\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2337,26 +2273,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -71374085\n", + "Setting the LD random seed to 2062417135\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -2376,7 +2306,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 15 Mb of data\n" + "This run will generate roughly 2 Mb of data\n" ] }, { @@ -2385,13 +2315,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"I Quit My Job Blowing Leaves\" (Beck)\n", + "GROMACS reminds you: \"Your Bones Got a Little Machine\" (Pixies)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2400,11 +2328,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.05\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2434,26 +2363,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1173802941\n", + "Setting the LD random seed to -1225019537\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2473,7 +2396,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -2482,13 +2405,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"Welcome to the Power Age\" (2 Unlimited)\n", + "GROMACS reminds you: \"Naive you are if you believe life favours those who aren't naive.\" (Piet Hein)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2497,11 +2418,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.1\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2531,26 +2453,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1411402275\n", + "Setting the LD random seed to 1203762038\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2570,7 +2486,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -2579,13 +2495,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"Welcome to the Power Age\" (2 Unlimited)\n", + "GROMACS reminds you: \"Naive you are if you believe life favours those who aren't naive.\" (Piet Hein)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2594,11 +2508,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.2\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2628,26 +2543,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1678026753\n", + "Setting the LD random seed to -369033\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2667,7 +2576,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -2676,13 +2585,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"Like other defaulters, I like to lay half the blame on ill-fortune and adverse circumstances\" (Mr. Rochester in Jane Eyre by Charlotte Bronte)\n", + "GROMACS reminds you: \"Shake Yourself\" (YES)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2691,11 +2598,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.3\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2725,26 +2633,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -963675284\n", + "Setting the LD random seed to 1973943263\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2764,7 +2666,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -2773,13 +2675,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"GROMACS First : Making MD Great Again\" (Vedran Miletic)\n", + "GROMACS reminds you: \"Shake Yourself\" (YES)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2788,11 +2688,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.4\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2822,26 +2723,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -375586905\n", + "Setting the LD random seed to -118815233\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2861,7 +2756,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -2870,13 +2765,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"GROMACS First : Making MD Great Again\" (Vedran Miletic)\n", + "GROMACS reminds you: \"Science, my lad, is made up of mistakes, but they are mistakes which it is useful to make, because they lead little by little to the truth.\" (Jules Verne)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2885,11 +2778,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.5\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2919,26 +2813,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1658150910\n", + "Setting the LD random seed to -1100921521\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2958,7 +2846,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -2967,13 +2855,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"C has the power of assembly language and the convenience of... assembly language.\" (Dennis Ritchie)\n", + "GROMACS reminds you: \"You Can Always Go On Ricky Lake\" (Offspring)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2982,11 +2868,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.6\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3016,26 +2903,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -102768749\n", + "Setting the LD random seed to -1431325972\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3055,7 +2936,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -3064,13 +2945,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"C has the power of assembly language and the convenience of... assembly language.\" (Dennis Ritchie)\n", + "GROMACS reminds you: \"You Can Always Go On Ricky Lake\" (Offspring)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3079,11 +2958,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.65\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3113,26 +2993,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1126270785\n", + "Setting the LD random seed to 522582511\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3152,7 +3026,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -3161,13 +3035,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"I Have a Bad Case Of Purple Diarrhea\" (Urban Dance Squad)\n", + "GROMACS reminds you: \"As Always Your Logic Is Impeccable\" (Tuvok)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3176,11 +3048,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.7\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3210,26 +3083,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -265217\n", + "Setting the LD random seed to -1291878529\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3249,7 +3116,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -3258,13 +3125,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"I Have a Bad Case Of Purple Diarrhea\" (Urban Dance Squad)\n", + "GROMACS reminds you: \"As Always Your Logic Is Impeccable\" (Tuvok)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3273,11 +3138,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.75\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3307,26 +3173,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 2077204442\n", + "Setting the LD random seed to 1568472927\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3346,7 +3206,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -3355,13 +3215,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"Erwin with his psi can do / Calculations quite a few. / But one thing has not been seen / Just what psi really mean.\" (Felix Bloch)\n", + "GROMACS reminds you: \"Science Won't Change You\" (The Talking Heads)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3370,11 +3228,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.8\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3404,26 +3263,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -170917891\n", + "Setting the LD random seed to -35946561\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3443,7 +3296,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -3452,13 +3305,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"Erwin with his psi can do / Calculations quite a few. / But one thing has not been seen / Just what psi really mean.\" (Felix Bloch)\n", + "GROMACS reminds you: \"Computer system analysis is like child-rearing; you can do grievous damage, but you cannot ensure success.\" (Tom DeMarcho)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3467,11 +3318,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.85\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3501,26 +3353,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1128333313\n", + "Setting the LD random seed to -17572231\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3540,7 +3386,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -3549,13 +3395,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"Not everyone is capable of madness; and of those lucky enough to be capable, not many have the courage for it.\" (August Strindberg)\n", + "GROMACS reminds you: \"Computer system analysis is like child-rearing; you can do grievous damage, but you cannot ensure success.\" (Tom DeMarcho)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3564,11 +3408,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.9\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3598,26 +3443,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -143274449\n", + "Setting the LD random seed to 1806893055\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3637,7 +3476,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -3646,13 +3485,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it.\" (Max Planck)\n", + "GROMACS reminds you: \"The historical meaning of QM/MM: Quanto Mangi, Mamma Mia!\" (Attilio Vittorio Vargiu, at BioExcel 2022 Summer School in Sardinia)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3661,11 +3498,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=0.95\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3695,26 +3533,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1994323699\n", + "Setting the LD random seed to -1083769157\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3734,7 +3566,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -3743,13 +3575,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it.\" (Max Planck)\n", + "GROMACS reminds you: \"The historical meaning of QM/MM: Quanto Mangi, Mamma Mia!\" (Attilio Vittorio Vargiu, at BioExcel 2022 Summer School in Sardinia)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3758,11 +3588,12 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "mdpow.fep : INFO Preparing vdw for lambda=1\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3792,26 +3623,20 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n", - "\n", - "Back Off! I just backed up processed.top to ./#processed.top.1#\n" + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1484915985\n", + "Setting the LD random seed to -570441874\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3831,7 +3656,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -3840,13 +3665,11 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", - "\n", - "GROMACS reminds you: \"It always takes longer than you think even when you take Hofstadter's Law into account.\" (Hofstadter's Law)\n", + "GROMACS reminds you: \"Beware of bugs in the above code; I have only proved it correct, not tried it.\" (Donald Knuth)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3855,7 +3678,7 @@ "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output tpr = 'md.tpr'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] All files set up for a run time of 5000 ps (dt=0.02, nsteps=250000)\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", "mdpow.fep : INFO [vdw] Wrote array job scripts [None]\n", "mdpow.fep : INFO Saved state information to '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep'; reload later with G = Ghyd(filename='/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep').\n", @@ -3866,7 +3689,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -170164757\n", + "Setting the LD random seed to -311828649\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3886,7 +3709,7 @@ "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 17 Mb of data\n" + "This run will generate roughly 3 Mb of data\n" ] }, { @@ -3905,7 +3728,7 @@ " 'sc_alpha': 0.5,\n", " 'sc_power': 1,\n", " 'sc_sigma': 0.3,\n", - " 'separate-dhdl-file': 'yes',\n", + " 'separate-dhdl-file': 'no',\n", " 'ref_t': 300.0,\n", " 'gen_temp': 300.0,\n", " 'free_energy': 'yes',\n", @@ -3916,7 +3739,7 @@ " 'calc_lambda_neighbors': -1}" ] }, - "execution_count": 8, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } @@ -3925,37 +3748,29 @@ "import mdpow.fep\n", "\n", "gwat = mdpow.fep.Ghyd(simulation=sim, runtime=1e+3, mdp=str(RUN_FILE.absolute()))\n", - "gwat.setup(dt=0.02, edr=False)\n", + "gwat.setup(dt=0.02)\n", "\n", "# run multiple simulations on cluster" ] }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", - "\n", - "Back Off! I just backed up md.log to ./#md.log.1#\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", "\n", @@ -3967,35 +3782,27 @@ "Using 1 MPI thread\n", "Using 4 OpenMP threads \n", "\n", - "\n", - "Back Off! I just backed up md.xtc to ./#md.xtc.1#\n", - "\n", - "Back Off! I just backed up md.trr to ./#md.trr.1#\n", - "\n", - "Back Off! I just backed up md.edr to ./#md.edr.1#\n", - "\n", - "Back Off! I just backed up md.xvg to ./#md.xvg.1#\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 705.172 176.293 400.0\n", + " Time: 112.406 28.102 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2450.475 0.010\n", + "Performance: 3074.618 0.008\n", "\n", - "GROMACS reminds you: \"You always pass failure on the way to success.\" (Mickey Rooney)\n", + "GROMACS reminds you: \"Take Dehydrated Water On Your Desert Trips\" (Space Quest III)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4009,26 +3816,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 638.689 159.672 400.0\n", + " Time: 103.522 25.881 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2705.554 0.009\n", + "Performance: 3338.469 0.007\n", "\n", - "GROMACS reminds you: \"The first 90% of the code accounts for the first 90% of the development time. The remaining 10% of the code accounts for the other 90% of the development time.\" (Tom Cargill)\n", + "GROMACS reminds you: \"If everything seems under control, you're just not going fast enough.\" (Mario Andretti)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4042,26 +3849,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 661.083 165.271 400.0\n", + " Time: 111.958 27.989 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2613.900 0.009\n", + "Performance: 3086.935 0.008\n", "\n", - "GROMACS reminds you: \"In science it often happens that scientists say, 'You know that's a really good argument; my position is mistaken,' and then they would actually change their minds and you never hear that old view from them again. They really do it. It doesn't happen as often as it should, because scientists are human and change is sometimes painful. But it happens every day. I cannot recall the last time something like that happened in politics or religion.\" (Carl Sagan)\n", + "GROMACS reminds you: \"If all it takes to motivate you is a fancy picture and quote, you probably have a very easy job. The type of job computers will soon be doing.\" (Anonymous)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4075,26 +3882,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 637.299 159.325 400.0\n", + " Time: 91.919 22.980 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2711.452 0.009\n", + "Performance: 3759.912 0.006\n", "\n", - "GROMACS reminds you: \"With a Little Penknife\" (Nick Cave)\n", + "GROMACS reminds you: \"We're having an information explosion, among others, and it's certainly obvious that information is of no use unless it's available.\" (Sister Mary Kenneth Keller)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4108,26 +3915,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s 6400, remaining wall clock time: 126 s , remaining wall clock time: 71 s 168000, remaining wall clock time: 54 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s 900, remaining wall clock time: 20 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 662.486 165.622 400.0\n", + " Time: 109.086 27.272 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2608.366 0.009\n", + "Performance: 3168.202 0.008\n", "\n", - "GROMACS reminds you: \"Computer system analysis is like child-rearing; you can do grievous damage, but you cannot ensure success.\" (Tom DeMarcho)\n", + "GROMACS reminds you: \"I used to be blond and stupid, but now I dyed it black\" (Miss Li)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4141,26 +3948,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s 10200, remaining wall clock time: 20 s , remaining wall clock time: 19 s 24900, remaining wall clock time: 14 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 1004.487 251.122 400.0\n", + " Time: 106.914 26.729 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 1720.288 0.014\n", + "Performance: 3232.568 0.007\n", "\n", - "GROMACS reminds you: \"Torture numbers, and they'll confess to anything.\" (Greg Easterbrook)\n", + "GROMACS reminds you: \"Get Down In 3D\" (George Clinton)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4174,26 +3981,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s remaining wall clock time: 22 s 19900, remaining wall clock time: 15 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 723.325 180.831 400.0\n", + " Time: 121.145 30.286 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2388.977 0.010\n", + "Performance: 2852.835 0.008\n", "\n", - "GROMACS reminds you: \"UNIX is basically a simple operating system. It just takes a genius to understand its simplicity.\" (Dennis Ritchie)\n", + "GROMACS reminds you: \"Come on boys, Let's push it hard\" (P.J. Harvey)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4207,26 +4014,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s 9800, remaining wall clock time: 105 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 844.038 211.009 400.0\n", + " Time: 173.225 43.306 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2047.310 0.012\n", + "Performance: 1995.128 0.012\n", "\n", - "GROMACS reminds you: \"By denying scientific principles, one may maintain any paradox.\" (Galileo Galilei)\n", + "GROMACS reminds you: \"I can't help but think the model is ungrateful for all that nice data I gave it. Jerk.\" (Kate Stafford)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4240,26 +4047,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s 140200, remaining wall clock time: 105 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 1036.599 259.150 400.0\n", + " Time: 133.766 33.442 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 1666.996 0.014\n", + "Performance: 2583.656 0.009\n", "\n", - "GROMACS reminds you: \"What's the point, yo, what's the spread?\" (Red Hot Chili Peppers)\n", + "GROMACS reminds you: \"Don't waste pure thoughts on dirty enzymes.\" (Efraim Racker)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4273,26 +4080,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 992.378 248.095 400.0\n", + " Time: 145.685 36.421 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 1741.278 0.014\n", + "Performance: 2372.278 0.010\n", "\n", - "GROMACS reminds you: \"Being Great is Not So Good\" (Red Hot Chili Peppers)\n", + "GROMACS reminds you: \"Here's something fun to do: Next time you approach a conversation say 'I want to talk to someone technical... Oh! There's a woman!' and walk straight over to her.\" (Patty Lopez)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4306,26 +4113,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 946.990 236.748 400.0\n", + " Time: 119.297 29.824 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 1824.735 0.013\n", + "Performance: 2897.015 0.008\n", "\n", - "GROMACS reminds you: \"We must be clear that when it comes to atoms, language can be used only as in poetry. \" (Niels Bohr)\n", + "GROMACS reminds you: \"It's Not Dark Yet, But It's Getting There\" (Bob Dylan)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4339,26 +4146,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 1081.532 270.383 400.0\n", + " Time: 127.291 31.823 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 1597.740 0.015\n", + "Performance: 2715.098 0.009\n", "\n", - "GROMACS reminds you: \"Occams Razor is the scientific principle that, all things being equal, the simplest explanation is always the dog ate my homework.\" (Greg Tamblyn)\n", + "GROMACS reminds you: \"Science is the record of dead religions.\" (Oscar Wilde)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4372,26 +4179,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s 139100, remaining wall clock time: 276 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 1634.983 408.746 400.0\n", + " Time: 135.754 33.938 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 1056.896 0.023\n", + "Performance: 2545.836 0.009\n", "\n", - "GROMACS reminds you: \"Facts are stubborn things, but statistics are more pliable.\" (Laurence Peter)\n", + "GROMACS reminds you: \"Everybody Wants to Be Naked and Famous\" (Tricky)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4405,26 +4212,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s remaining wall clock time: 199 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 801.529 200.382 400.0\n", + " Time: 139.214 34.804 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2155.887 0.011\n", + "Performance: 2482.552 0.010\n", "\n", - "GROMACS reminds you: \"I'm Looking for a New Simulation\" (Stone Temple Pilots)\n", + "GROMACS reminds you: \"You see it through a charmed medium: you can not discern that the gilding is slime and the silk draperies cobwebs; that the marble is sordid slate, and the polished woods mere refuse chips and scale bark.\" (Mr. Rochester in Jane Eyre by Charlotte Bronte)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4438,26 +4245,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 675.882 168.971 400.0\n", + " Time: 130.245 32.561 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2556.668 0.009\n", + "Performance: 2653.511 0.009\n", "\n", - "GROMACS reminds you: \"It's Because Of the Metric System\" (Pulp Fiction)\n", + "GROMACS reminds you: \"To survive science you have to become science.\" (Gerrit Groenhof)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4471,26 +4278,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s , remaining wall clock time: 21 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 664.554 166.139 400.0\n", + " Time: 133.221 33.305 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2600.249 0.009\n", + "Performance: 2594.232 0.009\n", "\n", - "GROMACS reminds you: \"Research ! A mere excuse for idleness; it has never achieved, and will never achieve any results of the slightest value.\" (Benjamin Jowett, British theologian, 1817-93)\n", + "GROMACS reminds you: \"Your Proposal is Accepted\" (Men In Black)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4504,26 +4311,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 675.300 168.825 400.0\n", + " Time: 132.336 33.084 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2558.871 0.009\n", + "Performance: 2611.583 0.009\n", "\n", - "GROMACS reminds you: \"There was no preconception on what to do\" (Daft Punk)\n", + "GROMACS reminds you: \"Erwin with his psi can do / Calculations quite a few. / But one thing has not been seen / Just what psi really mean.\" (Felix Bloch)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4537,26 +4344,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s 4500, remaining wall clock time: 101 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 683.395 170.849 400.0\n", + " Time: 118.261 29.565 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2528.560 0.009\n", + "Performance: 2922.399 0.008\n", "\n", - "GROMACS reminds you: \"The easiest way to scale well is to have bad single-core performance\" (Blind Freddie)\n", + "GROMACS reminds you: \"Strength is just an accident arising from the weakness of others\" (Joseph Conrad)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4570,26 +4377,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s 5000, remaining wall clock time: 126 s , remaining wall clock time: 136 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s 39500, remaining wall clock time: 10 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 683.647 170.912 400.0\n", + " Time: 187.262 46.815 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2527.629 0.009\n", + "Performance: 1845.580 0.013\n", "\n", - "GROMACS reminds you: \"Mathematics is like love; a simple idea, but it can get complicated.\" (Anonymous)\n", + "GROMACS reminds you: \"Check Your Input\" (D. Van Der Spoel)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4603,26 +4410,26 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s 000, remaining wall clock time: 30 s 13200, remaining wall clock time: 22 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 658.028 164.507 400.0\n", + " Time: 137.558 34.390 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2626.036 0.009\n", + "Performance: 2512.442 0.010\n", "\n", - "GROMACS reminds you: \"The most exciting phrase to hear in science, the one that heralds new discoveries, is not \"Eureka\" but \"That's funny...\".\" (Isaac Asimov)\n", + "GROMACS reminds you: \"When It Starts to Start It'll Never Stop\" (Magnapop)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", @@ -4636,16 +4443,16 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "250000 steps, 5000.0 ps.\n", - "step 249900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps.\n", + "step 49900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", - "step 250000, remaining wall clock time: 0 s \n", + "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 657.966 164.492 400.0\n", + " Time: 133.675 33.419 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2626.283 0.009\n", + "Performance: 2585.423 0.009\n", "\n", - "GROMACS reminds you: \"I see they found out the universe is 80 million years older than we thought. It's also been lying about its weight.\" (Bill Maher)\n", + "GROMACS reminds you: \"Perfect is the enemy of good.\" (Voltaire)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n" ] @@ -4654,1403 +4461,1871 @@ "source": [ "for dir_ in gwat.fep_dirs():\n", " r = gromacs.run.MDrunner(\n", - " dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=\"md.xvg\"\n", + " dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=True\n", " )\n", " r.run() # runs mdrun in the python shell" ] }, { "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/water] Finding dgdl xvg files, reading with stride=1 permissive=False.\n", - "mdpow.fep : INFO Analysis stride is 1.\n", - "mdpow.fep : INFO Analyzing stored data.\n", - "mdpow.fep : INFO [BENZ coulomb] Computing averages and errors for 5 lambda values.\n", - "numkit.integration: WARNING Approximating Simpson integration statistical error with the average spacing.\n", - "mdpow.fep : INFO [BENZ vdw] Computing averages and errors for 16 lambda values.\n", - "numkit.integration: WARNING Approximating Simpson integration statistical error with the average spacing.\n", - "mdpow.fep : INFO DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n", - "mdpow.fep : INFO [BENZ] Water solvation free energy (coulomb) -34014.8 (4.01) kJ/mol\n", - "mdpow.fep : INFO [BENZ] Water solvation free energy (vdw) -34012 (2.23) kJ/mol\n", - "mdpow.fep : INFO [BENZ] Water solvation free energy (Gibbs) 68026.8 (4.59) kJ/mol\n" - ] - }, - { - "data": { - "image/png": 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", - "text/plain": [ - "
" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "gwat.collect_alchemlyb()\n", - "gwat.analyze_alchemlyb()\n", - "gwat.plot()" - ] - }, - { - "cell_type": "code", - "execution_count": 16, + "execution_count": 18, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation' (newly created)...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/octanol.gro'...\n", - " :-) GROMACS - gmx editconf, 2023.2 (-:\n", + "mdpow.fep : INFO [FEP/water] Converting EDR -> XVG.bz2\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 4.0\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n", "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"C is not a high-level language.\" (Brian Kernighan, C author)\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", "\n", - " :-) GROMACS - gmx solvate, 2023.2 (-:\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx solvate -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -cp boxed.gro -cs /home/awsm/MDPOW/doc/examples/martini/octanol.gro -o solvated.gro\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n", "\n", - "Reading solute configuration\n", - "Reading solvent configuration\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "Initialising inter-atomic distances...\n", - "Generating solvent configuration\n", - "Will generate new solvent configuration of 2x2x2 boxes\n", - "Solvent box contains 5943 atoms in 1981 residues\n", - "Removed 828 solvent atoms due to solvent-solvent overlap\n", - "Removed 3 solvent atoms due to solute-solvent overlap\n", - "Sorting configuration\n", - "Found 1 molecule type:\n", - " OCO ( 3 atoms): 1704 residues\n", - "Generated solvent containing 5112 atoms in 1704 residues\n", - "Writing generated configuration to solvated.gro\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", "\n", - "Output configuration contains 5115 atoms in 1705 residues\n", - "Volume : 399.981 (nm^3)\n", - "Density : 389.199 (g/l)\n", - "Number of solvent molecules: 1704 \n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", - "Processing topology\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n", "\n", - "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/#system.top.1#\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"C is not a high-level language.\" (Brian Kernighan, C author)\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", "\n", - "gromacs.setup: INFO Solvated system with /home/awsm/MDPOW/doc/examples/martini/octanol.gro\n" + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 130 time 520.000 " ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Note that major changes are planned in future for editconf, to improve usability and utility.\n", - "Read 3 atoms\n", - "Volume: 4050 nm^3, corresponds to roughly 1822500 electrons\n", - "No velocities found\n", - " system size : 0.210 0.160 0.248 (nm)\n", - " diameter : 0.270 (nm)\n", - " center : 2.987 0.606 2.315 (nm)\n", - " box vectors : 15.000 15.000 18.000 (nm)\n", - " box angles : 90.00 90.00 90.00 (degrees)\n", - " box volume :4050.00 (nm^3)\n", - " shift : 3.216 5.597 0.609 (nm)\n", - "new center : 6.203 6.203 2.924 (nm)\n", - "new box vectors : 8.270 8.270 8.270 (nm)\n", - "new box angles : 60.00 60.00 90.00 (degrees)\n", - "new box volume : 399.98 (nm^3)\n", "\n", - "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n", - " based on residue and atom names, since they could not be\n", - " definitively assigned from the information in your input\n", - " files. These guessed numbers might deviate from the mass\n", - " and radius of the atom type. Please check the output\n", - " files if necessary. Note, that this functionality may\n", - " be removed in a future GROMACS version. Please, consider\n", - " using another file format for your input.\n", "\n", - "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n", - "from the source below. This means the results may be different\n", - "compared to previous GROMACS versions.\n", + "Wrote 8 lambda values with 5001 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n", "\n", - "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n", - "A. Bondi\n", - "van der Waals Volumes and Radii\n", - "J. Phys. Chem. 68 (1964) pp. 441-451\n", - "-------- -------- --- Thank You --- -------- --------\n", "\n", - "Adding line for 1704 solvent molecules with resname (OCO) to topology file (/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top)\n" + "Wrote 8 lambda values with 5001 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 5001 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 5001 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 5001 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "gromacs.cbook: INFO system total charge qtot = 0\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] After solvation: total charge qtot = 0 = 0\n", - "gromacs.cbook: INFO system total charge qtot = 0\n", - "gromacs.setup: INFO Building the main index file 'main.ndx'...\n", - " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx make_ndx -f ionized.tpr -o main.ndx\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n", "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "Reading structure file\n", - "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", - "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", "\n", - "GROMACS reminds you: \"You Leave Me Dry\" (P.J. Harvey)\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", - " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx make_ndx -f ionized.tpr -n main.ndx -o main.ndx\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 " + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ "\n", - "Reading structure file\n", - "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", - "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "\n", - "Back Off! I just backed up main.ndx to ./#main.ndx.1#\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n", "\n", - "GROMACS reminds you: \"You Leave Me Dry\" (P.J. Harvey)\n", "\n", - " :-) GROMACS - gmx trjconv, 2023.2 (-:\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx trjconv -ur compact -center -boxcenter tric -pbc mol -f ionized.gro -s ionized.tpr -o compact.pdb -n main.ndx\n", - "\n", - "Will write pdb: Protein data bank file\n", - "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", - "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", - "Group 0 ( System) has 5115 elements\n", - "Group 1 ( Other) has 5115 elements\n", - "Group 2 ( BENZ) has 3 elements\n", - "Group 3 ( OCO) has 5112 elements\n", - "Group 4 ( __main__) has 3 elements\n", - "Group 5 (__environment__) has 5112 elements\n", - "Select a group: Group 0 ( System) has 5115 elements\n", - "Group 1 ( Other) has 5115 elements\n", - "Group 2 ( BENZ) has 3 elements\n", - "Group 3 ( OCO) has 5112 elements\n", - "Group 4 ( __main__) has 3 elements\n", - "Group 5 (__environment__) has 5112 elements\n", - "Select a group: Reading frames from gro file 'This is an auto generated system', 5115 atoms.\n", - "Reading frame 0 time 0.000 \n", - "Precision of ionized.gro is 0.001 (nm)\n", - "Last frame 0 time 0.000 \n", - " -> frame 0 time 0.000 \n", - "Last written: frame 0 time 0.000\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n", "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"You Leave Me Dry\" (P.J. Harvey)\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", "\n", - " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -f /tmp/tmpwoe68rau.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -nov\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n", "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "NOTE 1 [file /tmp/tmpwoe68rau.mdp]:\n", - " For a correct single-point energy evaluation with nsteps = 0, use\n", - " continuation = yes to avoid constraining the input coordinates.\n", - "\n" + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 200 time 800.000 " ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Note that major changes are planned in future for trjconv, to improve usability and utility.\n", - "Select group for centering\n", - "Selected 4: '__main__'\n", - "Select group for output\n", - "Selected 0: 'System'\n" + "\n", + "\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ + "Last energy frame read 250 time 1000.000 \n", "\n", - "NOTE 2 [file system.top, line 28]:\n", - " For energy conservation with LINCS, lincs_iter should be 2 or larger.\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", - "Number of degrees of freedom in T-Coupling group rest is 15339.00\n", - "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n", "\n", - "NOTE 3 [file /tmp/tmpwoe68rau.mdp]:\n", - " NVE simulation with an initial temperature of zero: will use a Verlet\n", - " buffer of 10%. Check your energy drift!\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", "\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", "\n", - "There were 3 NOTEs\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", - "GROMACS reminds you: \"Research ! A mere excuse for idleness; it has never achieved, and will never achieve any results of the slightest value.\" (Benjamin Jowett, British theologian, 1817-93)\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n", "\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top', mdp='em.mdp' ...\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em' (newly created)...\n", - "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n", - "gromacs.cbook: WARNING Not substituted in 'em.mdp': ['maxwarn', 'pp']\n", - "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", - "{'maxwarn': 1, 'pp': 'processed.top'}\n", - "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", - "{'maxwarn': 1, 'pp': 'processed.top'}\n", - " warnings.warn(wmsg, category=UsageWarning)\n", - " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -maxwarn 1 -pp processed.top\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n", "\n", - "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", - "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n" + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 140 time 560.000 " ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -394305602\n", "\n", - "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", - "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n", "\n", - "Excluding 1 bonded neighbours molecule type 'OCO'\n", - "Analysing residue names:\n", - "There are: 1705 Other residues\n", - "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", "\n", - "This run will generate roughly 0 Mb of data\n" + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "Number of degrees of freedom in T-Coupling group rest is 15339.00\n", - "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Research ! A mere excuse for idleness; it has never achieved, and will never achieve any results of the slightest value.\" (Benjamin Jowett, British theologian, 1817-93)\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", "\n", - "gromacs.run : WARNING No 'mdrun_d' binary found so trying 'mdrun' instead.\n", - "(Note that energy minimization runs better with mdrun_d.)\n", - "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/run.py:423: AutoCorrectionWarning: No 'mdrun_d' binary found so trying 'mdrun' instead.\n", - "(Note that energy minimization runs better with mdrun_d.)\n", - " warnings.warn(wmsg, category=AutoCorrectionWarning)\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx mdrun -v -stepout 10 -deffnm em -c em.pdb\n", - "\n" + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 180 time 720.000 " ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1843264573\n", "\n", - "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", - "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n", "\n", - "Excluding 1 bonded neighbours molecule type 'OCO'\n", - "Analysing residue names:\n", - "There are: 1705 Other residues\n", - "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", "\n", - "This run will generate roughly 1 Mb of data\n" + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "Reading file em.tpr, VERSION 2023.2 (single precision)\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + "Last energy frame read 250 time 1000.000 \n", "\n", + "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", "\n", - "Steepest Descents:\n", - " Tolerance (Fmax) = 1.00000e+01\n", - " Number of steps = 1000\n", - "Step= 0, Dmax= 1.0e-02 nm, Epot= 1.02801e+07 Fmax= 2.05315e+07, atom= 5083\n", - "Step= 1, Dmax= 1.0e-02 nm, Epot= 7.41994e+06 Fmax= 5.74654e+06, atom= 3110\n", - "Step= 2, Dmax= 1.2e-02 nm, Epot= 4.40326e+06 Fmax= 2.44532e+06, atom= 4997\n", - "Step= 3, Dmax= 1.4e-02 nm, Epot= 2.73794e+06 Fmax= 9.51879e+05, atom= 1685\n", - "Step= 4, Dmax= 1.7e-02 nm, Epot= 1.53428e+06 Fmax= 4.51665e+05, atom= 1684\n", - "Step= 5, Dmax= 2.1e-02 nm, Epot= 8.87445e+05 Fmax= 1.90248e+05, atom= 1990\n", - "Step= 6, Dmax= 2.5e-02 nm, Epot= 4.61156e+05 Fmax= 1.05731e+05, atom= 3691\n", - "Step= 7, Dmax= 3.0e-02 nm, Epot= 2.59013e+05 Fmax= 7.39295e+04, atom= 3626\n", - "Step= 8, Dmax= 3.6e-02 nm, Epot= 1.57144e+05 Fmax= 4.51091e+04, atom= 3691\n", - "Step= 9, Dmax= 4.3e-02 nm, Epot= 8.70638e+04 Fmax= 3.11807e+04, atom= 3047\n", - "Step= 10, Dmax= 5.2e-02 nm, Epot= 4.74060e+04 Fmax= 1.09883e+05, atom= 3020\n", - "Step= 11, Dmax= 6.2e-02 nm, Epot= 3.89493e+04 Fmax= 1.54250e+04, atom= 1088\n", - "Step= 12, Dmax= 7.4e-02 nm, Epot= 6.83724e+03 Fmax= 1.68745e+04, atom= 1088\n", - "Step= 13, Dmax= 8.9e-02 nm, Epot= -4.12860e+03 Fmax= 1.03436e+04, atom= 1088\n", - "Step= 14, Dmax= 1.1e-01 nm, Epot= -1.13032e+04 Fmax= 1.60196e+05, atom= 4\n", - "Step= 15, Dmax= 1.3e-01 nm, Epot= -1.48685e+04 Fmax= 1.22377e+04, atom= 4\n", - "Step= 16, Dmax= 1.5e-01 nm, Epot= -2.01121e+04 Fmax= 3.01369e+04, atom= 4\n", - "Step= 17, Dmax= 1.8e-01 nm, Epot= -2.17950e+04 Fmax= 4.10930e+04, atom= 2520\n", - "Step= 18, Dmax= 2.2e-01 nm, Epot= -2.41455e+04 Fmax= 2.58498e+04, atom= 4\n", - "Step= 19, Dmax= 2.7e-01 nm, Epot= -2.66240e+04 Fmax= 2.69402e+04, atom= 835\n", - "Step= 23, Dmax= 4.0e-02 nm, Epot= -2.72905e+04 Fmax= 1.12462e+04, atom= 5360\n", - "Step= 24, Dmax= 4.8e-02 nm, Epot= -2.82618e+04 Fmax= 8.89258e+03, atom= 3110\n", - "Step= 25, Dmax= 5.8e-02 nm, Epot= -2.94485e+04 Fmax= 7.02500e+03, atom= 835\n", - "Step= 26, Dmax= 6.9e-02 nm, Epot= -3.10718e+04 Fmax= 4.20735e+03, atom= 835\n", - "Step= 27, Dmax= 8.3e-02 nm, Epot= -3.33640e+04 Fmax= 1.18144e+04, atom= 835\n", - "Step= 28, Dmax= 9.9e-02 nm, Epot= -3.46020e+04 Fmax= 2.13260e+03, atom= 3110\n", - "Step= 29, Dmax= 1.2e-01 nm, Epot= -3.82089e+04 Fmax= 4.27695e+04, atom= 3110\n", - "Step= 30, Dmax= 1.4e-01 nm, Epot= -3.94408e+04 Fmax= 2.82754e+03, atom= 536\n", - "Step= 31, Dmax= 1.7e-01 nm, Epot= -3.97104e+04 Fmax= 1.20557e+05, atom= 413\n", - "Step= 33, Dmax= 1.0e-01 nm, Epot= -4.13529e+04 Fmax= 3.83121e+04, atom= 413\n", - "Step= 34, Dmax= 1.2e-01 nm, Epot= -4.20900e+04 Fmax= 3.46040e+03, atom= 5051\n", - "Step= 35, Dmax= 1.5e-01 nm, Epot= -4.35923e+04 Fmax= 8.93873e+03, atom= 5051\n", - "Step= 36, Dmax= 1.8e-01 nm, Epot= -4.39487e+04 Fmax= 3.05296e+03, atom= 413\n", - "Step= 37, Dmax= 2.1e-01 nm, Epot= -4.53159e+04 Fmax= 8.39938e+03, atom= 5051\n", - "Step= 39, Dmax= 1.3e-01 nm, Epot= -4.58889e+04 Fmax= 6.37810e+03, atom= 4135\n", - "Step= 40, Dmax= 1.5e-01 nm, Epot= -4.66503e+04 Fmax= 2.17876e+03, atom= 413\n", - "Step= 42, Dmax= 9.2e-02 nm, Epot= -4.73329e+04 Fmax= 3.49740e+03, atom= 4130\n", - "Step= 43, Dmax= 1.1e-01 nm, Epot= -4.76411e+04 Fmax= 5.47566e+03, atom= 5050\n", - "Step= 44, Dmax= 1.3e-01 nm, Epot= -4.79772e+04 Fmax= 6.20737e+03, atom= 1883\n", - "Step= 45, Dmax= 1.6e-01 nm, Epot= -4.80615e+04 Fmax= 1.18165e+04, atom= 1883\n", - "Step= 47, Dmax= 9.6e-02 nm, Epot= -4.85170e+04 Fmax= 1.25836e+03, atom= 2244\n", - "Step= 48, Dmax= 1.1e-01 nm, Epot= -4.93841e+04 Fmax= 4.12020e+03, atom= 1883\n", - "Step= 49, Dmax= 1.4e-01 nm, Epot= -4.98325e+04 Fmax= 6.95321e+02, atom= 1883\n", - "Step= 51, Dmax= 8.3e-02 nm, Epot= -5.06075e+04 Fmax= 4.29779e+03, atom= 5062\n", - "Step= 52, Dmax= 9.9e-02 nm, Epot= -5.08344e+04 Fmax= 1.55311e+03, atom= 1684\n", - "Step= 54, Dmax= 6.0e-02 nm, Epot= -5.10811e+04 Fmax= 2.58606e+03, atom= 1684\n", - "Step= 55, Dmax= 7.1e-02 nm, Epot= -5.12316e+04 Fmax= 1.94541e+03, atom= 1684\n", - "Step= 56, Dmax= 8.6e-02 nm, Epot= -5.14540e+04 Fmax= 3.79274e+03, atom= 1684\n", - "Step= 57, Dmax= 1.0e-01 nm, Epot= -5.15757e+04 Fmax= 2.28648e+03, atom= 1684\n", - "Step= 58, Dmax= 1.2e-01 nm, Epot= -5.17068e+04 Fmax= 5.86852e+03, atom= 1684\n", - "Step= 59, Dmax= 1.5e-01 nm, Epot= -5.17809e+04 Fmax= 4.05461e+03, atom= 1684\n", - "Step= 61, Dmax= 8.9e-02 nm, Epot= -5.21152e+04 Fmax= 1.19647e+03, atom= 5089\n", - "Step= 62, Dmax= 1.1e-01 nm, Epot= -5.24892e+04 Fmax= 1.98810e+03, atom= 1685\n", - "Step= 63, Dmax= 1.3e-01 nm, Epot= -5.25173e+04 Fmax= 3.38293e+03, atom= 1685\n", - "Step= 65, Dmax= 7.7e-02 nm, Epot= -5.28031e+04 Fmax= 1.59406e+03, atom= 15\n", - "Step= 66, Dmax= 9.2e-02 nm, Epot= -5.30527e+04 Fmax= 1.02223e+03, atom= 2171\n", - "Step= 67, Dmax= 1.1e-01 nm, Epot= -5.30732e+04 Fmax= 7.81743e+03, atom= 2171\n", - "Step= 68, Dmax= 1.3e-01 nm, Epot= -5.34332e+04 Fmax= 6.62480e+02, atom= 1684\n", - "Step= 70, Dmax= 8.0e-02 nm, Epot= -5.35749e+04 Fmax= 5.88957e+03, atom= 3179\n", - "Step= 71, Dmax= 9.6e-02 nm, Epot= -5.37497e+04 Fmax= 2.39396e+03, atom= 2567\n", - "Step= 72, Dmax= 1.1e-01 nm, Epot= -5.38901e+04 Fmax= 1.90550e+03, atom= 1079\n", - "Step= 73, Dmax= 1.4e-01 nm, Epot= -5.39738e+04 Fmax= 2.74704e+03, atom= 2366\n", - "Step= 75, Dmax= 8.3e-02 nm, Epot= -5.41336e+04 Fmax= 2.65971e+03, atom= 4446\n", - "Step= 77, Dmax= 5.0e-02 nm, Epot= -5.42250e+04 Fmax= 1.30975e+03, atom= 3046\n", - "Step= 78, Dmax= 5.9e-02 nm, Epot= -5.43393e+04 Fmax= 8.65460e+02, atom= 3046\n", - "Step= 79, Dmax= 7.1e-02 nm, Epot= -5.44704e+04 Fmax= 1.58444e+03, atom= 3046\n", - "Step= 80, Dmax= 8.6e-02 nm, Epot= -5.45726e+04 Fmax= 1.36866e+03, atom= 3046\n", - "Step= 81, Dmax= 1.0e-01 nm, Epot= -5.46030e+04 Fmax= 5.03876e+03, atom= 444\n", - "Step= 82, Dmax= 1.2e-01 nm, Epot= -5.47013e+04 Fmax= 2.52246e+03, atom= 2366\n", - "Step= 83, Dmax= 1.5e-01 nm, Epot= -5.47871e+04 Fmax= 3.43336e+03, atom= 1079\n", - "Step= 84, Dmax= 1.8e-01 nm, Epot= -5.49199e+04 Fmax= 1.89007e+03, atom= 2559\n", - "Step= 85, Dmax= 2.1e-01 nm, Epot= -5.49722e+04 Fmax= 3.24062e+03, atom= 2559\n", - "Step= 87, Dmax= 1.3e-01 nm, Epot= -5.50446e+04 Fmax= 4.58713e+03, atom= 2760\n", - "Step= 89, Dmax= 7.7e-02 nm, Epot= -5.51553e+04 Fmax= 1.82867e+03, atom= 4360\n", - "Step= 90, Dmax= 9.2e-02 nm, Epot= -5.52639e+04 Fmax= 5.26539e+02, atom= 2261\n", - "Step= 91, Dmax= 1.1e-01 nm, Epot= -5.53684e+04 Fmax= 5.66826e+03, atom= 4360\n", - "Step= 92, Dmax= 1.3e-01 nm, Epot= -5.55561e+04 Fmax= 4.54173e+02, atom= 4360\n", - "Step= 93, Dmax= 1.6e-01 nm, Epot= -5.55593e+04 Fmax= 4.81414e+03, atom= 4360\n", - "Step= 95, Dmax= 9.5e-02 nm, Epot= -5.57775e+04 Fmax= 5.16815e+03, atom= 4360\n", - "Step= 96, Dmax= 1.1e-01 nm, Epot= -5.59213e+04 Fmax= 8.86091e+02, atom= 2568\n", - "Step= 97, Dmax= 1.4e-01 nm, Epot= -5.59392e+04 Fmax= 4.13422e+03, atom= 2568\n", - "Step= 99, Dmax= 8.2e-02 nm, Epot= -5.60849e+04 Fmax= 5.59378e+02, atom= 2760\n", - "Step= 100, Dmax= 9.9e-02 nm, Epot= -5.61778e+04 Fmax= 7.36354e+02, atom= 2261\n", - "Step= 102, Dmax= 5.9e-02 nm, Epot= -5.63295e+04 Fmax= 3.84610e+02, atom= 2567\n", - "Step= 103, Dmax= 7.1e-02 nm, Epot= -5.63583e+04 Fmax= 1.33306e+03, atom= 2567\n", - "Step= 104, Dmax= 8.5e-02 nm, Epot= -5.64837e+04 Fmax= 6.59975e+02, atom= 2567\n", - "Step= 106, Dmax= 5.1e-02 nm, Epot= -5.65690e+04 Fmax= 2.71290e+02, atom= 2567\n", - "Step= 107, Dmax= 6.2e-02 nm, Epot= -5.65777e+04 Fmax= 1.65116e+03, atom= 3180\n", - "Step= 108, Dmax= 7.4e-02 nm, Epot= -5.67310e+04 Fmax= 4.94173e+02, atom= 2567\n", - "Step= 109, Dmax= 8.9e-02 nm, Epot= -5.67486e+04 Fmax= 1.94536e+03, atom= 2567\n", - "Step= 110, Dmax= 1.1e-01 nm, Epot= -5.68570e+04 Fmax= 4.43982e+02, atom= 3179\n", - "Step= 112, Dmax= 6.4e-02 nm, Epot= -5.69402e+04 Fmax= 4.47751e+02, atom= 3179\n", - "Step= 113, Dmax= 7.7e-02 nm, Epot= -5.69597e+04 Fmax= 9.20285e+02, atom= 2139\n", - "Step= 114, Dmax= 9.2e-02 nm, Epot= -5.70078e+04 Fmax= 9.37800e+02, atom= 2139\n", - "Step= 116, Dmax= 5.5e-02 nm, Epot= -5.71175e+04 Fmax= 2.86563e+02, atom= 1078\n", - "Step= 117, Dmax= 6.6e-02 nm, Epot= -5.71881e+04 Fmax= 4.72104e+02, atom= 2567\n", - "Step= 119, Dmax= 4.0e-02 nm, Epot= -5.72505e+04 Fmax= 3.34971e+02, atom= 3179\n", - "Step= 120, Dmax= 4.8e-02 nm, Epot= -5.72684e+04 Fmax= 6.68821e+02, atom= 1088\n", - "Step= 121, Dmax= 5.7e-02 nm, Epot= -5.73208e+04 Fmax= 5.89958e+02, atom= 1088\n", - "Step= 122, Dmax= 6.9e-02 nm, Epot= -5.73273e+04 Fmax= 1.00541e+03, atom= 1088\n", - "Step= 123, Dmax= 8.2e-02 nm, Epot= -5.73823e+04 Fmax= 9.18556e+02, atom= 1088\n", - "Step= 125, Dmax= 4.9e-02 nm, Epot= -5.74540e+04 Fmax= 3.33559e+02, atom= 1088\n", - "Step= 126, Dmax= 5.9e-02 nm, Epot= -5.75094e+04 Fmax= 7.16891e+02, atom= 1088\n", - "Step= 127, Dmax= 7.1e-02 nm, Epot= -5.75464e+04 Fmax= 5.50998e+02, atom= 1088\n", - "Step= 128, Dmax= 8.5e-02 nm, Epot= -5.75679e+04 Fmax= 1.20153e+03, atom= 1088\n", - "Step= 129, Dmax= 1.0e-01 nm, Epot= -5.76115e+04 Fmax= 6.52398e+02, atom= 1088\n", - "Step= 131, Dmax= 6.1e-02 nm, Epot= -5.76713e+04 Fmax= 2.53581e+02, atom= 1088\n", - "Step= 133, Dmax= 3.7e-02 nm, Epot= -5.77124e+04 Fmax= 3.86314e+02, atom= 1088\n", - "Step= 134, Dmax= 4.4e-02 nm, Epot= -5.77482e+04 Fmax= 3.73108e+02, atom= 1088\n", - "Step= 135, Dmax= 5.3e-02 nm, Epot= -5.77629e+04 Fmax= 5.31183e+02, atom= 1088\n", - "Step= 136, Dmax= 6.4e-02 nm, Epot= -5.77879e+04 Fmax= 6.43519e+02, atom= 2750\n", - "Step= 138, Dmax= 3.8e-02 nm, Epot= -5.78558e+04 Fmax= 1.85832e+02, atom= 2750\n", - "Step= 139, Dmax= 4.6e-02 nm, Epot= -5.78925e+04 Fmax= 1.09288e+03, atom= 2750\n", - "Step= 140, Dmax= 5.5e-02 nm, Epot= -5.79367e+04 Fmax= 2.69548e+02, atom= 2750\n", - "Step= 141, Dmax= 6.6e-02 nm, Epot= -5.79484e+04 Fmax= 1.95160e+03, atom= 2750\n", - "Step= 142, Dmax= 7.9e-02 nm, Epot= -5.80068e+04 Fmax= 2.88227e+02, atom= 2750\n", - "Step= 144, Dmax= 4.8e-02 nm, Epot= -5.80458e+04 Fmax= 3.98323e+02, atom= 2750\n", - "Step= 145, Dmax= 5.7e-02 nm, Epot= -5.80633e+04 Fmax= 5.81518e+02, atom= 2750\n", - "Step= 146, Dmax= 6.8e-02 nm, Epot= -5.80932e+04 Fmax= 6.58553e+02, atom= 2750\n", - "Step= 147, Dmax= 8.2e-02 nm, Epot= -5.80940e+04 Fmax= 7.38113e+02, atom= 2750\n", - "Step= 148, Dmax= 9.9e-02 nm, Epot= -5.80943e+04 Fmax= 1.21411e+03, atom= 2750\n", - "Step= 149, Dmax= 1.2e-01 nm, Epot= -5.81100e+04 Fmax= 9.10252e+02, atom= 2750\n", - "Step= 151, Dmax= 7.1e-02 nm, Epot= -5.82095e+04 Fmax= 2.71693e+02, atom= 1416\n", - "Step= 153, Dmax= 4.3e-02 nm, Epot= -5.82354e+04 Fmax= 3.70157e+02, atom= 1037\n", - "Step= 154, Dmax= 5.1e-02 nm, Epot= -5.82509e+04 Fmax= 5.47522e+02, atom= 1037\n", - "Step= 155, Dmax= 6.1e-02 nm, Epot= -5.82635e+04 Fmax= 5.14065e+02, atom= 1037\n", - "Step= 157, Dmax= 3.7e-02 nm, Epot= -5.83180e+04 Fmax= 1.92017e+02, atom= 5043\n", - "Step= 158, Dmax= 4.4e-02 nm, Epot= -5.83328e+04 Fmax= 9.64419e+02, atom= 4635\n", - "Step= 159, Dmax= 5.3e-02 nm, Epot= -5.83731e+04 Fmax= 3.20299e+02, atom= 4635\n", - "Step= 160, Dmax= 6.4e-02 nm, Epot= -5.83903e+04 Fmax= 9.33434e+02, atom= 4635\n", - "Step= 161, Dmax= 7.6e-02 nm, Epot= -5.84114e+04 Fmax= 4.89153e+02, atom= 4635\n", - "Step= 163, Dmax= 4.6e-02 nm, Epot= -5.84404e+04 Fmax= 3.90576e+02, atom= 2855\n", - "Step= 164, Dmax= 5.5e-02 nm, Epot= -5.84639e+04 Fmax= 3.89971e+02, atom= 285\n", - "Step= 166, Dmax= 3.3e-02 nm, Epot= -5.84896e+04 Fmax= 1.85394e+02, atom= 285\n", - "Step= 167, Dmax= 4.0e-02 nm, Epot= -5.85081e+04 Fmax= 6.35285e+02, atom= 285\n", - "Step= 168, Dmax= 4.7e-02 nm, Epot= -5.85385e+04 Fmax= 2.95014e+02, atom= 285\n", - "Step= 169, Dmax= 5.7e-02 nm, Epot= -5.85451e+04 Fmax= 9.77754e+02, atom= 285\n", - "Step= 170, Dmax= 6.8e-02 nm, Epot= -5.85778e+04 Fmax= 3.63391e+02, atom= 285\n", - "Step= 172, Dmax= 4.1e-02 nm, Epot= -5.86024e+04 Fmax= 2.02615e+02, atom= 5043\n", - "Step= 174, Dmax= 2.5e-02 nm, Epot= -5.86247e+04 Fmax= 2.03310e+02, atom= 2855\n", - "Step= 175, Dmax= 3.0e-02 nm, Epot= -5.86436e+04 Fmax= 2.96942e+02, atom= 285\n", - "Step= 176, Dmax= 3.5e-02 nm, Epot= -5.86611e+04 Fmax= 3.10824e+02, atom= 285\n", - "Step= 177, Dmax= 4.3e-02 nm, Epot= -5.86736e+04 Fmax= 4.93776e+02, atom= 285\n", - "Step= 178, Dmax= 5.1e-02 nm, Epot= -5.86940e+04 Fmax= 3.89987e+02, atom= 285\n", - "Step= 180, Dmax= 3.1e-02 nm, Epot= -5.87218e+04 Fmax= 1.06833e+02, atom= 5043\n", - "Step= 181, Dmax= 3.7e-02 nm, Epot= -5.87361e+04 Fmax= 6.44166e+02, atom= 4635\n", - "Step= 182, Dmax= 4.4e-02 nm, Epot= -5.87811e+04 Fmax= 3.19544e+02, atom= 4635\n", - "Step= 183, Dmax= 5.3e-02 nm, Epot= -5.87921e+04 Fmax= 4.90715e+02, atom= 4635\n", - "Step= 184, Dmax= 6.3e-02 nm, Epot= -5.87959e+04 Fmax= 7.74901e+02, atom= 285\n", - "Step= 185, Dmax= 7.6e-02 nm, Epot= -5.88137e+04 Fmax= 5.99807e+02, atom= 285\n", - "Step= 187, Dmax= 4.6e-02 nm, Epot= -5.88498e+04 Fmax= 1.62855e+02, atom= 1551\n", - "Step= 188, Dmax= 5.5e-02 nm, Epot= -5.88566e+04 Fmax= 5.94842e+02, atom= 1550\n", - "Step= 189, Dmax= 6.6e-02 nm, Epot= -5.88797e+04 Fmax= 7.11423e+02, atom= 285\n", - "Step= 190, Dmax= 7.9e-02 nm, Epot= -5.88856e+04 Fmax= 6.80859e+02, atom= 4635\n", - "Step= 192, Dmax= 4.7e-02 nm, Epot= -5.89348e+04 Fmax= 2.08451e+02, atom= 5043\n", - "Step= 193, Dmax= 5.7e-02 nm, Epot= -5.89433e+04 Fmax= 6.04278e+02, atom= 4635\n", - "Step= 194, Dmax= 6.8e-02 nm, Epot= -5.89509e+04 Fmax= 9.42196e+02, atom= 4635\n", - "Step= 195, Dmax= 8.2e-02 nm, Epot= -5.89724e+04 Fmax= 7.30556e+02, atom= 285\n", - "Step= 196, Dmax= 9.8e-02 nm, Epot= -5.89776e+04 Fmax= 5.60661e+02, atom= 285\n", - "Step= 198, Dmax= 5.9e-02 nm, Epot= -5.90097e+04 Fmax= 3.13266e+02, atom= 284\n", - "Step= 200, Dmax= 3.5e-02 nm, Epot= -5.90345e+04 Fmax= 2.61433e+02, atom= 284\n", - "Step= 201, Dmax= 4.2e-02 nm, Epot= -5.90393e+04 Fmax= 3.44039e+02, atom= 284\n", - "Step= 203, Dmax= 2.5e-02 nm, Epot= -5.90742e+04 Fmax= 6.14359e+01, atom= 4625\n", - "Step= 204, Dmax= 3.1e-02 nm, Epot= -5.90799e+04 Fmax= 4.51359e+02, atom= 4625\n", - "Step= 205, Dmax= 3.7e-02 nm, Epot= -5.91354e+04 Fmax= 1.74673e+02, atom= 2162\n", - "Step= 207, Dmax= 2.2e-02 nm, Epot= -5.91481e+04 Fmax= 1.95328e+02, atom= 2162\n", - "Step= 208, Dmax= 2.6e-02 nm, Epot= -5.91559e+04 Fmax= 2.55103e+02, atom= 2162\n", - "Step= 209, Dmax= 3.2e-02 nm, Epot= -5.91669e+04 Fmax= 2.86077e+02, atom= 2750\n", - "Step= 210, Dmax= 3.8e-02 nm, Epot= -5.91675e+04 Fmax= 3.50601e+02, atom= 2162\n", - "Step= 211, Dmax= 4.6e-02 nm, Epot= -5.91689e+04 Fmax= 4.72392e+02, atom= 2750\n", - "Step= 212, Dmax= 5.5e-02 nm, Epot= -5.91789e+04 Fmax= 4.46180e+02, atom= 2750\n", - "Step= 214, Dmax= 3.3e-02 nm, Epot= -5.92348e+04 Fmax= 9.62019e+01, atom= 1037\n", - "Step= 216, Dmax= 2.0e-02 nm, Epot= -5.92468e+04 Fmax= 2.07440e+02, atom= 1037\n", - "Step= 217, Dmax= 2.4e-02 nm, Epot= -5.92606e+04 Fmax= 2.08207e+02, atom= 1037\n", - "Step= 218, Dmax= 2.8e-02 nm, Epot= -5.92666e+04 Fmax= 2.65871e+02, atom= 1037\n", - "Step= 219, Dmax= 3.4e-02 nm, Epot= -5.92731e+04 Fmax= 3.31445e+02, atom= 1037\n", - "Step= 220, Dmax= 4.1e-02 nm, Epot= -5.92789e+04 Fmax= 3.56153e+02, atom= 1037\n", - "Step= 222, Dmax= 2.5e-02 nm, Epot= -5.93179e+04 Fmax= 5.21486e+01, atom= 1037\n", - "Step= 223, Dmax= 2.9e-02 nm, Epot= -5.93196e+04 Fmax= 4.67079e+02, atom= 5050\n", - "Step= 224, Dmax= 3.5e-02 nm, Epot= -5.93757e+04 Fmax= 1.66102e+02, atom= 5050\n", - "Step= 226, Dmax= 2.1e-02 nm, Epot= -5.93867e+04 Fmax= 1.66684e+02, atom= 5051\n", - "Step= 227, Dmax= 2.5e-02 nm, Epot= -5.93889e+04 Fmax= 2.47359e+02, atom= 1037\n", - "Step= 228, Dmax= 3.1e-02 nm, Epot= -5.93961e+04 Fmax= 2.66854e+02, atom= 1037\n", - "Step= 230, Dmax= 1.8e-02 nm, Epot= -5.94274e+04 Fmax= 5.09855e+01, atom= 5050\n", - "Step= 231, Dmax= 2.2e-02 nm, Epot= -5.94429e+04 Fmax= 3.58031e+02, atom= 5050\n", - "Step= 232, Dmax= 2.6e-02 nm, Epot= -5.94728e+04 Fmax= 1.08357e+02, atom= 5050\n", - "Step= 234, Dmax= 1.6e-02 nm, Epot= -5.94838e+04 Fmax= 1.43123e+02, atom= 5051\n", - "Step= 235, Dmax= 1.9e-02 nm, Epot= -5.94932e+04 Fmax= 1.72068e+02, atom= 5051\n", - "Step= 236, Dmax= 2.3e-02 nm, Epot= -5.95016e+04 Fmax= 2.04237e+02, atom= 5051\n", - "Step= 237, Dmax= 2.7e-02 nm, Epot= -5.95070e+04 Fmax= 2.48763e+02, atom= 5051\n", - "Step= 238, Dmax= 3.3e-02 nm, Epot= -5.95103e+04 Fmax= 2.89528e+02, atom= 5051\n", - "Step= 240, Dmax= 2.0e-02 nm, Epot= -5.95414e+04 Fmax= 5.12312e+01, atom= 5050\n", - "Step= 241, Dmax= 2.4e-02 nm, Epot= -5.95550e+04 Fmax= 3.89078e+02, atom= 5050\n", - "Step= 242, Dmax= 2.8e-02 nm, Epot= -5.95861e+04 Fmax= 1.10845e+02, atom= 5050\n", - "Step= 244, Dmax= 1.7e-02 nm, Epot= -5.95961e+04 Fmax= 1.58399e+02, atom= 5051\n", - "Step= 245, Dmax= 2.0e-02 nm, Epot= -5.96051e+04 Fmax= 1.78986e+02, atom= 5051\n", - "Step= 246, Dmax= 2.4e-02 nm, Epot= -5.96118e+04 Fmax= 2.22749e+02, atom= 5051\n", - "Step= 247, Dmax= 2.9e-02 nm, Epot= -5.96166e+04 Fmax= 2.61684e+02, atom= 5051\n", - "Step= 248, Dmax= 3.5e-02 nm, Epot= -5.96172e+04 Fmax= 3.13383e+02, atom= 5051\n", - "Step= 250, Dmax= 2.1e-02 nm, Epot= -5.96506e+04 Fmax= 4.86983e+01, atom= 5050\n", - "Step= 251, Dmax= 2.5e-02 nm, Epot= -5.96578e+04 Fmax= 4.31252e+02, atom= 5050\n", - "Step= 252, Dmax= 3.0e-02 nm, Epot= -5.96961e+04 Fmax= 1.11653e+02, atom= 5050\n", - "Step= 254, Dmax= 1.8e-02 nm, Epot= -5.97045e+04 Fmax= 1.70830e+02, atom= 5051\n", - "Step= 255, Dmax= 2.2e-02 nm, Epot= -5.97121e+04 Fmax= 1.91495e+02, atom= 5051\n", - "Step= 256, Dmax= 2.6e-02 nm, Epot= -5.97167e+04 Fmax= 2.38105e+02, atom= 5051\n", - "Step= 257, Dmax= 3.2e-02 nm, Epot= -5.97191e+04 Fmax= 2.79075e+02, atom= 5051\n", - "Step= 259, Dmax= 1.9e-02 nm, Epot= -5.97454e+04 Fmax= 4.23782e+01, atom= 1319\n", - "Step= 260, Dmax= 2.3e-02 nm, Epot= -5.97519e+04 Fmax= 3.81711e+02, atom= 1319\n", - "Step= 261, Dmax= 2.7e-02 nm, Epot= -5.97869e+04 Fmax= 1.28726e+02, atom= 1319\n", - "Step= 263, Dmax= 1.6e-02 nm, Epot= -5.97949e+04 Fmax= 1.65876e+02, atom= 1319\n", - "Step= 264, Dmax= 2.0e-02 nm, Epot= -5.98026e+04 Fmax= 1.75747e+02, atom= 1319\n", - "Step= 265, Dmax= 2.4e-02 nm, Epot= -5.98091e+04 Fmax= 2.40416e+02, atom= 1319\n", - "Step= 266, Dmax= 2.8e-02 nm, Epot= -5.98163e+04 Fmax= 2.55718e+02, atom= 1319\n", - "Step= 267, Dmax= 3.4e-02 nm, Epot= -5.98209e+04 Fmax= 3.39142e+02, atom= 1319\n", - "Step= 268, Dmax= 4.1e-02 nm, Epot= -5.98261e+04 Fmax= 3.75544e+02, atom= 1319\n", - "Step= 269, Dmax= 4.9e-02 nm, Epot= -5.98282e+04 Fmax= 4.73619e+02, atom= 1319\n", - "Step= 271, Dmax= 2.9e-02 nm, Epot= -5.98530e+04 Fmax= 6.18993e+01, atom= 1318\n", - "Step= 272, Dmax= 3.5e-02 nm, Epot= -5.98663e+04 Fmax= 6.46697e+02, atom= 1318\n", - "Step= 273, Dmax= 4.2e-02 nm, Epot= -5.98917e+04 Fmax= 1.65695e+02, atom= 1319\n", - "Step= 275, Dmax= 2.5e-02 nm, Epot= -5.98978e+04 Fmax= 2.94874e+02, atom= 1319\n", - "Step= 276, Dmax= 3.0e-02 nm, Epot= -5.99062e+04 Fmax= 2.35808e+02, atom= 1319\n", - "Step= 277, Dmax= 3.6e-02 nm, Epot= -5.99087e+04 Fmax= 4.06924e+02, atom= 1319\n", - "Step= 278, Dmax= 4.4e-02 nm, Epot= -5.99171e+04 Fmax= 3.61301e+02, atom= 1319\n", - "Step= 280, Dmax= 2.6e-02 nm, Epot= -5.99307e+04 Fmax= 8.87213e+01, atom= 1319\n", - "Step= 281, Dmax= 3.2e-02 nm, Epot= -5.99414e+04 Fmax= 4.18033e+02, atom= 1319\n", - "Step= 282, Dmax= 3.8e-02 nm, Epot= -5.99546e+04 Fmax= 2.32465e+02, atom= 1319\n", - "Step= 284, Dmax= 2.3e-02 nm, Epot= -5.99621e+04 Fmax= 1.65416e+02, atom= 1319\n", - "Step= 285, Dmax= 2.7e-02 nm, Epot= -5.99676e+04 Fmax= 3.08849e+02, atom= 1319\n", - "Step= 286, Dmax= 3.3e-02 nm, Epot= -5.99752e+04 Fmax= 2.63161e+02, atom= 1319\n", - "Step= 287, Dmax= 3.9e-02 nm, Epot= -5.99774e+04 Fmax= 4.18453e+02, atom= 1319\n", - "Step= 288, Dmax= 4.7e-02 nm, Epot= -5.99840e+04 Fmax= 4.04201e+02, atom= 1319\n", - "Step= 290, Dmax= 2.8e-02 nm, Epot= -5.99987e+04 Fmax= 7.64403e+01, atom= 1319\n", - "Step= 291, Dmax= 3.4e-02 nm, Epot= -6.00103e+04 Fmax= 4.72924e+02, atom= 1319\n", - "Step= 292, Dmax= 4.1e-02 nm, Epot= -6.00260e+04 Fmax= 2.28258e+02, atom= 1319\n", - "Step= 294, Dmax= 2.4e-02 nm, Epot= -6.00327e+04 Fmax= 2.01055e+02, atom= 1319\n", - "Step= 295, Dmax= 2.9e-02 nm, Epot= -6.00376e+04 Fmax= 3.03494e+02, atom= 1319\n", - "Step= 296, Dmax= 3.5e-02 nm, Epot= -6.00436e+04 Fmax= 3.08345e+02, atom= 1319\n", - "Step= 297, Dmax= 4.2e-02 nm, Epot= -6.00463e+04 Fmax= 4.17414e+02, atom= 1319\n", - "Step= 298, Dmax= 5.1e-02 nm, Epot= -6.00499e+04 Fmax= 4.61089e+02, atom= 1319\n", - "Step= 299, Dmax= 6.1e-02 nm, Epot= -6.00500e+04 Fmax= 5.76279e+02, atom= 1319\n", - "Step= 301, Dmax= 3.6e-02 nm, Epot= -6.00740e+04 Fmax= 6.92350e+01, atom= 1318\n", - "Step= 303, Dmax= 2.2e-02 nm, Epot= -6.00849e+04 Fmax= 2.97816e+02, atom= 1319\n", - "Step= 304, Dmax= 2.6e-02 nm, Epot= -6.00940e+04 Fmax= 1.74488e+02, atom= 1319\n", - "Step= 305, Dmax= 3.1e-02 nm, Epot= -6.00963e+04 Fmax= 3.76278e+02, atom= 1319\n", - "Step= 306, Dmax= 3.8e-02 nm, Epot= -6.01053e+04 Fmax= 2.84534e+02, atom= 1319\n", - "Step= 308, Dmax= 2.3e-02 nm, Epot= -6.01145e+04 Fmax= 1.02150e+02, atom= 1319\n", - "Step= 309, Dmax= 2.7e-02 nm, Epot= -6.01210e+04 Fmax= 3.51456e+02, atom= 1319\n", - "Step= 310, Dmax= 3.3e-02 nm, Epot= -6.01310e+04 Fmax= 2.05725e+02, atom= 1319\n", - "Step= 312, Dmax= 2.0e-02 nm, Epot= -6.01375e+04 Fmax= 1.32276e+02, atom= 1319\n", - "Step= 313, Dmax= 2.3e-02 nm, Epot= -6.01429e+04 Fmax= 2.71747e+02, atom= 1319\n", - "Step= 314, Dmax= 2.8e-02 nm, Epot= -6.01498e+04 Fmax= 2.17193e+02, atom= 1319\n", - "Step= 315, Dmax= 3.4e-02 nm, Epot= -6.01523e+04 Fmax= 3.63914e+02, atom= 1319\n", - "Step= 316, Dmax= 4.1e-02 nm, Epot= -6.01588e+04 Fmax= 3.39846e+02, atom= 1319\n", - "Step= 318, Dmax= 2.4e-02 nm, Epot= -6.01697e+04 Fmax= 7.37318e+01, atom= 1319\n", - "Step= 319, Dmax= 2.9e-02 nm, Epot= -6.01788e+04 Fmax= 4.13958e+02, atom= 1319\n", - "Step= 320, Dmax= 3.5e-02 nm, Epot= -6.01916e+04 Fmax= 1.86138e+02, atom= 1319\n", - "Step= 322, Dmax= 2.1e-02 nm, Epot= -6.01974e+04 Fmax= 1.78388e+02, atom= 1319\n", - "Step= 323, Dmax= 2.5e-02 nm, Epot= -6.02022e+04 Fmax= 2.51869e+02, atom= 1319\n", - "Step= 324, Dmax= 3.0e-02 nm, Epot= -6.02074e+04 Fmax= 2.70618e+02, atom= 1319\n", - "Step= 325, Dmax= 3.6e-02 nm, Epot= -6.02108e+04 Fmax= 3.49031e+02, atom= 1319\n", - "Step= 326, Dmax= 4.4e-02 nm, Epot= -6.02141e+04 Fmax= 4.02081e+02, atom= 1319\n", - "Step= 327, Dmax= 5.2e-02 nm, Epot= -6.02156e+04 Fmax= 4.86209e+02, atom= 1319\n", - "Step= 329, Dmax= 3.1e-02 nm, Epot= -6.02336e+04 Fmax= 5.71155e+01, atom= 1319\n", - "Step= 330, Dmax= 3.8e-02 nm, Epot= -6.02368e+04 Fmax= 6.64340e+02, atom= 1318\n", - "Step= 331, Dmax= 4.5e-02 nm, Epot= -6.02655e+04 Fmax= 1.83676e+02, atom= 1319\n", - "Step= 333, Dmax= 2.7e-02 nm, Epot= -6.02695e+04 Fmax= 2.91250e+02, atom= 1319\n", - "Step= 334, Dmax= 3.3e-02 nm, Epot= -6.02756e+04 Fmax= 2.63202e+02, atom= 1319\n", - "Step= 335, Dmax= 3.9e-02 nm, Epot= -6.02765e+04 Fmax= 4.03992e+02, atom= 1319\n", - "Step= 336, Dmax= 4.7e-02 nm, Epot= -6.02819e+04 Fmax= 3.98621e+02, atom= 1319\n", - "Step= 338, Dmax= 2.8e-02 nm, Epot= -6.02956e+04 Fmax= 7.60762e+01, atom= 1319\n", - "Step= 339, Dmax= 3.4e-02 nm, Epot= -6.03017e+04 Fmax= 4.77231e+02, atom= 1319\n", - "Step= 340, Dmax= 4.1e-02 nm, Epot= -6.03171e+04 Fmax= 2.15730e+02, atom= 1319\n", - "Step= 342, Dmax= 2.4e-02 nm, Epot= -6.03227e+04 Fmax= 2.03128e+02, atom= 1319\n", - "Step= 343, Dmax= 2.9e-02 nm, Epot= -6.03264e+04 Fmax= 2.89043e+02, atom= 1319\n", - "Step= 344, Dmax= 3.5e-02 nm, Epot= -6.03312e+04 Fmax= 3.08965e+02, atom= 1319\n", - "Step= 345, Dmax= 4.2e-02 nm, Epot= -6.03330e+04 Fmax= 4.00348e+02, atom= 1319\n", - "Step= 346, Dmax= 5.0e-02 nm, Epot= -6.03353e+04 Fmax= 4.58882e+02, atom= 1319\n", - "Step= 348, Dmax= 3.0e-02 nm, Epot= -6.03520e+04 Fmax= 5.05216e+01, atom= 1319\n", - "Step= 349, Dmax= 3.6e-02 nm, Epot= -6.03634e+04 Fmax= 5.51052e+02, atom= 1319\n", - "Step= 350, Dmax= 4.4e-02 nm, Epot= -6.03847e+04 Fmax= 2.08449e+02, atom= 1319\n", - "Step= 352, Dmax= 2.6e-02 nm, Epot= -6.03894e+04 Fmax= 2.48168e+02, atom= 1319\n", - "Step= 353, Dmax= 3.1e-02 nm, Epot= -6.03939e+04 Fmax= 2.78026e+02, atom= 1319\n", - "Step= 354, Dmax= 3.8e-02 nm, Epot= -6.03962e+04 Fmax= 3.63994e+02, atom= 1319\n", - "Step= 355, Dmax= 4.5e-02 nm, Epot= -6.04000e+04 Fmax= 3.95144e+02, atom= 1319\n", - "Step= 357, Dmax= 2.7e-02 nm, Epot= -6.04132e+04 Fmax= 6.51975e+01, atom= 1319\n", - "Step= 358, Dmax= 3.3e-02 nm, Epot= -6.04186e+04 Fmax= 4.91131e+02, atom= 1319\n", - "Step= 359, Dmax= 3.9e-02 nm, Epot= -6.04361e+04 Fmax= 1.93860e+02, atom= 1319\n", - "Step= 361, Dmax= 2.3e-02 nm, Epot= -6.04414e+04 Fmax= 2.04614e+02, atom= 1319\n", - "Step= 362, Dmax= 2.8e-02 nm, Epot= -6.04453e+04 Fmax= 2.67362e+02, atom= 1319\n", - "Step= 363, Dmax= 3.4e-02 nm, Epot= -6.04495e+04 Fmax= 3.00671e+02, atom= 1319\n", - "Step= 364, Dmax= 4.0e-02 nm, Epot= -6.04514e+04 Fmax= 3.83352e+02, atom= 1319\n", - "Step= 365, Dmax= 4.9e-02 nm, Epot= -6.04542e+04 Fmax= 4.30970e+02, atom= 1319\n", - "Step= 367, Dmax= 2.9e-02 nm, Epot= -6.04695e+04 Fmax= 6.18336e+01, atom= 1319\n", - "Step= 368, Dmax= 3.5e-02 nm, Epot= -6.04722e+04 Fmax= 5.46742e+02, atom= 1319\n", - "Step= 369, Dmax= 4.2e-02 nm, Epot= -6.04944e+04 Fmax= 1.96927e+02, atom= 1319\n", - "Step= 371, Dmax= 2.5e-02 nm, Epot= -6.04991e+04 Fmax= 2.32225e+02, atom= 1319\n", - "Step= 372, Dmax= 3.0e-02 nm, Epot= -6.05030e+04 Fmax= 2.73007e+02, atom= 1319\n", - "Step= 373, Dmax= 3.6e-02 nm, Epot= -6.05060e+04 Fmax= 3.36710e+02, atom= 1319\n", - "Step= 374, Dmax= 4.4e-02 nm, Epot= -6.05082e+04 Fmax= 3.96413e+02, atom= 1319\n", - "Step= 375, Dmax= 5.2e-02 nm, Epot= -6.05088e+04 Fmax= 4.76611e+02, atom= 1319\n", - "Step= 377, Dmax= 3.1e-02 nm, Epot= -6.05272e+04 Fmax= 5.16323e+01, atom= 1319\n", - "Step= 378, Dmax= 3.8e-02 nm, Epot= -6.05276e+04 Fmax= 6.14499e+02, atom= 1319\n", - "Step= 379, Dmax= 4.5e-02 nm, Epot= -6.05569e+04 Fmax= 2.03659e+02, atom= 1319\n", - "Step= 381, Dmax= 2.7e-02 nm, Epot= -6.05610e+04 Fmax= 2.60531e+02, atom= 1319\n", - "Step= 382, Dmax= 3.2e-02 nm, Epot= -6.05650e+04 Fmax= 2.79866e+02, atom= 1319\n", - "Step= 383, Dmax= 3.9e-02 nm, Epot= -6.05663e+04 Fmax= 3.74775e+02, atom= 1319\n", - "Step= 384, Dmax= 4.7e-02 nm, Epot= -6.05691e+04 Fmax= 4.11038e+02, atom= 1319\n", - "Step= 386, Dmax= 2.8e-02 nm, Epot= -6.05838e+04 Fmax= 5.79211e+01, atom= 1319\n", - "Step= 387, Dmax= 3.4e-02 nm, Epot= -6.05889e+04 Fmax= 4.89873e+02, atom= 1319\n", - "Step= 388, Dmax= 4.0e-02 nm, Epot= -6.06071e+04 Fmax= 1.97414e+02, atom= 1319\n", - "Step= 390, Dmax= 2.4e-02 nm, Epot= -6.06115e+04 Fmax= 2.17537e+02, atom= 1319\n", - "Step= 391, Dmax= 2.9e-02 nm, Epot= -6.06147e+04 Fmax= 2.68041e+02, atom= 1319\n", - "Step= 392, Dmax= 3.5e-02 nm, Epot= -6.06174e+04 Fmax= 3.21251e+02, atom= 1319\n", - "Step= 393, Dmax= 4.2e-02 nm, Epot= -6.06190e+04 Fmax= 3.79032e+02, atom= 1319\n", - "Step= 395, Dmax= 2.5e-02 nm, Epot= -6.06328e+04 Fmax= 4.36223e+01, atom= 1319\n", - "Step= 396, Dmax= 3.0e-02 nm, Epot= -6.06401e+04 Fmax= 4.74855e+02, atom= 1319\n", - "Step= 397, Dmax= 3.6e-02 nm, Epot= -6.06604e+04 Fmax= 1.57750e+02, atom= 1319\n", - "Step= 399, Dmax= 2.2e-02 nm, Epot= -6.06641e+04 Fmax= 2.12313e+02, atom= 1319\n", - "Step= 400, Dmax= 2.6e-02 nm, Epot= -6.06682e+04 Fmax= 2.24630e+02, atom= 1319\n", - "Step= 401, Dmax= 3.1e-02 nm, Epot= -6.06700e+04 Fmax= 3.00293e+02, atom= 1319\n", - "Step= 402, Dmax= 3.8e-02 nm, Epot= -6.06728e+04 Fmax= 3.31786e+02, atom= 1319\n", - "Step= 404, Dmax= 2.3e-02 nm, Epot= -6.06847e+04 Fmax= 4.53620e+01, atom= 1319\n", - "Step= 405, Dmax= 2.7e-02 nm, Epot= -6.06914e+04 Fmax= 4.01247e+02, atom= 1319\n", - "Step= 406, Dmax= 3.2e-02 nm, Epot= -6.07079e+04 Fmax= 1.48220e+02, atom= 1319\n", - "Step= 408, Dmax= 1.9e-02 nm, Epot= -6.07116e+04 Fmax= 1.84527e+02, atom= 1319\n", - "Step= 409, Dmax= 2.3e-02 nm, Epot= -6.07151e+04 Fmax= 2.06689e+02, atom= 1319\n", - "Step= 410, Dmax= 2.8e-02 nm, Epot= -6.07169e+04 Fmax= 2.67366e+02, atom= 1319\n", - "Step= 411, Dmax= 3.4e-02 nm, Epot= -6.07192e+04 Fmax= 2.96362e+02, atom= 1319\n", - "Step= 413, Dmax= 2.0e-02 nm, Epot= -6.07315e+04 Fmax= 4.34829e+01, atom= 1319\n", - "Step= 414, Dmax= 2.4e-02 nm, Epot= -6.07318e+04 Fmax= 3.67845e+02, atom= 1319\n", - "Step= 415, Dmax= 2.9e-02 nm, Epot= -6.07518e+04 Fmax= 1.31639e+02, atom= 1319\n", - "Step= 417, Dmax= 1.7e-02 nm, Epot= -6.07548e+04 Fmax= 1.63602e+02, atom= 1319\n", - "Step= 418, Dmax= 2.1e-02 nm, Epot= -6.07572e+04 Fmax= 1.88990e+02, atom= 1319\n", - "Step= 419, Dmax= 2.5e-02 nm, Epot= -6.07577e+04 Fmax= 2.32875e+02, atom= 1319\n", - "Step= 421, Dmax= 1.5e-02 nm, Epot= -6.07708e+04 Fmax= 3.30466e+01, atom= 2326\n", - "Step= 422, Dmax= 1.8e-02 nm, Epot= -6.07767e+04 Fmax= 3.04932e+02, atom= 2326\n", - "Step= 423, Dmax= 2.2e-02 nm, Epot= -6.07912e+04 Fmax= 9.78066e+01, atom= 1223\n", - "Step= 425, Dmax= 1.3e-02 nm, Epot= -6.07950e+04 Fmax= 1.25476e+02, atom= 1223\n", - "Step= 426, Dmax= 1.6e-02 nm, Epot= -6.07985e+04 Fmax= 1.45130e+02, atom= 1223\n", - "Step= 427, Dmax= 1.9e-02 nm, Epot= -6.08015e+04 Fmax= 1.89108e+02, atom= 1223\n", - "Step= 428, Dmax= 2.2e-02 nm, Epot= -6.08046e+04 Fmax= 2.04297e+02, atom= 1223\n", - "Step= 429, Dmax= 2.7e-02 nm, Epot= -6.08059e+04 Fmax= 2.74445e+02, atom= 1223\n", - "Step= 430, Dmax= 3.2e-02 nm, Epot= -6.08084e+04 Fmax= 2.93029e+02, atom= 1223\n", - "Step= 432, Dmax= 1.9e-02 nm, Epot= -6.08203e+04 Fmax= 4.92068e+01, atom= 1223\n", - "Step= 433, Dmax= 2.3e-02 nm, Epot= -6.08255e+04 Fmax= 3.74352e+02, atom= 1223\n", - "Step= 434, Dmax= 2.8e-02 nm, Epot= -6.08374e+04 Fmax= 1.59570e+02, atom= 1223\n", - "Step= 436, Dmax= 1.7e-02 nm, Epot= -6.08415e+04 Fmax= 1.18581e+02, atom= 1223\n", - "Step= 437, Dmax= 2.0e-02 nm, Epot= -6.08439e+04 Fmax= 2.38973e+02, atom= 1223\n", - "Step= 438, Dmax= 2.4e-02 nm, Epot= -6.08490e+04 Fmax= 1.78082e+02, atom= 1223\n", - "Step= 440, Dmax= 1.4e-02 nm, Epot= -6.08539e+04 Fmax= 7.59461e+01, atom= 1223\n", - "Step= 441, Dmax= 1.7e-02 nm, Epot= -6.08580e+04 Fmax= 2.27286e+02, atom= 1223\n", - "Step= 442, Dmax= 2.1e-02 nm, Epot= -6.08635e+04 Fmax= 1.44711e+02, atom= 1223\n", - "Step= 443, Dmax= 2.5e-02 nm, Epot= -6.08645e+04 Fmax= 2.95004e+02, atom= 1223\n", - "Step= 444, Dmax= 3.0e-02 nm, Epot= -6.08700e+04 Fmax= 2.32901e+02, atom= 1223\n", - "Step= 446, Dmax= 1.8e-02 nm, Epot= -6.08762e+04 Fmax= 7.04377e+01, atom= 1223\n", - "Step= 447, Dmax= 2.2e-02 nm, Epot= -6.08777e+04 Fmax= 3.43073e+02, atom= 1223\n", - "Step= 448, Dmax= 2.6e-02 nm, Epot= -6.08879e+04 Fmax= 1.24836e+02, atom= 1223\n", - "Step= 450, Dmax= 1.6e-02 nm, Epot= -6.08917e+04 Fmax= 1.42072e+02, atom= 1223\n", - "Step= 451, Dmax= 1.9e-02 nm, Epot= -6.08948e+04 Fmax= 1.81305e+02, atom= 1223\n", - "Step= 452, Dmax= 2.2e-02 nm, Epot= -6.08980e+04 Fmax= 2.14994e+02, atom= 1223\n", - "Step= 453, Dmax= 2.7e-02 nm, Epot= -6.09003e+04 Fmax= 2.53778e+02, atom= 1223\n", - "Step= 454, Dmax= 3.2e-02 nm, Epot= -6.09020e+04 Fmax= 3.13246e+02, atom= 1223\n", - "Step= 455, Dmax= 3.9e-02 nm, Epot= -6.09029e+04 Fmax= 3.64355e+02, atom= 1223\n", - "Step= 457, Dmax= 2.3e-02 nm, Epot= -6.09160e+04 Fmax= 4.65659e+01, atom= 1223\n", - "Step= 458, Dmax= 2.8e-02 nm, Epot= -6.09208e+04 Fmax= 4.79801e+02, atom= 1223\n", - "Step= 459, Dmax= 3.4e-02 nm, Epot= -6.09356e+04 Fmax= 1.97644e+02, atom= 1223\n", - "Step= 461, Dmax= 2.0e-02 nm, Epot= -6.09399e+04 Fmax= 1.28547e+02, atom= 1223\n", - "Step= 462, Dmax= 2.4e-02 nm, Epot= -6.09409e+04 Fmax= 3.01190e+02, atom= 1223\n", - "Step= 463, Dmax= 2.9e-02 nm, Epot= -6.09471e+04 Fmax= 1.97468e+02, atom= 1223\n", - "Step= 465, Dmax= 1.7e-02 nm, Epot= -6.09522e+04 Fmax= 1.00804e+02, atom= 1223\n", - "Step= 466, Dmax= 2.1e-02 nm, Epot= -6.09543e+04 Fmax= 2.63690e+02, atom= 1223\n", - "Step= 467, Dmax= 2.5e-02 nm, Epot= -6.09602e+04 Fmax= 1.78006e+02, atom= 1223\n", - "Step= 469, Dmax= 1.5e-02 nm, Epot= -6.09647e+04 Fmax= 7.47557e+01, atom= 1223\n", - "Step= 470, Dmax= 1.8e-02 nm, Epot= -6.09677e+04 Fmax= 2.55234e+02, atom= 1223\n", - "Step= 471, Dmax= 2.2e-02 nm, Epot= -6.09741e+04 Fmax= 1.22540e+02, atom= 1223\n", - "Step= 473, Dmax= 1.3e-02 nm, Epot= -6.09779e+04 Fmax= 1.02993e+02, atom= 1223\n", - "Step= 474, Dmax= 1.6e-02 nm, Epot= -6.09811e+04 Fmax= 1.64853e+02, atom= 1223\n", - "Step= 475, Dmax= 1.9e-02 nm, Epot= -6.09848e+04 Fmax= 1.64522e+02, atom= 1223\n", - "Step= 476, Dmax= 2.2e-02 nm, Epot= -6.09870e+04 Fmax= 2.23727e+02, atom= 1223\n", - "Step= 477, Dmax= 2.7e-02 nm, Epot= -6.09899e+04 Fmax= 2.47590e+02, atom= 1223\n", - "Step= 478, Dmax= 3.2e-02 nm, Epot= -6.09907e+04 Fmax= 3.14368e+02, atom= 1223\n", - "Step= 479, Dmax= 3.9e-02 nm, Epot= -6.09921e+04 Fmax= 3.58548e+02, atom= 1223\n", - "Step= 481, Dmax= 2.3e-02 nm, Epot= -6.10042e+04 Fmax= 6.45564e+01, atom= 2326\n", - "Step= 482, Dmax= 2.8e-02 nm, Epot= -6.10077e+04 Fmax= 4.22201e+02, atom= 2326\n", - "Step= 483, Dmax= 3.3e-02 nm, Epot= -6.10168e+04 Fmax= 1.82764e+02, atom= 1223\n", - "Step= 485, Dmax= 2.0e-02 nm, Epot= -6.10212e+04 Fmax= 1.44877e+02, atom= 1223\n", - "Step= 487, Dmax= 1.2e-02 nm, Epot= -6.10253e+04 Fmax= 6.19955e+01, atom= 1223\n", - "Step= 488, Dmax= 1.4e-02 nm, Epot= -6.10291e+04 Fmax= 2.01341e+02, atom= 1223\n", - "Step= 489, Dmax= 1.7e-02 nm, Epot= -6.10341e+04 Fmax= 1.01983e+02, atom= 1223\n", - "Step= 490, Dmax= 2.1e-02 nm, Epot= -6.10347e+04 Fmax= 2.78053e+02, atom= 1223\n", - "Step= 491, Dmax= 2.5e-02 nm, Epot= -6.10412e+04 Fmax= 1.59365e+02, atom= 1223\n", - "Step= 493, Dmax= 1.5e-02 nm, Epot= -6.10456e+04 Fmax= 9.52809e+01, atom= 1223\n", - "Step= 494, Dmax= 1.8e-02 nm, Epot= -6.10477e+04 Fmax= 2.16944e+02, atom= 1223\n", - "Step= 495, Dmax= 2.2e-02 nm, Epot= -6.10526e+04 Fmax= 1.62664e+02, atom= 1223\n", - "Step= 497, Dmax= 1.3e-02 nm, Epot= -6.10568e+04 Fmax= 5.81613e+01, atom= 1223\n", - "Step= 498, Dmax= 1.6e-02 nm, Epot= -6.10605e+04 Fmax= 2.30065e+02, atom= 1223\n", - "Step= 499, Dmax= 1.9e-02 nm, Epot= -6.10663e+04 Fmax= 9.80535e+01, atom= 1223\n", - "Step= 501, Dmax= 1.1e-02 nm, Epot= -6.10697e+04 Fmax= 9.64444e+01, atom= 1223\n", - "Step= 502, Dmax= 1.3e-02 nm, Epot= -6.10728e+04 Fmax= 1.33882e+02, atom= 1223\n", - "Step= 503, Dmax= 1.6e-02 nm, Epot= -6.10759e+04 Fmax= 1.50261e+02, atom= 1223\n", - "Step= 504, Dmax= 1.9e-02 nm, Epot= -6.10785e+04 Fmax= 1.83555e+02, atom= 1223\n", - "Step= 505, Dmax= 2.3e-02 nm, Epot= -6.10809e+04 Fmax= 2.23775e+02, atom= 1223\n", - "Step= 506, Dmax= 2.8e-02 nm, Epot= -6.10828e+04 Fmax= 2.58840e+02, atom= 1223\n", - "Step= 507, Dmax= 3.3e-02 nm, Epot= -6.10835e+04 Fmax= 3.24092e+02, atom= 1223\n", - "Step= 508, Dmax= 4.0e-02 nm, Epot= -6.10837e+04 Fmax= 3.73191e+02, atom= 1223\n", - "Step= 510, Dmax= 2.4e-02 nm, Epot= -6.10974e+04 Fmax= 4.94931e+01, atom= 2002\n", - "Step= 511, Dmax= 2.9e-02 nm, Epot= -6.10982e+04 Fmax= 4.71037e+02, atom= 1223\n", - "Step= 512, Dmax= 3.5e-02 nm, Epot= -6.11131e+04 Fmax= 2.19061e+02, atom= 1223\n", - "Step= 514, Dmax= 2.1e-02 nm, Epot= -6.11176e+04 Fmax= 1.18684e+02, atom= 1223\n", - "Step= 516, Dmax= 1.2e-02 nm, Epot= -6.11210e+04 Fmax= 9.84646e+01, atom= 1223\n", - "Step= 517, Dmax= 1.5e-02 nm, Epot= -6.11240e+04 Fmax= 1.54585e+02, atom= 1223\n", - "Step= 518, Dmax= 1.8e-02 nm, Epot= -6.11271e+04 Fmax= 1.58661e+02, atom= 1223\n", - "Step= 519, Dmax= 2.2e-02 nm, Epot= -6.11292e+04 Fmax= 2.11798e+02, atom= 1223\n", - "Step= 520, Dmax= 2.6e-02 nm, Epot= -6.11315e+04 Fmax= 2.37670e+02, atom= 1223\n", - "Step= 521, Dmax= 3.1e-02 nm, Epot= -6.11322e+04 Fmax= 2.99094e+02, atom= 1223\n", - "Step= 522, Dmax= 3.7e-02 nm, Epot= -6.11330e+04 Fmax= 3.44767e+02, atom= 1223\n", - "Step= 524, Dmax= 2.2e-02 nm, Epot= -6.11447e+04 Fmax= 5.97056e+01, atom= 2326\n", - "Step= 525, Dmax= 2.7e-02 nm, Epot= -6.11474e+04 Fmax= 4.00193e+02, atom= 2326\n", - "Step= 526, Dmax= 3.2e-02 nm, Epot= -6.11562e+04 Fmax= 1.77130e+02, atom= 1223\n", - "Step= 528, Dmax= 1.9e-02 nm, Epot= -6.11602e+04 Fmax= 1.38647e+02, atom= 1223\n", - "Step= 530, Dmax= 1.2e-02 nm, Epot= -6.11639e+04 Fmax= 6.03498e+01, atom= 1223\n", - "Step= 531, Dmax= 1.4e-02 nm, Epot= -6.11672e+04 Fmax= 1.89772e+02, atom= 1223\n", - "Step= 532, Dmax= 1.7e-02 nm, Epot= -6.11718e+04 Fmax= 1.00613e+02, atom= 1223\n", - "Step= 533, Dmax= 2.0e-02 nm, Epot= -6.11721e+04 Fmax= 2.60538e+02, atom= 1223\n", - "Step= 534, Dmax= 2.4e-02 nm, Epot= -6.11779e+04 Fmax= 1.57938e+02, atom= 1223\n", - "Step= 536, Dmax= 1.4e-02 nm, Epot= -6.11822e+04 Fmax= 8.63103e+01, atom= 1223\n", - "Step= 537, Dmax= 1.7e-02 nm, Epot= -6.11839e+04 Fmax= 2.13303e+02, atom= 1223\n", - "Step= 538, Dmax= 2.1e-02 nm, Epot= -6.11888e+04 Fmax= 1.49692e+02, atom= 1223\n", - "Step= 540, Dmax= 1.2e-02 nm, Epot= -6.11926e+04 Fmax= 6.22881e+01, atom= 1223\n", - "Step= 541, Dmax= 1.5e-02 nm, Epot= -6.11953e+04 Fmax= 2.08925e+02, atom= 1223\n", - "Step= 542, Dmax= 1.8e-02 nm, Epot= -6.12004e+04 Fmax= 1.03819e+02, atom= 1223\n", - "Step= 544, Dmax= 1.1e-02 nm, Epot= -6.12036e+04 Fmax= 8.21175e+01, atom= 1223\n", - "Step= 545, Dmax= 1.3e-02 nm, Epot= -6.12064e+04 Fmax= 1.39020e+02, atom= 1223\n", - "Step= 546, Dmax= 1.5e-02 nm, Epot= -6.12096e+04 Fmax= 1.32133e+02, atom= 1223\n", - "Step= 547, Dmax= 1.9e-02 nm, Epot= -6.12115e+04 Fmax= 1.88047e+02, atom= 1223\n", - "Step= 548, Dmax= 2.2e-02 nm, Epot= -6.12142e+04 Fmax= 2.00684e+02, atom= 1223\n", - "Step= 549, Dmax= 2.7e-02 nm, Epot= -6.12150e+04 Fmax= 2.62648e+02, atom= 1223\n", - "Step= 550, Dmax= 3.2e-02 nm, Epot= -6.12166e+04 Fmax= 2.94405e+02, atom= 1223\n", - "Step= 552, Dmax= 1.9e-02 nm, Epot= -6.12259e+04 Fmax= 5.23357e+01, atom= 2326\n", - "Step= 553, Dmax= 2.3e-02 nm, Epot= -6.12293e+04 Fmax= 3.43597e+02, atom= 2326\n", - "Step= 554, Dmax= 2.8e-02 nm, Epot= -6.12373e+04 Fmax= 1.53810e+02, atom= 1223\n", - "Step= 556, Dmax= 1.7e-02 nm, Epot= -6.12409e+04 Fmax= 1.21731e+02, atom= 1223\n", - "Step= 557, Dmax= 2.0e-02 nm, Epot= -6.12416e+04 Fmax= 2.24143e+02, atom= 1223\n", - "Step= 558, Dmax= 2.4e-02 nm, Epot= -6.12460e+04 Fmax= 1.91440e+02, atom= 1223\n", - "Step= 560, Dmax= 1.4e-02 nm, Epot= -6.12510e+04 Fmax= 5.48196e+01, atom= 1223\n", - "Step= 561, Dmax= 1.7e-02 nm, Epot= -6.12531e+04 Fmax= 2.69031e+02, atom= 1223\n", - "Step= 562, Dmax= 2.1e-02 nm, Epot= -6.12605e+04 Fmax= 1.00313e+02, atom= 1223\n", - "Step= 564, Dmax= 1.2e-02 nm, Epot= -6.12635e+04 Fmax= 1.10796e+02, atom= 1223\n", - "Step= 565, Dmax= 1.5e-02 nm, Epot= -6.12661e+04 Fmax= 1.44672e+02, atom= 1223\n", - "Step= 566, Dmax= 1.8e-02 nm, Epot= -6.12687e+04 Fmax= 1.67308e+02, atom= 1223\n", - "Step= 567, Dmax= 2.1e-02 nm, Epot= -6.12706e+04 Fmax= 2.02282e+02, atom= 1223\n", - "Step= 568, Dmax= 2.6e-02 nm, Epot= -6.12724e+04 Fmax= 2.45964e+02, atom= 1223\n", - "Step= 569, Dmax= 3.1e-02 nm, Epot= -6.12732e+04 Fmax= 2.88150e+02, atom= 1223\n", - "Step= 571, Dmax= 1.9e-02 nm, Epot= -6.12828e+04 Fmax= 3.52276e+01, atom= 2002\n", - "Step= 572, Dmax= 2.2e-02 nm, Epot= -6.12895e+04 Fmax= 3.37060e+02, atom= 1223\n", - "Step= 573, Dmax= 2.7e-02 nm, Epot= -6.12994e+04 Fmax= 1.66757e+02, atom= 1223\n", - "Step= 575, Dmax= 1.6e-02 nm, Epot= -6.13033e+04 Fmax= 9.76431e+01, atom= 1223\n", - "Step= 576, Dmax= 1.9e-02 nm, Epot= -6.13042e+04 Fmax= 2.41500e+02, atom= 1223\n", - "Step= 577, Dmax= 2.3e-02 nm, Epot= -6.13096e+04 Fmax= 1.55215e+02, atom= 1223\n", - "Step= 579, Dmax= 1.4e-02 nm, Epot= -6.13136e+04 Fmax= 8.21985e+01, atom= 1223\n", - "Step= 580, Dmax= 1.7e-02 nm, Epot= -6.13156e+04 Fmax= 2.05423e+02, atom= 1223\n", - "Step= 581, Dmax= 2.0e-02 nm, Epot= -6.13203e+04 Fmax= 1.41518e+02, atom= 1223\n", - "Step= 583, Dmax= 1.2e-02 nm, Epot= -6.13241e+04 Fmax= 6.04040e+01, atom= 1223\n", - "Step= 584, Dmax= 1.4e-02 nm, Epot= -6.13270e+04 Fmax= 1.96301e+02, atom= 1223\n", - "Step= 585, Dmax= 1.7e-02 nm, Epot= -6.13321e+04 Fmax= 1.02305e+02, atom= 1223\n", - "Step= 587, Dmax= 1.0e-02 nm, Epot= -6.13353e+04 Fmax= 7.60511e+01, atom= 1223\n", - "Step= 588, Dmax= 1.2e-02 nm, Epot= -6.13383e+04 Fmax= 1.36678e+02, atom= 1223\n", - "Step= 589, Dmax= 1.5e-02 nm, Epot= -6.13417e+04 Fmax= 1.22432e+02, atom= 1223\n", - "Step= 590, Dmax= 1.8e-02 nm, Epot= -6.13436e+04 Fmax= 1.85066e+02, atom= 1223\n", - "Step= 591, Dmax= 2.1e-02 nm, Epot= -6.13467e+04 Fmax= 1.86598e+02, atom= 1223\n", - "Step= 592, Dmax= 2.6e-02 nm, Epot= -6.13471e+04 Fmax= 2.58182e+02, atom= 1223\n", - "Step= 593, Dmax= 3.1e-02 nm, Epot= -6.13494e+04 Fmax= 2.74523e+02, atom= 1223\n", - "Step= 595, Dmax= 1.9e-02 nm, Epot= -6.13585e+04 Fmax= 5.13218e+01, atom= 2326\n", - "Step= 596, Dmax= 2.2e-02 nm, Epot= -6.13605e+04 Fmax= 3.35681e+02, atom= 2326\n", - "Step= 597, Dmax= 2.7e-02 nm, Epot= -6.13702e+04 Fmax= 1.48336e+02, atom= 1223\n", - "Step= 599, Dmax= 1.6e-02 nm, Epot= -6.13739e+04 Fmax= 1.16013e+02, atom= 1223\n", - "Step= 600, Dmax= 1.9e-02 nm, Epot= -6.13748e+04 Fmax= 2.15015e+02, atom= 1223\n", - "Step= 601, Dmax= 2.3e-02 nm, Epot= -6.13792e+04 Fmax= 1.82102e+02, atom= 1223\n", - "Step= 603, Dmax= 1.4e-02 nm, Epot= -6.13843e+04 Fmax= 5.32855e+01, atom= 1223\n", - "Step= 604, Dmax= 1.7e-02 nm, Epot= -6.13867e+04 Fmax= 2.51868e+02, atom= 1223\n", - "Step= 605, Dmax= 2.0e-02 nm, Epot= -6.13940e+04 Fmax= 9.92775e+01, atom= 1223\n", - "Step= 607, Dmax= 1.2e-02 nm, Epot= -6.13972e+04 Fmax= 1.03082e+02, atom= 1223\n", - "Step= 608, Dmax= 1.4e-02 nm, Epot= -6.13998e+04 Fmax= 1.41508e+02, atom= 1223\n", - "Step= 609, Dmax= 1.7e-02 nm, Epot= -6.14026e+04 Fmax= 1.55968e+02, atom= 1223\n", - "Step= 610, Dmax= 2.1e-02 nm, Epot= -6.14045e+04 Fmax= 1.97491e+02, atom= 1223\n", - "Step= 611, Dmax= 2.5e-02 nm, Epot= -6.14066e+04 Fmax= 2.30065e+02, atom= 1223\n", - "Step= 612, Dmax= 3.0e-02 nm, Epot= -6.14071e+04 Fmax= 2.80509e+02, atom= 1223\n", - "Step= 613, Dmax= 3.6e-02 nm, Epot= -6.14073e+04 Fmax= 3.32363e+02, atom= 1223\n", - "Step= 615, Dmax= 2.1e-02 nm, Epot= -6.14204e+04 Fmax= 5.60515e+01, atom= 2326\n", - "Step= 616, Dmax= 2.6e-02 nm, Epot= -6.14238e+04 Fmax= 3.65824e+02, atom= 2326\n", - "Step= 617, Dmax= 3.1e-02 nm, Epot= -6.14322e+04 Fmax= 1.67807e+02, atom= 1223\n", - "Step= 619, Dmax= 1.8e-02 nm, Epot= -6.14361e+04 Fmax= 1.34038e+02, atom= 1223\n", - "Step= 621, Dmax= 1.1e-02 nm, Epot= -6.14401e+04 Fmax= 5.50527e+01, atom= 1223\n", - "Step= 622, Dmax= 1.3e-02 nm, Epot= -6.14435e+04 Fmax= 1.78651e+02, atom= 1223\n", - "Step= 623, Dmax= 1.6e-02 nm, Epot= -6.14483e+04 Fmax= 9.60041e+01, atom= 1223\n", - "Step= 624, Dmax= 1.9e-02 nm, Epot= -6.14486e+04 Fmax= 2.41824e+02, atom= 1223\n", - "Step= 625, Dmax= 2.3e-02 nm, Epot= -6.14546e+04 Fmax= 1.53190e+02, atom= 1223\n", - "Step= 627, Dmax= 1.4e-02 nm, Epot= -6.14590e+04 Fmax= 7.78358e+01, atom= 1223\n", - "Step= 628, Dmax= 1.7e-02 nm, Epot= -6.14606e+04 Fmax= 2.05742e+02, atom= 1223\n", - "Step= 629, Dmax= 2.0e-02 nm, Epot= -6.14660e+04 Fmax= 1.35763e+02, atom= 1223\n", - "Step= 631, Dmax= 1.2e-02 nm, Epot= -6.14699e+04 Fmax= 6.48805e+01, atom= 1223\n", - "Step= 632, Dmax= 1.4e-02 nm, Epot= -6.14724e+04 Fmax= 1.86673e+02, atom= 1223\n", - "Step= 633, Dmax= 1.7e-02 nm, Epot= -6.14775e+04 Fmax= 1.07111e+02, atom= 1223\n", - "Step= 635, Dmax= 1.0e-02 nm, Epot= -6.14809e+04 Fmax= 6.79335e+01, atom= 1223\n", - "Step= 636, Dmax= 1.2e-02 nm, Epot= -6.14839e+04 Fmax= 1.41408e+02, atom= 1223\n", - "Step= 637, Dmax= 1.5e-02 nm, Epot= -6.14877e+04 Fmax= 1.13284e+02, atom= 1223\n", - "Step= 638, Dmax= 1.8e-02 nm, Epot= -6.14891e+04 Fmax= 1.89173e+02, atom= 1223\n", - "Step= 639, Dmax= 2.1e-02 nm, Epot= -6.14928e+04 Fmax= 1.76115e+02, atom= 1223\n", - "Step= 641, Dmax= 1.3e-02 nm, Epot= -6.14983e+04 Fmax= 3.97391e+01, atom= 1223\n", - "Step= 642, Dmax= 1.5e-02 nm, Epot= -6.15019e+04 Fmax= 2.42423e+02, atom= 1223\n", - "Step= 643, Dmax= 1.8e-02 nm, Epot= -6.15104e+04 Fmax= 8.07222e+01, atom= 1223\n", - "Step= 645, Dmax= 1.1e-02 nm, Epot= -6.15136e+04 Fmax= 1.05926e+02, atom= 1223\n", - "Step= 646, Dmax= 1.3e-02 nm, Epot= -6.15166e+04 Fmax= 1.17903e+02, atom= 1223\n", - "Step= 647, Dmax= 1.6e-02 nm, Epot= -6.15191e+04 Fmax= 1.55289e+02, atom= 1223\n", - "Step= 648, Dmax= 1.9e-02 nm, Epot= -6.15218e+04 Fmax= 1.67975e+02, atom= 1223\n", - "Step= 649, Dmax= 2.3e-02 nm, Epot= -6.15228e+04 Fmax= 2.24444e+02, atom= 1223\n", - "Step= 650, Dmax= 2.8e-02 nm, Epot= -6.15247e+04 Fmax= 2.41343e+02, atom= 1223\n", - "Step= 652, Dmax= 1.7e-02 nm, Epot= -6.15343e+04 Fmax= 4.47053e+01, atom= 2002\n", - "Step= 653, Dmax= 2.0e-02 nm, Epot= -6.15378e+04 Fmax= 2.82850e+02, atom= 2002\n", - "Step= 654, Dmax= 2.4e-02 nm, Epot= -6.15469e+04 Fmax= 1.28913e+02, atom= 2003\n", - "Step= 656, Dmax= 1.4e-02 nm, Epot= -6.15506e+04 Fmax= 1.11679e+02, atom= 2003\n", - "Step= 657, Dmax= 1.7e-02 nm, Epot= -6.15523e+04 Fmax= 1.81701e+02, atom= 2003\n", - "Step= 658, Dmax= 2.1e-02 nm, Epot= -6.15561e+04 Fmax= 1.61320e+02, atom= 2003\n", - "Step= 660, Dmax= 1.2e-02 nm, Epot= -6.15613e+04 Fmax= 5.08633e+01, atom= 2003\n", - "Step= 661, Dmax= 1.5e-02 nm, Epot= -6.15649e+04 Fmax= 1.95413e+02, atom= 2003\n", - "Step= 662, Dmax= 1.8e-02 nm, Epot= -6.15705e+04 Fmax= 1.14628e+02, atom= 2003\n", - "Step= 664, Dmax= 1.1e-02 nm, Epot= -6.15742e+04 Fmax= 6.40345e+01, atom= 2003\n", - "Step= 665, Dmax= 1.3e-02 nm, Epot= -6.15775e+04 Fmax= 1.54010e+02, atom= 2003\n", - "Step= 666, Dmax= 1.5e-02 nm, Epot= -6.15816e+04 Fmax= 1.01478e+02, atom= 2003\n", - "Step= 667, Dmax= 1.8e-02 nm, Epot= -6.15825e+04 Fmax= 2.14265e+02, atom= 2003\n", - "Step= 668, Dmax= 2.2e-02 nm, Epot= -6.15877e+04 Fmax= 1.53961e+02, atom= 2003\n", - "Step= 670, Dmax= 1.3e-02 nm, Epot= -6.15923e+04 Fmax= 7.17153e+01, atom= 2003\n", - "Step= 671, Dmax= 1.6e-02 nm, Epot= -6.15944e+04 Fmax= 1.94172e+02, atom= 2003\n", - "Step= 672, Dmax= 1.9e-02 nm, Epot= -6.15995e+04 Fmax= 1.34465e+02, atom= 2003\n", - "Step= 674, Dmax= 1.1e-02 nm, Epot= -6.16035e+04 Fmax= 5.76225e+01, atom= 2003\n", - "Step= 675, Dmax= 1.4e-02 nm, Epot= -6.16069e+04 Fmax= 1.72810e+02, atom= 2003\n", - "Step= 676, Dmax= 1.7e-02 nm, Epot= -6.16116e+04 Fmax= 1.01823e+02, atom= 2003\n", - "Step= 677, Dmax= 2.0e-02 nm, Epot= -6.16117e+04 Fmax= 2.34006e+02, atom= 2003\n", - "Step= 678, Dmax= 2.4e-02 nm, Epot= -6.16176e+04 Fmax= 1.61353e+02, atom= 2003\n", - "Step= 680, Dmax= 1.4e-02 nm, Epot= -6.16223e+04 Fmax= 7.88245e+01, atom= 2003\n", - "Step= 681, Dmax= 1.7e-02 nm, Epot= -6.16237e+04 Fmax= 2.08074e+02, atom= 2003\n", - "Step= 682, Dmax= 2.1e-02 nm, Epot= -6.16290e+04 Fmax= 1.42235e+02, atom= 2003\n", - "Step= 684, Dmax= 1.2e-02 nm, Epot= -6.16332e+04 Fmax= 6.41023e+01, atom= 2003\n", - "Step= 685, Dmax= 1.5e-02 nm, Epot= -6.16361e+04 Fmax= 1.80185e+02, atom= 2003\n", - "Step= 686, Dmax= 1.8e-02 nm, Epot= -6.16408e+04 Fmax= 1.14791e+02, atom= 2003\n", - "Step= 688, Dmax= 1.1e-02 nm, Epot= -6.16442e+04 Fmax= 6.38684e+01, atom= 2003\n", - "Step= 689, Dmax= 1.3e-02 nm, Epot= -6.16473e+04 Fmax= 1.49940e+02, atom= 2003\n", - "Step= 690, Dmax= 1.5e-02 nm, Epot= -6.16512e+04 Fmax= 1.09117e+02, atom= 2003\n", - "Step= 691, Dmax= 1.8e-02 nm, Epot= -6.16525e+04 Fmax= 1.97989e+02, atom= 2003\n", - "Step= 692, Dmax= 2.2e-02 nm, Epot= -6.16564e+04 Fmax= 1.75100e+02, atom= 2003\n", - "Step= 694, Dmax= 1.3e-02 nm, Epot= -6.16616e+04 Fmax= 4.58183e+01, atom= 2003\n", - "Step= 695, Dmax= 1.6e-02 nm, Epot= -6.16655e+04 Fmax= 2.11814e+02, atom= 2003\n", - "Step= 696, Dmax= 1.9e-02 nm, Epot= -6.16717e+04 Fmax= 1.04387e+02, atom= 2003\n", - "Step= 698, Dmax= 1.1e-02 nm, Epot= -6.16749e+04 Fmax= 8.76908e+01, atom= 2003\n", - "Step= 699, Dmax= 1.4e-02 nm, Epot= -6.16773e+04 Fmax= 1.41051e+02, atom= 2003\n", - "Step= 700, Dmax= 1.6e-02 nm, Epot= -6.16805e+04 Fmax= 1.35624e+02, atom= 2003\n", - "Step= 701, Dmax= 2.0e-02 nm, Epot= -6.16816e+04 Fmax= 1.93555e+02, atom= 2003\n", - "Step= 702, Dmax= 2.4e-02 nm, Epot= -6.16840e+04 Fmax= 2.05078e+02, atom= 2003\n", - "Step= 704, Dmax= 1.4e-02 nm, Epot= -6.16913e+04 Fmax= 3.17197e+01, atom= 2003\n", - "Step= 705, Dmax= 1.7e-02 nm, Epot= -6.16949e+04 Fmax= 2.39624e+02, atom= 2003\n", - "Step= 706, Dmax= 2.1e-02 nm, Epot= -6.17050e+04 Fmax= 1.16014e+02, atom= 368\n", - "Step= 708, Dmax= 1.2e-02 nm, Epot= -6.17085e+04 Fmax= 9.90791e+01, atom= 368\n", - "Step= 709, Dmax= 1.5e-02 nm, Epot= -6.17102e+04 Fmax= 1.58602e+02, atom= 368\n", - "Step= 710, Dmax= 1.8e-02 nm, Epot= -6.17137e+04 Fmax= 1.48940e+02, atom= 368\n", - "Step= 711, Dmax= 2.1e-02 nm, Epot= -6.17142e+04 Fmax= 2.22296e+02, atom= 368\n", - "Step= 712, Dmax= 2.6e-02 nm, Epot= -6.17176e+04 Fmax= 2.19836e+02, atom= 368\n", - "Step= 714, Dmax= 1.5e-02 nm, Epot= -6.17245e+04 Fmax= 4.82357e+01, atom= 368\n", - "Step= 715, Dmax= 1.8e-02 nm, Epot= -6.17270e+04 Fmax= 2.75294e+02, atom= 368\n", - "Step= 716, Dmax= 2.2e-02 nm, Epot= -6.17349e+04 Fmax= 1.21547e+02, atom= 368\n", - "Step= 718, Dmax= 1.3e-02 nm, Epot= -6.17380e+04 Fmax= 1.10529e+02, atom= 368\n", - "Step= 719, Dmax= 1.6e-02 nm, Epot= -6.17404e+04 Fmax= 1.64026e+02, atom= 368\n", - "Step= 720, Dmax= 1.9e-02 nm, Epot= -6.17433e+04 Fmax= 1.66327e+02, atom= 368\n", - "Step= 721, Dmax= 2.3e-02 nm, Epot= -6.17447e+04 Fmax= 2.30901e+02, atom= 368\n", - "Step= 722, Dmax= 2.7e-02 nm, Epot= -6.17474e+04 Fmax= 2.43478e+02, atom= 368\n", - "Step= 724, Dmax= 1.6e-02 nm, Epot= -6.17534e+04 Fmax= 4.37707e+01, atom= 368\n", - "Step= 725, Dmax= 2.0e-02 nm, Epot= -6.17569e+04 Fmax= 3.06569e+02, atom= 368\n", - "Step= 726, Dmax= 2.4e-02 nm, Epot= -6.17655e+04 Fmax= 1.23357e+02, atom= 368\n", - "Step= 728, Dmax= 1.4e-02 nm, Epot= -6.17685e+04 Fmax= 1.27029e+02, atom= 368\n", - "Step= 729, Dmax= 1.7e-02 nm, Epot= -6.17709e+04 Fmax= 1.66765e+02, atom= 368\n", - "Step= 730, Dmax= 2.0e-02 nm, Epot= -6.17735e+04 Fmax= 1.88374e+02, atom= 368\n", - "Step= 731, Dmax= 2.5e-02 nm, Epot= -6.17750e+04 Fmax= 2.37119e+02, atom= 368\n", - "Step= 732, Dmax= 2.9e-02 nm, Epot= -6.17770e+04 Fmax= 2.72256e+02, atom= 368\n", - "Step= 734, Dmax= 1.8e-02 nm, Epot= -6.17841e+04 Fmax= 3.70225e+01, atom= 369\n", - "Step= 735, Dmax= 2.1e-02 nm, Epot= -6.17883e+04 Fmax= 3.60829e+02, atom= 369\n", - "Step= 736, Dmax= 2.5e-02 nm, Epot= -6.17994e+04 Fmax= 1.03095e+02, atom= 368\n", - "Step= 738, Dmax= 1.5e-02 nm, Epot= -6.18018e+04 Fmax= 1.70097e+02, atom= 368\n", - "Step= 739, Dmax= 1.8e-02 nm, Epot= -6.18051e+04 Fmax= 1.48555e+02, atom= 368\n", - "Step= 740, Dmax= 2.2e-02 nm, Epot= -6.18063e+04 Fmax= 2.35406e+02, atom= 368\n", - "Step= 741, Dmax= 2.6e-02 nm, Epot= -6.18094e+04 Fmax= 2.23330e+02, atom= 368\n", - "Step= 743, Dmax= 1.6e-02 nm, Epot= -6.18151e+04 Fmax= 4.97477e+01, atom= 368\n", - "Step= 744, Dmax= 1.9e-02 nm, Epot= -6.18197e+04 Fmax= 2.62392e+02, atom= 368\n", - "Step= 745, Dmax= 2.3e-02 nm, Epot= -6.18258e+04 Fmax= 1.29486e+02, atom= 368\n", - "Step= 747, Dmax= 1.4e-02 nm, Epot= -6.18288e+04 Fmax= 1.08641e+02, atom= 368\n", - "Step= 748, Dmax= 1.6e-02 nm, Epot= -6.18312e+04 Fmax= 1.74175e+02, atom= 368\n", - "Step= 749, Dmax= 2.0e-02 nm, Epot= -6.18341e+04 Fmax= 1.67198e+02, atom= 368\n", - "Step= 750, Dmax= 2.4e-02 nm, Epot= -6.18353e+04 Fmax= 2.41594e+02, atom= 368\n", - "Step= 751, Dmax= 2.8e-02 nm, Epot= -6.18378e+04 Fmax= 2.49320e+02, atom= 368\n", - "Step= 753, Dmax= 1.7e-02 nm, Epot= -6.18443e+04 Fmax= 4.28431e+01, atom= 368\n", - "Step= 754, Dmax= 2.0e-02 nm, Epot= -6.18492e+04 Fmax= 2.97137e+02, atom= 368\n", - "Step= 755, Dmax= 2.5e-02 nm, Epot= -6.18571e+04 Fmax= 1.26726e+02, atom= 368\n", - "Step= 757, Dmax= 1.5e-02 nm, Epot= -6.18600e+04 Fmax= 1.29646e+02, atom= 368\n", - "Step= 758, Dmax= 1.8e-02 nm, Epot= -6.18621e+04 Fmax= 1.73592e+02, atom= 368\n", - "Step= 759, Dmax= 2.1e-02 nm, Epot= -6.18645e+04 Fmax= 1.92137e+02, atom= 368\n", - "Step= 760, Dmax= 2.5e-02 nm, Epot= -6.18657e+04 Fmax= 2.46347e+02, atom= 368\n", - "Step= 761, Dmax= 3.1e-02 nm, Epot= -6.18670e+04 Fmax= 2.79095e+02, atom= 368\n", - "Step= 763, Dmax= 1.8e-02 nm, Epot= -6.18756e+04 Fmax= 3.45257e+01, atom= 368\n", - "Step= 764, Dmax= 2.2e-02 nm, Epot= -6.18806e+04 Fmax= 3.31107e+02, atom= 368\n", - "Step= 765, Dmax= 2.6e-02 nm, Epot= -6.18916e+04 Fmax= 1.29041e+02, atom= 368\n", - "Step= 767, Dmax= 1.6e-02 nm, Epot= -6.18942e+04 Fmax= 1.48210e+02, atom= 368\n", - "Step= 768, Dmax= 1.9e-02 nm, Epot= -6.18964e+04 Fmax= 1.76917e+02, atom= 368\n", - "Step= 769, Dmax= 2.3e-02 nm, Epot= -6.18979e+04 Fmax= 2.15149e+02, atom= 368\n", - "Step= 770, Dmax= 2.7e-02 nm, Epot= -6.18991e+04 Fmax= 2.55259e+02, atom= 368\n", - "Step= 772, Dmax= 1.6e-02 nm, Epot= -6.19071e+04 Fmax= 2.75736e+01, atom= 368\n", - "Step= 773, Dmax= 2.0e-02 nm, Epot= -6.19079e+04 Fmax= 3.44267e+02, atom= 2750\n", - "Step= 774, Dmax= 2.4e-02 nm, Epot= -6.19247e+04 Fmax= 1.08612e+02, atom= 2750\n", - "Step= 776, Dmax= 1.4e-02 nm, Epot= -6.19271e+04 Fmax= 1.35035e+02, atom= 2750\n", - "Step= 777, Dmax= 1.7e-02 nm, Epot= -6.19289e+04 Fmax= 1.61560e+02, atom= 2750\n", - "Step= 778, Dmax= 2.0e-02 nm, Epot= -6.19307e+04 Fmax= 2.00973e+02, atom= 2750\n", - "Step= 779, Dmax= 2.4e-02 nm, Epot= -6.19318e+04 Fmax= 2.24575e+02, atom= 2750\n", - "Step= 781, Dmax= 1.5e-02 nm, Epot= -6.19398e+04 Fmax= 1.91633e+01, atom= 1037\n", - "Step= 782, Dmax= 1.8e-02 nm, Epot= -6.19463e+04 Fmax= 2.75170e+02, atom= 1037\n", - "Step= 783, Dmax= 2.1e-02 nm, Epot= -6.19616e+04 Fmax= 1.25706e+02, atom= 2750\n", - "Step= 785, Dmax= 1.3e-02 nm, Epot= -6.19646e+04 Fmax= 9.91287e+01, atom= 2750\n", - "Step= 786, Dmax= 1.5e-02 nm, Epot= -6.19660e+04 Fmax= 1.77579e+02, atom= 2750\n", - "Step= 787, Dmax= 1.8e-02 nm, Epot= -6.19693e+04 Fmax= 1.46723e+02, atom= 2750\n", - "Step= 789, Dmax= 1.1e-02 nm, Epot= -6.19733e+04 Fmax= 3.79304e+01, atom= 2750\n", - "Step= 790, Dmax= 1.3e-02 nm, Epot= -6.19767e+04 Fmax= 1.93656e+02, atom= 2750\n", - "Step= 791, Dmax= 1.6e-02 nm, Epot= -6.19827e+04 Fmax= 8.18299e+01, atom= 2750\n", - "Step= 793, Dmax= 9.5e-03 nm, Epot= -6.19852e+04 Fmax= 8.65966e+01, atom= 2750\n", - "Step= 794, Dmax= 1.1e-02 nm, Epot= -6.19878e+04 Fmax= 1.16394e+02, atom= 2750\n", - "Step= 795, Dmax= 1.4e-02 nm, Epot= -6.19901e+04 Fmax= 1.24825e+02, atom= 2750\n", - "Step= 796, Dmax= 1.6e-02 nm, Epot= -6.19921e+04 Fmax= 1.68551e+02, atom= 2750\n", - "Step= 797, Dmax= 2.0e-02 nm, Epot= -6.19942e+04 Fmax= 1.76615e+02, atom= 2750\n", - "Step= 798, Dmax= 2.4e-02 nm, Epot= -6.19950e+04 Fmax= 2.48557e+02, atom= 2750\n", - "Step= 799, Dmax= 2.8e-02 nm, Epot= -6.19967e+04 Fmax= 2.45580e+02, atom= 2750\n", - "Step= 801, Dmax= 1.7e-02 nm, Epot= -6.20046e+04 Fmax= 3.22618e+01, atom= 2750\n", - "Step= 803, Dmax= 1.0e-02 nm, Epot= -6.20090e+04 Fmax= 1.51622e+02, atom= 2750\n", - "Step= 804, Dmax= 1.2e-02 nm, Epot= -6.20134e+04 Fmax= 6.78330e+01, atom= 2750\n", - "Step= 805, Dmax= 1.5e-02 nm, Epot= -6.20151e+04 Fmax= 1.80441e+02, atom= 2750\n", - "Step= 806, Dmax= 1.8e-02 nm, Epot= -6.20194e+04 Fmax= 1.23844e+02, atom= 2750\n", - "Step= 808, Dmax= 1.1e-02 nm, Epot= -6.20226e+04 Fmax= 6.75862e+01, atom= 2750\n", - "Step= 809, Dmax= 1.3e-02 nm, Epot= -6.20249e+04 Fmax= 1.62270e+02, atom= 2750\n", - "Step= 810, Dmax= 1.5e-02 nm, Epot= -6.20282e+04 Fmax= 1.10923e+02, atom= 2750\n", - "Step= 811, Dmax= 1.8e-02 nm, Epot= -6.20290e+04 Fmax= 2.22463e+02, atom= 2750\n", - "Step= 812, Dmax= 2.2e-02 nm, Epot= -6.20326e+04 Fmax= 1.67805e+02, atom= 2750\n", - "Step= 814, Dmax= 1.3e-02 nm, Epot= -6.20368e+04 Fmax= 5.20848e+01, atom= 2750\n", - "Step= 815, Dmax= 1.6e-02 nm, Epot= -6.20387e+04 Fmax= 2.22083e+02, atom= 2750\n", - "Step= 816, Dmax= 1.9e-02 nm, Epot= -6.20448e+04 Fmax= 1.07316e+02, atom= 2750\n", - "Step= 818, Dmax= 1.1e-02 nm, Epot= -6.20474e+04 Fmax= 9.50686e+01, atom= 2750\n", - "Step= 819, Dmax= 1.4e-02 nm, Epot= -6.20496e+04 Fmax= 1.49584e+02, atom= 2750\n", - "Step= 820, Dmax= 1.6e-02 nm, Epot= -6.20522e+04 Fmax= 1.39899e+02, atom= 2750\n", - "Step= 821, Dmax= 2.0e-02 nm, Epot= -6.20535e+04 Fmax= 2.13977e+02, atom= 2750\n", - "Step= 822, Dmax= 2.4e-02 nm, Epot= -6.20560e+04 Fmax= 2.00165e+02, atom= 2750\n", - "Step= 824, Dmax= 1.4e-02 nm, Epot= -6.20613e+04 Fmax= 3.38868e+01, atom= 2750\n", - "Step= 825, Dmax= 1.7e-02 nm, Epot= -6.20648e+04 Fmax= 2.65216e+02, atom= 2750\n", - "Step= 826, Dmax= 2.0e-02 nm, Epot= -6.20738e+04 Fmax= 9.39634e+01, atom= 2750\n", - "Step= 828, Dmax= 1.2e-02 nm, Epot= -6.20762e+04 Fmax= 1.19392e+02, atom= 2750\n", - "Step= 829, Dmax= 1.5e-02 nm, Epot= -6.20786e+04 Fmax= 1.40910e+02, atom= 2750\n", - "Step= 830, Dmax= 1.8e-02 nm, Epot= -6.20805e+04 Fmax= 1.67102e+02, atom= 2750\n", - "Step= 831, Dmax= 2.1e-02 nm, Epot= -6.20824e+04 Fmax= 2.10474e+02, atom= 2750\n", - "Step= 832, Dmax= 2.5e-02 nm, Epot= -6.20837e+04 Fmax= 2.30599e+02, atom= 2750\n", - "Step= 833, Dmax= 3.0e-02 nm, Epot= -6.20837e+04 Fmax= 3.17050e+02, atom= 2750\n", - "Step= 834, Dmax= 3.6e-02 nm, Epot= -6.20844e+04 Fmax= 3.14592e+02, atom= 2750\n", - "Step= 836, Dmax= 2.2e-02 nm, Epot= -6.20957e+04 Fmax= 4.04836e+01, atom= 1037\n", - "Step= 838, Dmax= 1.3e-02 nm, Epot= -6.20990e+04 Fmax= 1.77233e+02, atom= 2750\n", - "Step= 839, Dmax= 1.6e-02 nm, Epot= -6.21040e+04 Fmax= 1.12088e+02, atom= 2750\n", - "Step= 840, Dmax= 1.9e-02 nm, Epot= -6.21041e+04 Fmax= 2.09887e+02, atom= 2750\n", - "Step= 841, Dmax= 2.3e-02 nm, Epot= -6.21080e+04 Fmax= 1.85533e+02, atom= 2750\n", - "Step= 843, Dmax= 1.4e-02 nm, Epot= -6.21124e+04 Fmax= 6.45958e+01, atom= 2750\n", - "Step= 844, Dmax= 1.6e-02 nm, Epot= -6.21141e+04 Fmax= 2.37687e+02, atom= 2750\n", - "Step= 845, Dmax= 2.0e-02 nm, Epot= -6.21189e+04 Fmax= 1.20446e+02, atom= 2750\n", - "Step= 847, Dmax= 1.2e-02 nm, Epot= -6.21217e+04 Fmax= 7.95349e+01, atom= 2750\n", - "Step= 848, Dmax= 1.4e-02 nm, Epot= -6.21236e+04 Fmax= 1.65943e+02, atom= 2750\n", - "Step= 849, Dmax= 1.7e-02 nm, Epot= -6.21269e+04 Fmax= 1.29655e+02, atom= 2750\n", - "Step= 850, Dmax= 2.0e-02 nm, Epot= -6.21272e+04 Fmax= 2.19874e+02, atom= 2750\n", - "Step= 851, Dmax= 2.4e-02 nm, Epot= -6.21305e+04 Fmax= 2.08640e+02, atom= 2750\n", - "Step= 853, Dmax= 1.5e-02 nm, Epot= -6.21354e+04 Fmax= 6.09002e+01, atom= 2750\n", - "Step= 854, Dmax= 1.8e-02 nm, Epot= -6.21369e+04 Fmax= 2.68250e+02, atom= 2750\n", - "Step= 855, Dmax= 2.1e-02 nm, Epot= -6.21425e+04 Fmax= 1.20175e+02, atom= 2750\n", - "Step= 857, Dmax= 1.3e-02 nm, Epot= -6.21452e+04 Fmax= 9.50631e+01, atom= 2750\n", - "Step= 858, Dmax= 1.5e-02 nm, Epot= -6.21470e+04 Fmax= 1.68258e+02, atom= 2750\n", - "Step= 859, Dmax= 1.8e-02 nm, Epot= -6.21500e+04 Fmax= 1.50537e+02, atom= 2750\n", - "Step= 860, Dmax= 2.2e-02 nm, Epot= -6.21502e+04 Fmax= 2.25493e+02, atom= 2750\n", - "Step= 861, Dmax= 2.6e-02 nm, Epot= -6.21529e+04 Fmax= 2.37605e+02, atom= 2750\n", - "Step= 863, Dmax= 1.6e-02 nm, Epot= -6.21587e+04 Fmax= 5.47983e+01, atom= 2750\n", - "Step= 864, Dmax= 1.9e-02 nm, Epot= -6.21603e+04 Fmax= 3.04818e+02, atom= 2750\n", - "Step= 865, Dmax= 2.3e-02 nm, Epot= -6.21669e+04 Fmax= 1.19078e+02, atom= 2750\n", - "Step= 867, Dmax= 1.4e-02 nm, Epot= -6.21695e+04 Fmax= 1.12533e+02, atom= 2750\n", - "Step= 868, Dmax= 1.6e-02 nm, Epot= -6.21711e+04 Fmax= 1.70236e+02, atom= 2750\n", - "Step= 869, Dmax= 2.0e-02 nm, Epot= -6.21737e+04 Fmax= 1.73636e+02, atom= 2750\n", - "Step= 870, Dmax= 2.3e-02 nm, Epot= -6.21739e+04 Fmax= 2.31386e+02, atom= 2750\n", - "Step= 871, Dmax= 2.8e-02 nm, Epot= -6.21758e+04 Fmax= 2.68993e+02, atom= 2750\n", - "Step= 873, Dmax= 1.7e-02 nm, Epot= -6.21826e+04 Fmax= 4.84076e+01, atom= 2750\n", - "Step= 874, Dmax= 2.0e-02 nm, Epot= -6.21844e+04 Fmax= 3.47355e+02, atom= 2750\n", - "Step= 875, Dmax= 2.4e-02 nm, Epot= -6.21921e+04 Fmax= 1.17833e+02, atom= 2750\n", - "Step= 877, Dmax= 1.5e-02 nm, Epot= -6.21944e+04 Fmax= 1.31259e+02, atom= 2750\n", - "Step= 878, Dmax= 1.8e-02 nm, Epot= -6.21958e+04 Fmax= 1.72611e+02, atom= 2750\n", - "Step= 879, Dmax= 2.1e-02 nm, Epot= -6.21978e+04 Fmax= 1.98336e+02, atom= 2750\n", - "Step= 880, Dmax= 2.5e-02 nm, Epot= -6.21983e+04 Fmax= 2.37885e+02, atom= 2750\n", - "Step= 881, Dmax= 3.0e-02 nm, Epot= -6.21991e+04 Fmax= 3.02513e+02, atom= 2750\n", - "Step= 883, Dmax= 1.8e-02 nm, Epot= -6.22073e+04 Fmax= 4.21541e+01, atom= 2750\n", - "Step= 884, Dmax= 2.2e-02 nm, Epot= -6.22094e+04 Fmax= 3.98904e+02, atom= 2750\n", - "Step= 885, Dmax= 2.6e-02 nm, Epot= -6.22184e+04 Fmax= 1.17094e+02, atom= 2750\n", - "Step= 887, Dmax= 1.6e-02 nm, Epot= -6.22204e+04 Fmax= 1.50826e+02, atom= 2750\n", - "Step= 888, Dmax= 1.9e-02 nm, Epot= -6.22220e+04 Fmax= 1.75637e+02, atom= 2750\n", - "Step= 889, Dmax= 2.3e-02 nm, Epot= -6.22234e+04 Fmax= 2.24598e+02, atom= 2750\n", - "Step= 890, Dmax= 2.7e-02 nm, Epot= -6.22242e+04 Fmax= 2.45050e+02, atom= 2750\n", - "Step= 892, Dmax= 1.6e-02 nm, Epot= -6.22309e+04 Fmax= 2.27688e+01, atom= 1037\n", - "Step= 893, Dmax= 2.0e-02 nm, Epot= -6.22355e+04 Fmax= 3.11486e+02, atom= 2750\n", - "Step= 894, Dmax= 2.3e-02 nm, Epot= -6.22485e+04 Fmax= 1.37326e+02, atom= 2750\n", - "Step= 896, Dmax= 1.4e-02 nm, Epot= -6.22508e+04 Fmax= 1.12125e+02, atom= 2750\n", - "Step= 897, Dmax= 1.7e-02 nm, Epot= -6.22521e+04 Fmax= 1.91929e+02, atom= 2750\n", - "Step= 898, Dmax= 2.0e-02 nm, Epot= -6.22546e+04 Fmax= 1.66074e+02, atom= 2750\n", - "Step= 900, Dmax= 1.2e-02 nm, Epot= -6.22583e+04 Fmax= 3.72284e+01, atom= 2750\n", - "Step= 901, Dmax= 1.5e-02 nm, Epot= -6.22612e+04 Fmax= 2.21501e+02, atom= 2750\n", - "Step= 902, Dmax= 1.7e-02 nm, Epot= -6.22671e+04 Fmax= 8.47179e+01, atom= 2750\n", - "Step= 904, Dmax= 1.0e-02 nm, Epot= -6.22694e+04 Fmax= 1.01163e+02, atom= 2750\n", - "Step= 905, Dmax= 1.3e-02 nm, Epot= -6.22715e+04 Fmax= 1.22760e+02, atom= 2750\n", - "Step= 906, Dmax= 1.5e-02 nm, Epot= -6.22732e+04 Fmax= 1.43909e+02, atom= 2750\n", - "Step= 907, Dmax= 1.8e-02 nm, Epot= -6.22749e+04 Fmax= 1.80170e+02, atom= 2750\n", - "Step= 908, Dmax= 2.2e-02 nm, Epot= -6.22762e+04 Fmax= 2.01256e+02, atom= 2750\n", - "Step= 909, Dmax= 2.6e-02 nm, Epot= -6.22768e+04 Fmax= 2.68729e+02, atom= 2750\n", - "Step= 910, Dmax= 3.1e-02 nm, Epot= -6.22773e+04 Fmax= 2.77247e+02, atom= 2750\n", - "Step= 912, Dmax= 1.9e-02 nm, Epot= -6.22860e+04 Fmax= 3.04031e+01, atom= 1037\n", - "Step= 914, Dmax= 1.1e-02 nm, Epot= -6.22899e+04 Fmax= 1.66516e+02, atom= 2750\n", - "Step= 915, Dmax= 1.4e-02 nm, Epot= -6.22944e+04 Fmax= 8.28680e+01, atom= 2750\n", - "Step= 916, Dmax= 1.6e-02 nm, Epot= -6.22951e+04 Fmax= 1.92190e+02, atom= 2750\n", - "Step= 917, Dmax= 1.9e-02 nm, Epot= -6.22987e+04 Fmax= 1.44973e+02, atom= 2750\n", - "Step= 919, Dmax= 1.2e-02 nm, Epot= -6.23019e+04 Fmax= 6.82966e+01, atom= 2750\n", - "Step= 920, Dmax= 1.4e-02 nm, Epot= -6.23035e+04 Fmax= 1.87706e+02, atom= 2750\n", - "Step= 921, Dmax= 1.7e-02 nm, Epot= -6.23068e+04 Fmax= 1.17433e+02, atom= 2750\n", - "Step= 923, Dmax= 1.0e-02 nm, Epot= -6.23094e+04 Fmax= 5.49337e+01, atom= 2750\n", - "Step= 924, Dmax= 1.2e-02 nm, Epot= -6.23116e+04 Fmax= 1.58267e+02, atom= 2750\n", - "Step= 925, Dmax= 1.5e-02 nm, Epot= -6.23149e+04 Fmax= 9.58326e+01, atom= 2750\n", - "Step= 926, Dmax= 1.7e-02 nm, Epot= -6.23151e+04 Fmax= 2.06015e+02, atom= 2750\n", - "Step= 927, Dmax= 2.1e-02 nm, Epot= -6.23189e+04 Fmax= 1.60837e+02, atom= 2750\n", - "Step= 929, Dmax= 1.3e-02 nm, Epot= -6.23223e+04 Fmax= 6.87621e+01, atom= 2750\n", - "Step= 930, Dmax= 1.5e-02 nm, Epot= -6.23235e+04 Fmax= 2.08350e+02, atom= 2750\n", - "Step= 931, Dmax= 1.8e-02 nm, Epot= -6.23272e+04 Fmax= 1.20806e+02, atom= 2750\n", - "Step= 933, Dmax= 1.1e-02 nm, Epot= -6.23299e+04 Fmax= 6.43351e+01, atom= 2750\n", - "Step= 934, Dmax= 1.3e-02 nm, Epot= -6.23316e+04 Fmax= 1.64205e+02, atom= 2750\n", - "Step= 935, Dmax= 1.6e-02 nm, Epot= -6.23349e+04 Fmax= 1.09254e+02, atom= 2750\n", - "Step= 937, Dmax= 9.4e-03 nm, Epot= -6.23373e+04 Fmax= 6.08007e+01, atom= 2750\n", - "Step= 938, Dmax= 1.1e-02 nm, Epot= -6.23395e+04 Fmax= 1.41628e+02, atom= 2750\n", - "Step= 939, Dmax= 1.4e-02 nm, Epot= -6.23421e+04 Fmax= 1.01490e+02, atom= 2750\n", - "Step= 940, Dmax= 1.6e-02 nm, Epot= -6.23430e+04 Fmax= 1.92695e+02, atom= 2750\n", - "Step= 941, Dmax= 1.9e-02 nm, Epot= -6.23457e+04 Fmax= 1.54793e+02, atom= 2750\n", - "Step= 943, Dmax= 1.2e-02 nm, Epot= -6.23491e+04 Fmax= 4.20879e+01, atom= 2750\n", - "Step= 944, Dmax= 1.4e-02 nm, Epot= -6.23513e+04 Fmax= 2.05820e+02, atom= 2750\n", - "Step= 945, Dmax= 1.7e-02 nm, Epot= -6.23565e+04 Fmax= 8.83032e+01, atom= 2750\n", - "Step= 947, Dmax= 1.0e-02 nm, Epot= -6.23586e+04 Fmax= 9.22018e+01, atom= 2750\n", - "Step= 948, Dmax= 1.2e-02 nm, Epot= -6.23605e+04 Fmax= 1.23843e+02, atom= 2750\n", - "Step= 949, Dmax= 1.5e-02 nm, Epot= -6.23624e+04 Fmax= 1.34223e+02, atom= 2750\n", - "Step= 950, Dmax= 1.7e-02 nm, Epot= -6.23638e+04 Fmax= 1.78374e+02, atom= 2750\n", - "Step= 951, Dmax= 2.1e-02 nm, Epot= -6.23652e+04 Fmax= 1.90476e+02, atom= 2750\n", - "Step= 952, Dmax= 2.5e-02 nm, Epot= -6.23655e+04 Fmax= 2.62860e+02, atom= 2750\n", - "Step= 953, Dmax= 3.0e-02 nm, Epot= -6.23664e+04 Fmax= 2.64834e+02, atom= 2750\n", - "Step= 955, Dmax= 1.8e-02 nm, Epot= -6.23743e+04 Fmax= 3.04993e+01, atom= 2750\n", - "Step= 957, Dmax= 1.1e-02 nm, Epot= -6.23775e+04 Fmax= 1.70863e+02, atom= 2750\n", - "Step= 958, Dmax= 1.3e-02 nm, Epot= -6.23821e+04 Fmax= 6.69715e+01, atom= 2750\n", - "Step= 959, Dmax= 1.6e-02 nm, Epot= -6.23830e+04 Fmax= 1.95303e+02, atom= 2750\n", - "Step= 960, Dmax= 1.9e-02 nm, Epot= -6.23869e+04 Fmax= 1.25988e+02, atom= 2750\n", - "Step= 962, Dmax= 1.1e-02 nm, Epot= -6.23895e+04 Fmax= 7.82270e+01, atom= 2750\n", - "Step= 963, Dmax= 1.3e-02 nm, Epot= -6.23909e+04 Fmax= 1.66084e+02, atom= 2750\n", - "Step= 964, Dmax= 1.6e-02 nm, Epot= -6.23936e+04 Fmax= 1.25696e+02, atom= 2750\n", - "Step= 965, Dmax= 1.9e-02 nm, Epot= -6.23936e+04 Fmax= 2.28743e+02, atom= 2750\n", - "Step= 966, Dmax= 2.3e-02 nm, Epot= -6.23963e+04 Fmax= 1.87346e+02, atom= 2750\n", - "Step= 968, Dmax= 1.4e-02 nm, Epot= -6.24007e+04 Fmax= 4.61115e+01, atom= 2750\n", - "Step= 970, Dmax= 8.4e-03 nm, Epot= -6.24030e+04 Fmax= 1.06144e+02, atom= 2750\n", - "Step= 971, Dmax= 1.0e-02 nm, Epot= -6.24054e+04 Fmax= 7.16916e+01, atom= 2750\n", - "Step= 972, Dmax= 1.2e-02 nm, Epot= -6.24069e+04 Fmax= 1.41454e+02, atom= 2750\n", - "Step= 973, Dmax= 1.5e-02 nm, Epot= -6.24095e+04 Fmax= 1.13761e+02, atom= 2750\n", - "Step= 974, Dmax= 1.7e-02 nm, Epot= -6.24098e+04 Fmax= 1.90679e+02, atom= 2750\n", - "Step= 975, Dmax= 2.1e-02 nm, Epot= -6.24125e+04 Fmax= 1.79039e+02, atom= 2750\n", - "Step= 977, Dmax= 1.3e-02 nm, Epot= -6.24163e+04 Fmax= 5.29980e+01, atom= 2750\n", - "Step= 978, Dmax= 1.5e-02 nm, Epot= -6.24178e+04 Fmax= 2.26140e+02, atom= 2750\n", - "Step= 979, Dmax= 1.8e-02 nm, Epot= -6.24220e+04 Fmax= 1.06989e+02, atom= 2750\n", - "Step= 981, Dmax= 1.1e-02 nm, Epot= -6.24242e+04 Fmax= 7.87776e+01, atom= 2750\n", - "Step= 982, Dmax= 1.3e-02 nm, Epot= -6.24255e+04 Fmax= 1.49557e+02, atom= 2750\n", - "Step= 983, Dmax= 1.6e-02 nm, Epot= -6.24281e+04 Fmax= 1.24449e+02, atom= 2750\n", - "Step= 984, Dmax= 1.9e-02 nm, Epot= -6.24282e+04 Fmax= 2.01481e+02, atom= 2750\n", - "Step= 985, Dmax= 2.2e-02 nm, Epot= -6.24308e+04 Fmax= 1.95733e+02, atom= 2750\n", - "Step= 987, Dmax= 1.3e-02 nm, Epot= -6.24351e+04 Fmax= 5.41248e+01, atom= 2750\n", - "Step= 988, Dmax= 1.6e-02 nm, Epot= -6.24361e+04 Fmax= 2.48590e+02, atom= 2750\n", - "Step= 989, Dmax= 1.9e-02 nm, Epot= -6.24409e+04 Fmax= 1.11541e+02, atom= 2750\n", - "Step= 991, Dmax= 1.2e-02 nm, Epot= -6.24432e+04 Fmax= 8.77878e+01, atom= 2750\n", - "Step= 992, Dmax= 1.4e-02 nm, Epot= -6.24444e+04 Fmax= 1.57307e+02, atom= 2750\n", - "Step= 993, Dmax= 1.7e-02 nm, Epot= -6.24469e+04 Fmax= 1.37498e+02, atom= 2750\n", - "Step= 995, Dmax= 1.0e-02 nm, Epot= -6.24497e+04 Fmax= 4.70264e+01, atom= 2750\n", - "Step= 996, Dmax= 1.2e-02 nm, Epot= -6.24521e+04 Fmax= 1.72199e+02, atom= 2750\n", - "Step= 997, Dmax= 1.4e-02 nm, Epot= -6.24552e+04 Fmax= 9.22409e+01, atom= 2750\n", - "Step= 998, Dmax= 1.7e-02 nm, Epot= -6.24554e+04 Fmax= 2.27634e+02, atom= 2750\n", - "Step= 999, Dmax= 2.1e-02 nm, Epot= -6.24590e+04 Fmax= 1.49093e+02, atom= 2750\n", - "Step= 1000, Dmax= 2.5e-02 nm, Epot= -6.24568e+04 Fmax= 3.15809e+02, atom= 2750\n", - "Energy minimization reached the maximum number of steps before the forces\n", - "reached the requested precision Fmax < 10.\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", - "writing lowest energy coordinates.\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n", "\n", - "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n", - "Potential Energy = -6.2459031e+04\n", - "Maximum force = 1.4909303e+02 on atom 2750\n", - "Norm of force = 4.0432186e+00\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"The aim of science is not to open the door to infinite wisdom, but to set a limit to infinite error.\" (Bertolt Brecht, Life of Galileo)\n", + "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", "\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed' (newly created)...\n", - "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n", - "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp']\n", - "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", - "{'pp': 'processed.top'}\n", - "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", - "{'pp': 'processed.top'}\n", - " warnings.warn(wmsg, category=UsageWarning)\n", - " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n", "\n", - "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"If we knew what it was we were doing, it would not be called research, would it?\" (Albert Einstein)\n", + "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", "\n", - "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", - "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", - "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] All files set up for a run time of 1000 ps (dt=0.01, nsteps=100000)\n" + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 30 time 120.000 " ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -554193827\n", - "\n", - "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", - "Excluding 1 bonded neighbours molecule type 'BENZ'\n", - "\n", - "Excluding 1 bonded neighbours molecule type 'OCO'\n", "\n", - "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.125 nm, buffer size 0.025 nm\n", "\n", - "Set rlist, assuming 4x4 atom pair-list, to 1.100 nm, buffer size 0.000 nm\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n", "\n", - "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 3 Mb of data\n" + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n" ] }, - { - "data": { - "text/plain": [ - "{'struct': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro',\n", - " 'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top',\n", - " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx',\n", - " 'qscript': ['./local.sh'],\n", - " 'mainselection': None,\n", - " 'deffnm': 'md',\n", - " 'includes': ['/home/awsm/MDPOW/mdpow/top',\n", - " '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top']}" - ] - }, - "execution_count": 16, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "from mdpow.equil import OctanolSimulation\n", - "\n", - "oct_sim = OctanolSimulation(\n", - " molecule=\"BENZ\",\n", - " ff_class=MARTINI,\n", - " mdp={\n", - " \"energy_minimize\": str(EM_FILE.absolute()),\n", - " \"MD_relaxed\": str(EQ_FILE.absolute()),\n", - " \"MD_NPT\": str(EQ_FILE.absolute()),\n", - " \"MD_restrained\": str(RUN_FILE.absolute()),\n", - " },\n", - " distance=4.0,\n", - ")\n", - "oct_sim.topology(str(BENZENE_ITP))\n", - "oct_sim.solvate(struct=MARTINI_BENZENE, maxwarn=1)\n", - "oct_sim.energy_minimize(maxwarn=1)\n", - "oct_sim.MD_relaxed(runtime=1e3, dt=0.01)" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n", "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 10 to 50, rlist from 1.1 to 1.233\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the GPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "100000 steps, 1000.0 ps.\n", + "mdpow.fep : INFO Analysis stride is 1.\n", + "mdpow.fep : INFO Analysis starts from frame 0.\n", + "mdpow.fep : INFO Analysis stops at frame None.\n", + "mdpow.fep : INFO Analyzing stored data.\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/pymbar/other_estimators.py:510: RuntimeWarning: invalid value encountered in sqrt\n", + " dDeltaF = np.sqrt(variance)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ "\n", - "Step 0 Warning: pressure scaling more than 1%, mu: 0.971025 0.971025 0.971025\n", - "step 0\n", - "Step 50 Warning: pressure scaling more than 1%, mu: 1.01107 1.01107 1.01107\n", - "step 99900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 100000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 297.037 74.259 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 1163.502 0.021\n", "\n", - "GROMACS reminds you: \"There's so many shades of black\" (The Raconteurs)\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + "\n", + "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (coulomb) -1.10771e-15 (nan) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (vdw) -6.88405 (0.28) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (Gibbs) 6.88405 (nan) kJ/mol\n" ] }, { "data": { "text/plain": [ - "0" + "6.88405 (nan)" ] }, - "execution_count": 17, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "r = gromacs.run.MDrunner(\n", - " dirname=oct_sim.dirs[\"MD_relaxed\"],\n", - " deffnm=\"md\",\n", - " c=\"md.pdb\",\n", - " cpi=True,\n", - " v=True,\n", - ")\n", - "r.run() # runs mdrun in the python shell" + "gwat.convert_edr()\n", + "gwat.analyze_alchemlyb()" ] }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import seaborn as sb\n", + "\n", + "def plot_results(gsolv: mdpow.fep.Gsolv):\n", + " \"\"\"Plot the results of thermodynamic integration.\"\"\"\n", + " fep_dfs: dict[str, pd.DataFrame] = {component: tuple_[1] for component, tuple_ in gsolv.results.xvg.items()}\n", + " \n", + " # Each df has one column for each lambda value\n", + " # We want several rows for each lambda value\n", + " formatted_data = {\"Component\": [], \"Lambda\": [], \"dvdl\": []}\n", + " for component, df in fep_dfs.items():\n", + " for lambda_ in df.columns:\n", + " entries = df.loc[:, lambda_].values\n", + " n_entries = len(entries)\n", + "\n", + " formatted_data[\"Component\"] += [component] * n_entries\n", + " formatted_data[\"Lambda\"] += [lambda_] * n_entries\n", + " formatted_data[\"dvdl\"].extend(entries)\n", + " \n", + " plot_df = pd.DataFrame(formatted_data)\n", + " return sb.catplot(data=plot_df, x=\"Lambda\", y=\"dvdl\", errorbar=\"se\", col=\"Component\")\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "plot_results(gwat)" + ] + }, + { + "cell_type": "code", + "execution_count": 19, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "mdpow.equil : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro').\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT' (newly created)...\n", - "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n", - "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 't']\n", - "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", - "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt'}\n", - "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", - "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt'}\n", - " warnings.warn(wmsg, category=UsageWarning)\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top' (newly created)...\n", + "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/octanol.gro'...\n", + " :-) GROMACS - gmx editconf, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 4.0\n", + "\n", + "\n", + "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "\n", + " :-) GROMACS - gmx solvate, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx solvate -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -cp boxed.gro -cs /home/awsm/MDPOW/doc/examples/martini/octanol.gro -o solvated.gro\n", + "\n", + "Reading solute configuration\n", + "Reading solvent configuration\n", + "\n", + "Initialising inter-atomic distances...\n", + "Generating solvent configuration\n", + "Will generate new solvent configuration of 2x2x2 boxes\n", + "Solvent box contains 5943 atoms in 1981 residues\n", + "Removed 828 solvent atoms due to solvent-solvent overlap\n", + "Removed 3 solvent atoms due to solute-solvent overlap\n", + "Sorting configuration\n", + "Found 1 molecule type:\n", + " OCO ( 3 atoms): 1704 residues\n", + "Generated solvent containing 5112 atoms in 1704 residues\n", + "Writing generated configuration to solvated.gro\n", + "\n", + "Output configuration contains 5115 atoms in 1705 residues\n", + "Volume : 399.981 (nm^3)\n", + "Density : 389.199 (g/l)\n", + "Number of solvent molecules: 1704 \n", + "\n", + "Processing topology\n", + "\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/#system.top.1#\n", + "\n", + "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "\n", + "gromacs.setup: INFO Solvated system with /home/awsm/MDPOW/doc/examples/martini/octanol.gro\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Note that major changes are planned in future for editconf, to improve usability and utility.\n", + "Read 3 atoms\n", + "Volume: 4050 nm^3, corresponds to roughly 1822500 electrons\n", + "No velocities found\n", + " system size : 0.210 0.160 0.248 (nm)\n", + " diameter : 0.270 (nm)\n", + " center : 2.987 0.606 2.315 (nm)\n", + " box vectors : 15.000 15.000 18.000 (nm)\n", + " box angles : 90.00 90.00 90.00 (degrees)\n", + " box volume :4050.00 (nm^3)\n", + " shift : 3.216 5.597 0.609 (nm)\n", + "new center : 6.203 6.203 2.924 (nm)\n", + "new box vectors : 8.270 8.270 8.270 (nm)\n", + "new box angles : 60.00 60.00 90.00 (degrees)\n", + "new box volume : 399.98 (nm^3)\n", + "\n", + "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n", + " based on residue and atom names, since they could not be\n", + " definitively assigned from the information in your input\n", + " files. These guessed numbers might deviate from the mass\n", + " and radius of the atom type. Please check the output\n", + " files if necessary. Note, that this functionality may\n", + " be removed in a future GROMACS version. Please, consider\n", + " using another file format for your input.\n", + "\n", + "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n", + "from the source below. This means the results may be different\n", + "compared to previous GROMACS versions.\n", + "\n", + "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n", + "A. Bondi\n", + "van der Waals Volumes and Radii\n", + "J. Phys. Chem. 68 (1964) pp. 441-451\n", + "-------- -------- --- Thank You --- -------- --------\n", + "\n", + "Adding line for 1704 solvent molecules with resname (OCO) to topology file (/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.cbook: INFO system total charge qtot = 0\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] After solvation: total charge qtot = 0 = 0\n", + "gromacs.cbook: INFO system total charge qtot = 0\n", + "gromacs.setup: INFO Building the main index file 'main.ndx'...\n", + " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx make_ndx -f ionized.tpr -o main.ndx\n", + "\n", + "\n", + "Reading structure file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "GROMACS reminds you: \"Welcome to the Power Age\" (2 Unlimited)\n", + "\n", + " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx make_ndx -f ionized.tpr -n main.ndx -o main.ndx\n", + "\n", + "\n", + "Reading structure file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.1#\n", + "\n", + "GROMACS reminds you: \"Welcome to the Power Age\" (2 Unlimited)\n", + "\n", + " :-) GROMACS - gmx trjconv, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n", + "Command line:\n", + " gmx trjconv -ur compact -center -boxcenter tric -pbc mol -f ionized.gro -s ionized.tpr -o compact.pdb -n main.ndx\n", + "\n", + "Will write pdb: Protein data bank file\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", + "Group 0 ( System) has 5115 elements\n", + "Group 1 ( Other) has 5115 elements\n", + "Group 2 ( BENZ) has 3 elements\n", + "Group 3 ( OCO) has 5112 elements\n", + "Group 4 ( __main__) has 3 elements\n", + "Group 5 (__environment__) has 5112 elements\n", + "Select a group: Group 0 ( System) has 5115 elements\n", + "Group 1 ( Other) has 5115 elements\n", + "Group 2 ( BENZ) has 3 elements\n", + "Group 3 ( OCO) has 5112 elements\n", + "Group 4 ( __main__) has 3 elements\n", + "Group 5 (__environment__) has 5112 elements\n", + "Select a group: Reading frames from gro file 'This is an auto generated system', 5115 atoms.\n", + "Reading frame 0 time 0.000 \n", + "Precision of ionized.gro is 0.001 (nm)\n", + "Last frame 0 time 0.000 \n", + " -> frame 0 time 0.000 \n", + "Last written: frame 0 time 0.000\n", + "\n", + "\n", + "GROMACS reminds you: \"Welcome to the Power Age\" (2 Unlimited)\n", + "\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -f /tmp/tmp2_aikyq2.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -nov\n", + "\n", + "\n", + "NOTE 1 [file /tmp/tmp2_aikyq2.mdp]:\n", + " For a correct single-point energy evaluation with nsteps = 0, use\n", + " continuation = yes to avoid constraining the input coordinates.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Note that major changes are planned in future for trjconv, to improve usability and utility.\n", + "Select group for centering\n", + "Selected 4: '__main__'\n", + "Select group for output\n", + "Selected 0: 'System'\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n", + "NOTE 2 [file system.top, line 28]:\n", + " For energy conservation with LINCS, lincs_iter should be 2 or larger.\n", + "\n", + "\n", + "Number of degrees of freedom in T-Coupling group rest is 15339.00\n", + "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "\n", + "NOTE 3 [file /tmp/tmp2_aikyq2.mdp]:\n", + " NVE simulation with an initial temperature of zero: will use a Verlet\n", + " buffer of 10%. Check your energy drift!\n", + "\n", + "\n", + "There were 3 NOTEs\n", + "\n", + "GROMACS reminds you: \"You should call it 'entropy'. No one knows what entropy really is, so in a debate you will always have the advantage.\" (John von Neumann to Claude Shannon, on why he should borrow the term for information theory)\n", + "\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top', mdp='em.mdp' ...\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'em.mdp': ['maxwarn', 'pp']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'maxwarn': 1, 'pp': 'processed.top'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'maxwarn': 1, 'pp': 'processed.top'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em\n", + "Command line:\n", + " gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -maxwarn 1 -pp processed.top\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1669599249\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "Analysing residue names:\n", + "There are: 1705 Other residues\n", + "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", + "\n", + "This run will generate roughly 0 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group rest is 15339.00\n", + "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", + "\n", + "GROMACS reminds you: \"You should call it 'entropy'. No one knows what entropy really is, so in a debate you will always have the advantage.\" (John von Neumann to Claude Shannon, on why he should borrow the term for information theory)\n", + "\n", + "gromacs.run : WARNING No 'mdrun_d' binary found so trying 'mdrun' instead.\n", + "(Note that energy minimization runs better with mdrun_d.)\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/run.py:423: AutoCorrectionWarning: No 'mdrun_d' binary found so trying 'mdrun' instead.\n", + "(Note that energy minimization runs better with mdrun_d.)\n", + " warnings.warn(wmsg, category=AutoCorrectionWarning)\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em\n", + "Command line:\n", + " gmx mdrun -v -stepout 10 -deffnm em -c em.pdb\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -538320998\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "Analysing residue names:\n", + "There are: 1705 Other residues\n", + "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n", + "\n", + "This run will generate roughly 1 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Reading file em.tpr, VERSION 2023.2 (single precision)\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "\n", + "Steepest Descents:\n", + " Tolerance (Fmax) = 1.00000e+01\n", + " Number of steps = 1000\n", + "Step= 0, Dmax= 1.0e-02 nm, Epot= 1.02801e+07 Fmax= 2.05315e+07, atom= 5083\n", + "Step= 1, Dmax= 1.0e-02 nm, Epot= 7.41994e+06 Fmax= 5.74654e+06, atom= 3110\n", + "Step= 2, Dmax= 1.2e-02 nm, Epot= 4.40326e+06 Fmax= 2.44532e+06, atom= 4997\n", + "Step= 3, Dmax= 1.4e-02 nm, Epot= 2.73795e+06 Fmax= 9.51879e+05, atom= 1685\n", + "Step= 4, Dmax= 1.7e-02 nm, Epot= 1.53428e+06 Fmax= 4.51665e+05, atom= 1684\n", + "Step= 5, Dmax= 2.1e-02 nm, Epot= 8.87445e+05 Fmax= 1.90248e+05, atom= 1990\n", + "Step= 6, Dmax= 2.5e-02 nm, Epot= 4.61156e+05 Fmax= 1.05731e+05, atom= 3691\n", + "Step= 7, Dmax= 3.0e-02 nm, Epot= 2.59013e+05 Fmax= 7.39295e+04, atom= 3626\n", + "Step= 8, Dmax= 3.6e-02 nm, Epot= 1.57144e+05 Fmax= 4.51091e+04, atom= 3691\n", + "Step= 9, Dmax= 4.3e-02 nm, Epot= 8.70638e+04 Fmax= 3.11807e+04, atom= 3047\n", + "Step= 10, Dmax= 5.2e-02 nm, Epot= 4.74060e+04 Fmax= 1.09883e+05, atom= 3020\n", + "Step= 11, Dmax= 6.2e-02 nm, Epot= 3.89493e+04 Fmax= 1.54250e+04, atom= 1088\n", + "Step= 12, Dmax= 7.4e-02 nm, Epot= 6.83725e+03 Fmax= 1.68745e+04, atom= 1088\n", + "Step= 13, Dmax= 8.9e-02 nm, Epot= -4.12859e+03 Fmax= 1.03437e+04, atom= 1088\n", + "Step= 14, Dmax= 1.1e-01 nm, Epot= -1.13033e+04 Fmax= 1.60187e+05, atom= 4\n", + "Step= 15, Dmax= 1.3e-01 nm, Epot= -1.48685e+04 Fmax= 1.22382e+04, atom= 4\n", + "Step= 16, Dmax= 1.5e-01 nm, Epot= -2.01120e+04 Fmax= 3.01354e+04, atom= 4\n", + "Step= 17, Dmax= 1.8e-01 nm, Epot= -2.17950e+04 Fmax= 4.10907e+04, atom= 2520\n", + "Step= 18, Dmax= 2.2e-01 nm, Epot= -2.41451e+04 Fmax= 2.58663e+04, atom= 4\n", + "Step= 19, Dmax= 2.7e-01 nm, Epot= -2.66228e+04 Fmax= 2.69286e+04, atom= 835\n", + "Step= 23, Dmax= 4.0e-02 nm, Epot= -2.72892e+04 Fmax= 1.12464e+04, atom= 5360\n", + "Step= 24, Dmax= 4.8e-02 nm, Epot= -2.82606e+04 Fmax= 8.89099e+03, atom= 3110\n", + "Step= 25, Dmax= 5.8e-02 nm, Epot= -2.94476e+04 Fmax= 7.02441e+03, atom= 835\n", + "Step= 26, Dmax= 6.9e-02 nm, Epot= -3.10712e+04 Fmax= 4.20767e+03, atom= 835\n", + "Step= 27, Dmax= 8.3e-02 nm, Epot= -3.33635e+04 Fmax= 1.18104e+04, atom= 835\n", + "Step= 28, Dmax= 9.9e-02 nm, Epot= -3.46017e+04 Fmax= 2.13437e+03, atom= 3110\n", + "Step= 29, Dmax= 1.2e-01 nm, Epot= -3.82056e+04 Fmax= 4.27338e+04, atom= 3110\n", + "Step= 30, Dmax= 1.4e-01 nm, Epot= -3.94374e+04 Fmax= 2.83113e+03, atom= 536\n", + "Step= 31, Dmax= 1.7e-01 nm, Epot= -3.95423e+04 Fmax= 1.29043e+05, atom= 413\n", + "Step= 33, Dmax= 1.0e-01 nm, Epot= -4.13777e+04 Fmax= 3.66374e+04, atom= 413\n", + "Step= 34, Dmax= 1.2e-01 nm, Epot= -4.20921e+04 Fmax= 3.45667e+03, atom= 5051\n", + "Step= 35, Dmax= 1.5e-01 nm, Epot= -4.35935e+04 Fmax= 9.64975e+03, atom= 5051\n", + "Step= 36, Dmax= 1.8e-01 nm, Epot= -4.38149e+04 Fmax= 8.18688e+03, atom= 413\n", + "Step= 38, Dmax= 1.1e-01 nm, Epot= -4.40733e+04 Fmax= 1.07000e+04, atom= 5050\n", + "Step= 39, Dmax= 1.3e-01 nm, Epot= -4.43300e+04 Fmax= 2.05335e+04, atom= 5113\n", + "Step= 40, Dmax= 1.5e-01 nm, Epot= -4.47992e+04 Fmax= 6.05413e+03, atom= 1883\n", + "Step= 41, Dmax= 1.8e-01 nm, Epot= -4.49074e+04 Fmax= 3.01743e+04, atom= 1883\n", + "Step= 43, Dmax= 1.1e-01 nm, Epot= -4.56484e+04 Fmax= 1.52506e+03, atom= 4743\n", + "Step= 44, Dmax= 1.3e-01 nm, Epot= -4.68200e+04 Fmax= 1.07854e+04, atom= 5051\n", + "Step= 46, Dmax= 8.0e-02 nm, Epot= -4.73751e+04 Fmax= 2.52220e+03, atom= 5051\n", + "Step= 47, Dmax= 9.6e-02 nm, Epot= -4.79770e+04 Fmax= 4.87343e+03, atom= 5051\n", + "Step= 48, Dmax= 1.1e-01 nm, Epot= -4.82572e+04 Fmax= 1.91275e+03, atom= 413\n", + "Step= 49, Dmax= 1.4e-01 nm, Epot= -4.89999e+04 Fmax= 8.15021e+03, atom= 413\n", + "Step= 50, Dmax= 1.7e-01 nm, Epot= -4.90237e+04 Fmax= 7.20306e+03, atom= 5050\n", + "Step= 52, Dmax= 9.9e-02 nm, Epot= -4.94243e+04 Fmax= 1.62333e+03, atom= 5113\n", + "Step= 53, Dmax= 1.2e-01 nm, Epot= -5.00761e+04 Fmax= 1.83149e+03, atom= 1883\n", + "Step= 54, Dmax= 1.4e-01 nm, Epot= -5.05800e+04 Fmax= 3.35992e+03, atom= 1883\n", + "Step= 55, Dmax= 1.7e-01 nm, Epot= -5.07979e+04 Fmax= 6.36579e+03, atom= 4743\n", + "Step= 56, Dmax= 2.1e-01 nm, Epot= -5.10603e+04 Fmax= 3.91558e+03, atom= 4743\n", + "Step= 58, Dmax= 1.2e-01 nm, Epot= -5.12744e+04 Fmax= 4.35122e+03, atom= 1361\n", + "Step= 59, Dmax= 1.5e-01 nm, Epot= -5.12777e+04 Fmax= 1.09249e+04, atom= 644\n", + "Step= 60, Dmax= 1.8e-01 nm, Epot= -5.13083e+04 Fmax= 1.53387e+04, atom= 4715\n", + "Step= 62, Dmax= 1.1e-01 nm, Epot= -5.16633e+04 Fmax= 9.15874e+02, atom= 4715\n", + "Step= 63, Dmax= 1.3e-01 nm, Epot= -5.22662e+04 Fmax= 2.03880e+03, atom= 1684\n", + "Step= 65, Dmax= 7.7e-02 nm, Epot= -5.24549e+04 Fmax= 2.91928e+03, atom= 1684\n", + "Step= 66, Dmax= 9.2e-02 nm, Epot= -5.26368e+04 Fmax= 1.72494e+03, atom= 5089\n", + "Step= 67, Dmax= 1.1e-01 nm, Epot= -5.27366e+04 Fmax= 5.74404e+03, atom= 1684\n", + "Step= 68, Dmax= 1.3e-01 nm, Epot= -5.28955e+04 Fmax= 4.63541e+03, atom= 1684\n", + "Step= 70, Dmax= 8.0e-02 nm, Epot= -5.29997e+04 Fmax= 1.91787e+03, atom= 5063\n", + "Step= 71, Dmax= 9.6e-02 nm, Epot= -5.32217e+04 Fmax= 6.49572e+02, atom= 431\n", + "Step= 72, Dmax= 1.1e-01 nm, Epot= -5.34501e+04 Fmax= 9.63944e+03, atom= 5063\n", + "Step= 73, Dmax= 1.4e-01 nm, Epot= -5.37606e+04 Fmax= 8.94016e+02, atom= 431\n", + "Step= 74, Dmax= 1.7e-01 nm, Epot= -5.39605e+04 Fmax= 2.52140e+03, atom= 1684\n", + "Step= 76, Dmax= 9.9e-02 nm, Epot= -5.42504e+04 Fmax= 6.83333e+02, atom= 1684\n", + "Step= 77, Dmax= 1.2e-01 nm, Epot= -5.42770e+04 Fmax= 8.26019e+03, atom= 1684\n", + "Step= 78, Dmax= 1.4e-01 nm, Epot= -5.45678e+04 Fmax= 2.83134e+03, atom= 5062\n", + "Step= 80, Dmax= 8.6e-02 nm, Epot= -5.46790e+04 Fmax= 2.38991e+03, atom= 5101\n", + "Step= 81, Dmax= 1.0e-01 nm, Epot= -5.47846e+04 Fmax= 7.86056e+02, atom= 413\n", + "Step= 82, Dmax= 1.2e-01 nm, Epot= -5.49908e+04 Fmax= 1.47592e+03, atom= 413\n", + "Step= 83, Dmax= 1.5e-01 nm, Epot= -5.50680e+04 Fmax= 1.37360e+03, atom= 5101\n", + "Step= 85, Dmax= 8.9e-02 nm, Epot= -5.52757e+04 Fmax= 8.87388e+02, atom= 5062\n", + "Step= 86, Dmax= 1.1e-01 nm, Epot= -5.53671e+04 Fmax= 3.01079e+03, atom= 1684\n", + "Step= 87, Dmax= 1.3e-01 nm, Epot= -5.53722e+04 Fmax= 4.76861e+03, atom= 14\n", + "Step= 89, Dmax= 7.7e-02 nm, Epot= -5.54904e+04 Fmax= 1.28290e+03, atom= 2172\n", + "Step= 90, Dmax= 9.2e-02 nm, Epot= -5.55903e+04 Fmax= 5.29342e+02, atom= 1967\n", + "Step= 91, Dmax= 1.1e-01 nm, Epot= -5.56311e+04 Fmax= 3.79409e+03, atom= 2172\n", + "Step= 92, Dmax= 1.3e-01 nm, Epot= -5.58242e+04 Fmax= 8.02267e+02, atom= 2172\n", + "Step= 93, Dmax= 1.6e-01 nm, Epot= -5.58868e+04 Fmax= 2.26917e+03, atom= 5084\n", + "Step= 95, Dmax= 9.5e-02 nm, Epot= -5.59963e+04 Fmax= 2.49396e+03, atom= 14\n", + "Step= 96, Dmax= 1.1e-01 nm, Epot= -5.60698e+04 Fmax= 1.52605e+03, atom= 2171\n", + "Step= 97, Dmax= 1.4e-01 nm, Epot= -5.61231e+04 Fmax= 1.90551e+03, atom= 1966\n", + "Step= 98, Dmax= 1.6e-01 nm, Epot= -5.61786e+04 Fmax= 1.84995e+03, atom= 661\n", + "Step= 100, Dmax= 9.9e-02 nm, Epot= -5.62628e+04 Fmax= 6.51040e+02, atom= 1622\n", + "Step= 101, Dmax= 1.2e-01 nm, Epot= -5.63016e+04 Fmax= 1.70613e+03, atom= 667\n", + "Step= 102, Dmax= 1.4e-01 nm, Epot= -5.64090e+04 Fmax= 1.54019e+03, atom= 881\n", + "Step= 103, Dmax= 1.7e-01 nm, Epot= -5.64727e+04 Fmax= 8.08136e+02, atom= 968\n", + "Step= 105, Dmax= 1.0e-01 nm, Epot= -5.65925e+04 Fmax= 8.57638e+02, atom= 968\n", + "Step= 106, Dmax= 1.2e-01 nm, Epot= -5.66342e+04 Fmax= 9.91126e+02, atom= 968\n", + "Step= 108, Dmax= 7.4e-02 nm, Epot= -5.67794e+04 Fmax= 2.13723e+02, atom= 968\n", + "Step= 109, Dmax= 8.9e-02 nm, Epot= -5.67891e+04 Fmax= 1.98010e+03, atom= 969\n", + "Step= 110, Dmax= 1.1e-01 nm, Epot= -5.70265e+04 Fmax= 3.42698e+02, atom= 589\n", + "Step= 112, Dmax= 6.4e-02 nm, Epot= -5.71025e+04 Fmax= 5.63475e+02, atom= 590\n", + "Step= 113, Dmax= 7.7e-02 nm, Epot= -5.71615e+04 Fmax= 5.79251e+02, atom= 590\n", + "Step= 114, Dmax= 9.2e-02 nm, Epot= -5.71927e+04 Fmax= 8.66274e+02, atom= 590\n", + "Step= 115, Dmax= 1.1e-01 nm, Epot= -5.72416e+04 Fmax= 8.34020e+02, atom= 590\n", + "Step= 117, Dmax= 6.6e-02 nm, Epot= -5.73480e+04 Fmax= 1.76306e+02, atom= 590\n", + "Step= 119, Dmax= 4.0e-02 nm, Epot= -5.74114e+04 Fmax= 3.97555e+02, atom= 590\n", + "Step= 120, Dmax= 4.8e-02 nm, Epot= -5.74583e+04 Fmax= 3.61480e+02, atom= 590\n", + "Step= 121, Dmax= 5.7e-02 nm, Epot= -5.74646e+04 Fmax= 5.43998e+02, atom= 1268\n", + "Step= 122, Dmax= 6.9e-02 nm, Epot= -5.74734e+04 Fmax= 6.51600e+02, atom= 2750\n", + "Step= 124, Dmax= 4.1e-02 nm, Epot= -5.76075e+04 Fmax= 1.62744e+02, atom= 3420\n", + "Step= 125, Dmax= 4.9e-02 nm, Epot= -5.76634e+04 Fmax= 9.86603e+02, atom= 1037\n", + "Step= 126, Dmax= 5.9e-02 nm, Epot= -5.77230e+04 Fmax= 2.50357e+02, atom= 1037\n", + "Step= 127, Dmax= 7.1e-02 nm, Epot= -5.77331e+04 Fmax= 2.54090e+03, atom= 1037\n", + "Step= 128, Dmax= 8.5e-02 nm, Epot= -5.78134e+04 Fmax= 3.28038e+02, atom= 342\n", + "Step= 130, Dmax= 5.1e-02 nm, Epot= -5.78580e+04 Fmax= 3.56783e+02, atom= 1037\n", + "Step= 131, Dmax= 6.1e-02 nm, Epot= -5.78686e+04 Fmax= 6.76955e+02, atom= 1037\n", + "Step= 132, Dmax= 7.4e-02 nm, Epot= -5.79020e+04 Fmax= 5.59506e+02, atom= 1037\n", + "Step= 134, Dmax= 4.4e-02 nm, Epot= -5.79598e+04 Fmax= 2.36282e+02, atom= 1037\n", + "Step= 136, Dmax= 2.7e-02 nm, Epot= -5.79889e+04 Fmax= 2.18827e+02, atom= 4446\n", + "Step= 137, Dmax= 3.2e-02 nm, Epot= -5.80023e+04 Fmax= 5.21913e+02, atom= 444\n", + "Step= 138, Dmax= 3.8e-02 nm, Epot= -5.80462e+04 Fmax= 2.84451e+02, atom= 2366\n", + "Step= 139, Dmax= 4.6e-02 nm, Epot= -5.80608e+04 Fmax= 8.97149e+02, atom= 2366\n", + "Step= 140, Dmax= 5.5e-02 nm, Epot= -5.80975e+04 Fmax= 3.42887e+02, atom= 2366\n", + "Step= 142, Dmax= 3.3e-02 nm, Epot= -5.81282e+04 Fmax= 1.36145e+02, atom= 3046\n", + "Step= 143, Dmax= 4.0e-02 nm, Epot= -5.81573e+04 Fmax= 6.49999e+02, atom= 444\n", + "Step= 144, Dmax= 4.8e-02 nm, Epot= -5.81985e+04 Fmax= 5.85509e+02, atom= 444\n", + "Step= 145, Dmax= 5.7e-02 nm, Epot= -5.82168e+04 Fmax= 5.20569e+02, atom= 2366\n", + "Step= 146, Dmax= 6.8e-02 nm, Epot= -5.82348e+04 Fmax= 7.49805e+02, atom= 2366\n", + "Step= 147, Dmax= 8.2e-02 nm, Epot= -5.82399e+04 Fmax= 8.13908e+02, atom= 444\n", + "Step= 149, Dmax= 4.9e-02 nm, Epot= -5.82909e+04 Fmax= 1.92976e+02, atom= 3046\n", + "Step= 150, Dmax= 5.9e-02 nm, Epot= -5.83183e+04 Fmax= 7.54840e+02, atom= 3046\n", + "Step= 151, Dmax= 7.1e-02 nm, Epot= -5.83438e+04 Fmax= 7.57133e+02, atom= 444\n", + "Step= 152, Dmax= 8.5e-02 nm, Epot= -5.83492e+04 Fmax= 1.18558e+03, atom= 2366\n", + "Step= 153, Dmax= 1.0e-01 nm, Epot= -5.83833e+04 Fmax= 6.94247e+02, atom= 1079\n", + "Step= 155, Dmax= 6.1e-02 nm, Epot= -5.84236e+04 Fmax= 2.60608e+02, atom= 2759\n", + "Step= 156, Dmax= 7.4e-02 nm, Epot= -5.84247e+04 Fmax= 1.01250e+03, atom= 1079\n", + "Step= 157, Dmax= 8.8e-02 nm, Epot= -5.84664e+04 Fmax= 7.38344e+02, atom= 1079\n", + "Step= 159, Dmax= 5.3e-02 nm, Epot= -5.85081e+04 Fmax= 3.14148e+02, atom= 2366\n", + "Step= 160, Dmax= 6.4e-02 nm, Epot= -5.85283e+04 Fmax= 4.62261e+02, atom= 2366\n", + "Step= 162, Dmax= 3.8e-02 nm, Epot= -5.85613e+04 Fmax= 1.20716e+02, atom= 2056\n", + "Step= 163, Dmax= 4.6e-02 nm, Epot= -5.85799e+04 Fmax= 5.28588e+02, atom= 2056\n", + "Step= 164, Dmax= 5.5e-02 nm, Epot= -5.86070e+04 Fmax= 6.41145e+02, atom= 444\n", + "Step= 165, Dmax= 6.6e-02 nm, Epot= -5.86313e+04 Fmax= 6.33683e+02, atom= 2366\n", + "Step= 166, Dmax= 7.9e-02 nm, Epot= -5.86481e+04 Fmax= 4.59080e+02, atom= 2366\n", + "Step= 168, Dmax= 4.7e-02 nm, Epot= -5.86816e+04 Fmax= 2.75045e+02, atom= 4446\n", + "Step= 170, Dmax= 2.8e-02 nm, Epot= -5.87073e+04 Fmax= 1.67651e+02, atom= 2567\n", + "Step= 172, Dmax= 1.7e-02 nm, Epot= -5.87271e+04 Fmax= 1.31748e+02, atom= 1088\n", + "Step= 173, Dmax= 2.1e-02 nm, Epot= -5.87449e+04 Fmax= 2.22822e+02, atom= 1088\n", + "Step= 174, Dmax= 2.5e-02 nm, Epot= -5.87632e+04 Fmax= 2.10901e+02, atom= 2558\n", + "Step= 175, Dmax= 3.0e-02 nm, Epot= -5.87758e+04 Fmax= 3.27185e+02, atom= 2558\n", + "Step= 176, Dmax= 3.5e-02 nm, Epot= -5.87944e+04 Fmax= 3.08317e+02, atom= 2558\n", + "Step= 177, Dmax= 4.3e-02 nm, Epot= -5.88020e+04 Fmax= 4.61500e+02, atom= 2558\n", + "Step= 178, Dmax= 5.1e-02 nm, Epot= -5.88195e+04 Fmax= 4.45693e+02, atom= 2558\n", + "Step= 180, Dmax= 3.1e-02 nm, Epot= -5.88535e+04 Fmax= 8.54541e+01, atom= 2558\n", + "Step= 181, Dmax= 3.7e-02 nm, Epot= -5.88827e+04 Fmax= 5.40215e+02, atom= 2558\n", + "Step= 182, Dmax= 4.4e-02 nm, Epot= -5.89190e+04 Fmax= 2.35271e+02, atom= 2558\n", + "Step= 184, Dmax= 2.6e-02 nm, Epot= -5.89342e+04 Fmax= 2.30083e+02, atom= 2558\n", + "Step= 185, Dmax= 3.2e-02 nm, Epot= -5.89464e+04 Fmax= 3.31008e+02, atom= 2558\n", + "Step= 186, Dmax= 3.8e-02 nm, Epot= -5.89608e+04 Fmax= 3.34787e+02, atom= 2558\n", + "Step= 187, Dmax= 4.6e-02 nm, Epot= -5.89667e+04 Fmax= 4.70588e+02, atom= 2558\n", + "Step= 188, Dmax= 5.5e-02 nm, Epot= -5.89793e+04 Fmax= 4.82120e+02, atom= 2558\n", + "Step= 190, Dmax= 3.3e-02 nm, Epot= -5.90132e+04 Fmax= 7.92084e+01, atom= 2750\n", + "Step= 192, Dmax= 2.0e-02 nm, Epot= -5.90341e+04 Fmax= 3.02839e+02, atom= 2750\n", + "Step= 193, Dmax= 2.4e-02 nm, Epot= -5.90526e+04 Fmax= 1.38626e+02, atom= 2750\n", + "Step= 194, Dmax= 2.8e-02 nm, Epot= -5.90647e+04 Fmax= 4.28440e+02, atom= 2750\n", + "Step= 195, Dmax= 3.4e-02 nm, Epot= -5.90850e+04 Fmax= 2.04448e+02, atom= 2750\n", + "Step= 196, Dmax= 4.1e-02 nm, Epot= -5.90885e+04 Fmax= 6.34782e+02, atom= 2750\n", + "Step= 197, Dmax= 4.9e-02 nm, Epot= -5.91141e+04 Fmax= 2.81753e+02, atom= 2750\n", + "Step= 199, Dmax= 2.9e-02 nm, Epot= -5.91302e+04 Fmax= 1.71736e+02, atom= 2750\n", + "Step= 200, Dmax= 3.5e-02 nm, Epot= -5.91366e+04 Fmax= 4.23679e+02, atom= 1037\n", + "Step= 201, Dmax= 4.2e-02 nm, Epot= -5.91595e+04 Fmax= 3.24522e+02, atom= 1037\n", + "Step= 203, Dmax= 2.5e-02 nm, Epot= -5.91755e+04 Fmax= 1.34946e+02, atom= 2750\n", + "Step= 204, Dmax= 3.1e-02 nm, Epot= -5.91877e+04 Fmax= 4.69017e+02, atom= 2750\n", + "Step= 205, Dmax= 3.7e-02 nm, Epot= -5.92069e+04 Fmax= 2.09146e+02, atom= 2750\n", + "Step= 206, Dmax= 4.4e-02 nm, Epot= -5.92081e+04 Fmax= 6.84871e+02, atom= 2750\n", + "Step= 207, Dmax= 5.3e-02 nm, Epot= -5.92339e+04 Fmax= 2.91752e+02, atom= 2750\n", + "Step= 209, Dmax= 3.2e-02 nm, Epot= -5.92494e+04 Fmax= 1.91073e+02, atom= 1037\n", + "Step= 210, Dmax= 3.8e-02 nm, Epot= -5.92536e+04 Fmax= 4.45564e+02, atom= 1037\n", + "Step= 211, Dmax= 4.6e-02 nm, Epot= -5.92755e+04 Fmax= 3.48115e+02, atom= 1037\n", + "Step= 213, Dmax= 2.7e-02 nm, Epot= -5.92914e+04 Fmax= 1.36146e+02, atom= 2750\n", + "Step= 214, Dmax= 3.3e-02 nm, Epot= -5.93009e+04 Fmax= 5.12191e+02, atom= 2750\n", + "Step= 215, Dmax= 3.9e-02 nm, Epot= -5.93214e+04 Fmax= 2.14140e+02, atom= 2750\n", + "Step= 217, Dmax= 2.4e-02 nm, Epot= -5.93342e+04 Fmax= 1.60744e+02, atom= 1037\n", + "Step= 218, Dmax= 2.8e-02 nm, Epot= -5.93443e+04 Fmax= 3.17338e+02, atom= 1037\n", + "Step= 219, Dmax= 3.4e-02 nm, Epot= -5.93589e+04 Fmax= 2.73929e+02, atom= 1037\n", + "Step= 220, Dmax= 4.1e-02 nm, Epot= -5.93638e+04 Fmax= 4.06981e+02, atom= 1037\n", + "Step= 221, Dmax= 4.9e-02 nm, Epot= -5.93762e+04 Fmax= 4.42758e+02, atom= 1037\n", + "Step= 222, Dmax= 5.9e-02 nm, Epot= -5.93764e+04 Fmax= 5.38567e+02, atom= 1037\n", + "Step= 223, Dmax= 7.1e-02 nm, Epot= -5.93817e+04 Fmax= 6.85024e+02, atom= 1037\n", + "Step= 225, Dmax= 4.2e-02 nm, Epot= -5.94210e+04 Fmax= 1.13595e+02, atom= 2750\n", + "Step= 226, Dmax= 5.1e-02 nm, Epot= -5.94264e+04 Fmax= 1.12021e+03, atom= 2750\n", + "Step= 227, Dmax= 6.1e-02 nm, Epot= -5.94648e+04 Fmax= 2.13155e+02, atom= 2750\n", + "Step= 229, Dmax= 3.7e-02 nm, Epot= -5.94763e+04 Fmax= 3.40382e+02, atom= 2750\n", + "Step= 230, Dmax= 4.4e-02 nm, Epot= -5.94846e+04 Fmax= 3.72517e+02, atom= 2750\n", + "Step= 231, Dmax= 5.3e-02 nm, Epot= -5.94899e+04 Fmax= 5.17229e+02, atom= 2750\n", + "Step= 232, Dmax= 6.3e-02 nm, Epot= -5.94943e+04 Fmax= 5.04661e+02, atom= 2750\n", + "Step= 234, Dmax= 3.8e-02 nm, Epot= -5.95260e+04 Fmax= 1.10726e+02, atom= 1037\n", + "Step= 235, Dmax= 4.6e-02 nm, Epot= -5.95365e+04 Fmax= 5.90053e+02, atom= 1037\n", + "Step= 236, Dmax= 5.5e-02 nm, Epot= -5.95637e+04 Fmax= 3.74966e+02, atom= 1037\n", + "Step= 238, Dmax= 3.3e-02 nm, Epot= -5.95763e+04 Fmax= 1.82726e+02, atom= 1037\n", + "Step= 239, Dmax= 3.9e-02 nm, Epot= -5.95772e+04 Fmax= 5.49092e+02, atom= 1037\n", + "Step= 240, Dmax= 4.7e-02 nm, Epot= -5.95973e+04 Fmax= 2.75807e+02, atom= 2750\n", + "Step= 242, Dmax= 2.8e-02 nm, Epot= -5.96106e+04 Fmax= 1.84392e+02, atom= 1037\n", + "Step= 243, Dmax= 3.4e-02 nm, Epot= -5.96163e+04 Fmax= 3.79298e+02, atom= 1037\n", + "Step= 244, Dmax= 4.1e-02 nm, Epot= -5.96307e+04 Fmax= 3.13443e+02, atom= 1037\n", + "Step= 246, Dmax= 2.4e-02 nm, Epot= -5.96435e+04 Fmax= 1.07066e+02, atom= 1037\n", + "Step= 247, Dmax= 2.9e-02 nm, Epot= -5.96536e+04 Fmax= 4.31069e+02, atom= 1037\n", + "Step= 248, Dmax= 3.5e-02 nm, Epot= -5.96701e+04 Fmax= 1.86394e+02, atom= 2750\n", + "Step= 250, Dmax= 2.1e-02 nm, Epot= -5.96802e+04 Fmax= 1.64083e+02, atom= 1037\n", + "Step= 251, Dmax= 2.5e-02 nm, Epot= -5.96885e+04 Fmax= 2.59689e+02, atom= 1037\n", + "Step= 252, Dmax= 3.0e-02 nm, Epot= -5.96985e+04 Fmax= 2.61649e+02, atom= 1037\n", + "Step= 253, Dmax= 3.7e-02 nm, Epot= -5.97040e+04 Fmax= 3.45406e+02, atom= 1037\n", + "Step= 254, Dmax= 4.4e-02 nm, Epot= -5.97120e+04 Fmax= 4.06156e+02, atom= 1037\n", + "Step= 255, Dmax= 5.3e-02 nm, Epot= -5.97147e+04 Fmax= 4.66646e+02, atom= 1037\n", + "Step= 256, Dmax= 6.3e-02 nm, Epot= -5.97166e+04 Fmax= 6.15389e+02, atom= 1037\n", + "Step= 258, Dmax= 3.8e-02 nm, Epot= -5.97483e+04 Fmax= 8.18105e+01, atom= 2750\n", + "Step= 259, Dmax= 4.5e-02 nm, Epot= -5.97598e+04 Fmax= 9.54914e+02, atom= 2750\n", + "Step= 260, Dmax= 5.5e-02 nm, Epot= -5.97904e+04 Fmax= 1.91853e+02, atom= 2750\n", + "Step= 262, Dmax= 3.3e-02 nm, Epot= -5.97985e+04 Fmax= 3.15322e+02, atom= 2750\n", + "Step= 263, Dmax= 3.9e-02 nm, Epot= -5.98056e+04 Fmax= 3.21297e+02, atom= 2750\n", + "Step= 264, Dmax= 4.7e-02 nm, Epot= -5.98084e+04 Fmax= 4.68174e+02, atom= 2750\n", + "Step= 265, Dmax= 5.7e-02 nm, Epot= -5.98132e+04 Fmax= 4.44374e+02, atom= 2750\n", + "Step= 267, Dmax= 3.4e-02 nm, Epot= -5.98370e+04 Fmax= 1.04068e+02, atom= 1037\n", + "Step= 268, Dmax= 4.1e-02 nm, Epot= -5.98418e+04 Fmax= 5.35238e+02, atom= 1037\n", + "Step= 269, Dmax= 4.9e-02 nm, Epot= -5.98648e+04 Fmax= 2.99566e+02, atom= 1037\n", + "Step= 271, Dmax= 2.9e-02 nm, Epot= -5.98739e+04 Fmax= 1.89412e+02, atom= 1037\n", + "Step= 272, Dmax= 3.5e-02 nm, Epot= -5.98761e+04 Fmax= 4.27339e+02, atom= 1037\n", + "Step= 273, Dmax= 4.2e-02 nm, Epot= -5.98881e+04 Fmax= 2.85161e+02, atom= 1037\n", + "Step= 275, Dmax= 2.5e-02 nm, Epot= -5.98998e+04 Fmax= 1.31589e+02, atom= 1037\n", + "Step= 276, Dmax= 3.0e-02 nm, Epot= -5.99052e+04 Fmax= 3.66594e+02, atom= 1037\n", + "Step= 277, Dmax= 3.6e-02 nm, Epot= -5.99179e+04 Fmax= 2.45938e+02, atom= 1037\n", + "Step= 279, Dmax= 2.2e-02 nm, Epot= -5.99266e+04 Fmax= 1.22527e+02, atom= 1037\n", + "Step= 280, Dmax= 2.6e-02 nm, Epot= -5.99331e+04 Fmax= 3.36093e+02, atom= 1037\n", + "Step= 281, Dmax= 3.2e-02 nm, Epot= -5.99436e+04 Fmax= 1.97719e+02, atom= 1037\n", + "Step= 283, Dmax= 1.9e-02 nm, Epot= -5.99518e+04 Fmax= 1.17503e+02, atom= 1037\n", + "Step= 284, Dmax= 2.3e-02 nm, Epot= -5.99593e+04 Fmax= 2.56680e+02, atom= 1037\n", + "Step= 285, Dmax= 2.7e-02 nm, Epot= -5.99681e+04 Fmax= 2.03015e+02, atom= 1037\n", + "Step= 286, Dmax= 3.3e-02 nm, Epot= -5.99718e+04 Fmax= 3.34761e+02, atom= 1037\n", + "Step= 287, Dmax= 3.9e-02 nm, Epot= -5.99802e+04 Fmax= 3.27429e+02, atom= 1037\n", + "Step= 289, Dmax= 2.4e-02 nm, Epot= -5.99916e+04 Fmax= 7.51183e+01, atom= 1037\n", + "Step= 290, Dmax= 2.8e-02 nm, Epot= -6.00004e+04 Fmax= 4.44159e+02, atom= 1037\n", + "Step= 291, Dmax= 3.4e-02 nm, Epot= -6.00164e+04 Fmax= 1.52832e+02, atom= 2750\n", + "Step= 293, Dmax= 2.0e-02 nm, Epot= -6.00233e+04 Fmax= 1.84184e+02, atom= 1037\n", + "Step= 294, Dmax= 2.4e-02 nm, Epot= -6.00292e+04 Fmax= 2.23600e+02, atom= 1037\n", + "Step= 295, Dmax= 2.9e-02 nm, Epot= -6.00352e+04 Fmax= 2.76996e+02, atom= 1037\n", + "Step= 296, Dmax= 3.5e-02 nm, Epot= -6.00399e+04 Fmax= 3.08297e+02, atom= 1037\n", + "Step= 297, Dmax= 4.2e-02 nm, Epot= -6.00432e+04 Fmax= 4.13042e+02, atom= 1037\n", + "Step= 298, Dmax= 5.1e-02 nm, Epot= -6.00467e+04 Fmax= 4.27370e+02, atom= 1037\n", + "Step= 300, Dmax= 3.0e-02 nm, Epot= -6.00665e+04 Fmax= 6.86301e+01, atom= 1037\n", + "Step= 301, Dmax= 3.6e-02 nm, Epot= -6.00790e+04 Fmax= 4.94901e+02, atom= 1037\n", + "Step= 302, Dmax= 4.4e-02 nm, Epot= -6.00971e+04 Fmax= 2.47767e+02, atom= 1037\n", + "Step= 304, Dmax= 2.6e-02 nm, Epot= -6.01039e+04 Fmax= 1.85350e+02, atom= 1037\n", + "Step= 305, Dmax= 3.1e-02 nm, Epot= -6.01068e+04 Fmax= 3.56989e+02, atom= 1037\n", + "Step= 306, Dmax= 3.8e-02 nm, Epot= -6.01148e+04 Fmax= 2.75919e+02, atom= 1037\n", + "Step= 308, Dmax= 2.3e-02 nm, Epot= -6.01246e+04 Fmax= 9.78715e+01, atom= 1037\n", + "Step= 309, Dmax= 2.7e-02 nm, Epot= -6.01309e+04 Fmax= 3.46739e+02, atom= 1037\n", + "Step= 310, Dmax= 3.3e-02 nm, Epot= -6.01421e+04 Fmax= 1.98503e+02, atom= 1037\n", + "Step= 312, Dmax= 2.0e-02 nm, Epot= -6.01487e+04 Fmax= 1.28477e+02, atom= 1037\n", + "Step= 313, Dmax= 2.3e-02 nm, Epot= -6.01540e+04 Fmax= 2.75405e+02, atom= 1037\n", + "Step= 314, Dmax= 2.8e-02 nm, Epot= -6.01613e+04 Fmax= 1.98013e+02, atom= 1037\n", + "Step= 315, Dmax= 3.4e-02 nm, Epot= -6.01626e+04 Fmax= 3.86317e+02, atom= 1037\n", + "Step= 316, Dmax= 4.1e-02 nm, Epot= -6.01711e+04 Fmax= 2.95692e+02, atom= 1037\n", + "Step= 318, Dmax= 2.4e-02 nm, Epot= -6.01816e+04 Fmax= 1.05991e+02, atom= 1037\n", + "Step= 319, Dmax= 2.9e-02 nm, Epot= -6.01859e+04 Fmax= 3.70320e+02, atom= 1037\n", + "Step= 320, Dmax= 3.5e-02 nm, Epot= -6.01977e+04 Fmax= 2.15025e+02, atom= 1037\n", + "Step= 322, Dmax= 2.1e-02 nm, Epot= -6.02042e+04 Fmax= 1.36626e+02, atom= 1037\n", + "Step= 323, Dmax= 2.5e-02 nm, Epot= -6.02085e+04 Fmax= 2.97344e+02, atom= 1037\n", + "Step= 324, Dmax= 3.0e-02 nm, Epot= -6.02160e+04 Fmax= 2.11920e+02, atom= 1037\n", + "Step= 326, Dmax= 1.8e-02 nm, Epot= -6.02232e+04 Fmax= 9.05070e+01, atom= 1037\n", + "Step= 327, Dmax= 2.2e-02 nm, Epot= -6.02299e+04 Fmax= 2.67235e+02, atom= 1037\n", + "Step= 328, Dmax= 2.6e-02 nm, Epot= -6.02379e+04 Fmax= 1.71430e+02, atom= 1037\n", + "Step= 329, Dmax= 3.1e-02 nm, Epot= -6.02398e+04 Fmax= 3.43862e+02, atom= 1037\n", + "Step= 330, Dmax= 3.8e-02 nm, Epot= -6.02481e+04 Fmax= 2.87984e+02, atom= 1037\n", + "Step= 332, Dmax= 2.3e-02 nm, Epot= -6.02567e+04 Fmax= 9.48735e+01, atom= 1037\n", + "Step= 333, Dmax= 2.7e-02 nm, Epot= -6.02606e+04 Fmax= 3.83167e+02, atom= 1037\n", + "Step= 334, Dmax= 3.3e-02 nm, Epot= -6.02722e+04 Fmax= 1.74631e+02, atom= 1037\n", + "Step= 336, Dmax= 2.0e-02 nm, Epot= -6.02781e+04 Fmax= 1.53774e+02, atom= 1037\n", + "Step= 337, Dmax= 2.3e-02 nm, Epot= -6.02825e+04 Fmax= 2.35394e+02, atom= 1037\n", + "Step= 338, Dmax= 2.8e-02 nm, Epot= -6.02882e+04 Fmax= 2.40650e+02, atom= 1037\n", + "Step= 339, Dmax= 3.4e-02 nm, Epot= -6.02907e+04 Fmax= 3.19053e+02, atom= 1037\n", + "Step= 340, Dmax= 4.1e-02 nm, Epot= -6.02951e+04 Fmax= 3.67076e+02, atom= 1037\n", + "Step= 341, Dmax= 4.9e-02 nm, Epot= -6.02952e+04 Fmax= 4.37482e+02, atom= 1037\n", + "Step= 342, Dmax= 5.8e-02 nm, Epot= -6.02956e+04 Fmax= 5.51808e+02, atom= 1037\n", + "Step= 344, Dmax= 3.5e-02 nm, Epot= -6.03189e+04 Fmax= 6.47657e+01, atom= 2750\n", + "Step= 346, Dmax= 2.1e-02 nm, Epot= -6.03278e+04 Fmax= 2.65796e+02, atom= 1037\n", + "Step= 347, Dmax= 2.5e-02 nm, Epot= -6.03354e+04 Fmax= 1.68249e+02, atom= 1037\n", + "Step= 348, Dmax= 3.0e-02 nm, Epot= -6.03359e+04 Fmax= 3.57357e+02, atom= 1037\n", + "Step= 349, Dmax= 3.6e-02 nm, Epot= -6.03444e+04 Fmax= 2.56839e+02, atom= 1037\n", + "Step= 351, Dmax= 2.2e-02 nm, Epot= -6.03533e+04 Fmax= 1.03634e+02, atom= 1037\n", + "Step= 352, Dmax= 2.6e-02 nm, Epot= -6.03569e+04 Fmax= 3.24418e+02, atom= 1037\n", + "Step= 353, Dmax= 3.1e-02 nm, Epot= -6.03665e+04 Fmax= 1.99515e+02, atom= 1037\n", + "Step= 355, Dmax= 1.9e-02 nm, Epot= -6.03724e+04 Fmax= 1.16216e+02, atom= 1037\n", + "Step= 356, Dmax= 2.3e-02 nm, Epot= -6.03766e+04 Fmax= 2.72102e+02, atom= 1037\n", + "Step= 357, Dmax= 2.7e-02 nm, Epot= -6.03834e+04 Fmax= 1.84755e+02, atom= 1037\n", + "Step= 358, Dmax= 3.3e-02 nm, Epot= -6.03837e+04 Fmax= 3.76645e+02, atom= 1037\n", + "Step= 359, Dmax= 3.9e-02 nm, Epot= -6.03916e+04 Fmax= 2.81100e+02, atom= 1037\n", + "Step= 361, Dmax= 2.3e-02 nm, Epot= -6.04007e+04 Fmax= 1.05848e+02, atom= 1037\n", + "Step= 362, Dmax= 2.8e-02 nm, Epot= -6.04037e+04 Fmax= 3.52774e+02, atom= 1037\n", + "Step= 363, Dmax= 3.4e-02 nm, Epot= -6.04139e+04 Fmax= 2.08901e+02, atom= 1037\n", + "Step= 365, Dmax= 2.0e-02 nm, Epot= -6.04196e+04 Fmax= 1.29971e+02, atom= 1037\n", + "Step= 366, Dmax= 2.4e-02 nm, Epot= -6.04232e+04 Fmax= 2.86343e+02, atom= 1037\n", + "Step= 367, Dmax= 2.9e-02 nm, Epot= -6.04299e+04 Fmax= 2.03936e+02, atom= 1037\n", + "Step= 369, Dmax= 1.7e-02 nm, Epot= -6.04360e+04 Fmax= 8.72055e+01, atom= 1037\n", + "Step= 370, Dmax= 2.1e-02 nm, Epot= -6.04418e+04 Fmax= 2.56841e+02, atom= 1037\n", + "Step= 371, Dmax= 2.5e-02 nm, Epot= -6.04488e+04 Fmax= 1.64364e+02, atom= 1037\n", + "Step= 372, Dmax= 3.0e-02 nm, Epot= -6.04502e+04 Fmax= 3.31834e+02, atom= 1037\n", + "Step= 373, Dmax= 3.6e-02 nm, Epot= -6.04576e+04 Fmax= 2.75539e+02, atom= 1037\n", + "Step= 375, Dmax= 2.2e-02 nm, Epot= -6.04652e+04 Fmax= 9.25214e+01, atom= 1037\n", + "Step= 376, Dmax= 2.6e-02 nm, Epot= -6.04683e+04 Fmax= 3.64517e+02, atom= 1037\n", + "Step= 377, Dmax= 3.1e-02 nm, Epot= -6.04785e+04 Fmax= 1.71353e+02, atom= 1037\n", + "Step= 379, Dmax= 1.9e-02 nm, Epot= -6.04837e+04 Fmax= 1.44810e+02, atom= 1037\n", + "Step= 380, Dmax= 2.3e-02 nm, Epot= -6.04875e+04 Fmax= 2.28991e+02, atom= 1037\n", + "Step= 381, Dmax= 2.7e-02 nm, Epot= -6.04926e+04 Fmax= 2.27742e+02, atom= 1037\n", + "Step= 382, Dmax= 3.2e-02 nm, Epot= -6.04946e+04 Fmax= 3.10242e+02, atom= 1037\n", + "Step= 383, Dmax= 3.9e-02 nm, Epot= -6.04986e+04 Fmax= 3.48585e+02, atom= 1037\n", + "Step= 385, Dmax= 2.3e-02 nm, Epot= -6.05092e+04 Fmax= 5.26484e+01, atom= 1037\n", + "Step= 386, Dmax= 2.8e-02 nm, Epot= -6.05155e+04 Fmax= 4.62501e+02, atom= 1037\n", + "Step= 387, Dmax= 3.4e-02 nm, Epot= -6.05316e+04 Fmax= 1.34614e+02, atom= 1037\n", + "Step= 389, Dmax= 2.0e-02 nm, Epot= -6.05356e+04 Fmax= 2.10017e+02, atom= 1037\n", + "Step= 390, Dmax= 2.4e-02 nm, Epot= -6.05402e+04 Fmax= 1.97335e+02, atom= 1037\n", + "Step= 391, Dmax= 2.9e-02 nm, Epot= -6.05424e+04 Fmax= 3.00593e+02, atom= 1037\n", + "Step= 392, Dmax= 3.5e-02 nm, Epot= -6.05469e+04 Fmax= 2.84566e+02, atom= 1037\n", + "Step= 394, Dmax= 2.1e-02 nm, Epot= -6.05561e+04 Fmax= 6.08198e+01, atom= 1037\n", + "Step= 395, Dmax= 2.5e-02 nm, Epot= -6.05637e+04 Fmax= 3.46049e+02, atom= 1037\n", + "Step= 396, Dmax= 3.0e-02 nm, Epot= -6.05739e+04 Fmax= 1.55490e+02, atom= 1037\n", + "Step= 398, Dmax= 1.8e-02 nm, Epot= -6.05785e+04 Fmax= 1.45502e+02, atom= 1037\n", + "Step= 399, Dmax= 2.2e-02 nm, Epot= -6.05822e+04 Fmax= 2.23874e+02, atom= 1037\n", + "Step= 400, Dmax= 2.6e-02 nm, Epot= -6.05867e+04 Fmax= 2.11393e+02, atom= 1037\n", + "Step= 401, Dmax= 3.1e-02 nm, Epot= -6.05885e+04 Fmax= 3.21945e+02, atom= 1037\n", + "Step= 402, Dmax= 3.8e-02 nm, Epot= -6.05929e+04 Fmax= 3.04826e+02, atom= 1037\n", + "Step= 404, Dmax= 2.3e-02 nm, Epot= -6.06024e+04 Fmax= 6.54186e+01, atom= 1037\n", + "Step= 405, Dmax= 2.7e-02 nm, Epot= -6.06084e+04 Fmax= 3.72286e+02, atom= 1037\n", + "Step= 406, Dmax= 3.2e-02 nm, Epot= -6.06196e+04 Fmax= 1.65258e+02, atom= 1037\n", + "Step= 408, Dmax= 1.9e-02 nm, Epot= -6.06240e+04 Fmax= 1.58314e+02, atom= 1037\n", + "Step= 409, Dmax= 2.3e-02 nm, Epot= -6.06274e+04 Fmax= 2.38066e+02, atom= 1037\n", + "Step= 410, Dmax= 2.8e-02 nm, Epot= -6.06317e+04 Fmax= 2.29244e+02, atom= 1037\n", + "Step= 411, Dmax= 3.4e-02 nm, Epot= -6.06331e+04 Fmax= 3.43271e+02, atom= 1037\n", + "Step= 412, Dmax= 4.0e-02 nm, Epot= -6.06371e+04 Fmax= 3.29533e+02, atom= 1037\n", + "Step= 414, Dmax= 2.4e-02 nm, Epot= -6.06478e+04 Fmax= 6.72159e+01, atom= 1037\n", + "Step= 415, Dmax= 2.9e-02 nm, Epot= -6.06522e+04 Fmax= 4.02576e+02, atom= 1037\n", + "Step= 416, Dmax= 3.5e-02 nm, Epot= -6.06652e+04 Fmax= 1.74136e+02, atom= 1037\n", + "Step= 418, Dmax= 2.1e-02 nm, Epot= -6.06694e+04 Fmax= 1.73671e+02, atom= 1037\n", + "Step= 419, Dmax= 2.5e-02 nm, Epot= -6.06725e+04 Fmax= 2.51593e+02, atom= 1037\n", + "Step= 420, Dmax= 3.0e-02 nm, Epot= -6.06764e+04 Fmax= 2.50038e+02, atom= 1037\n", + "Step= 421, Dmax= 3.6e-02 nm, Epot= -6.06770e+04 Fmax= 3.64277e+02, atom= 1037\n", + "Step= 422, Dmax= 4.3e-02 nm, Epot= -6.06804e+04 Fmax= 3.57519e+02, atom= 1037\n", + "Step= 424, Dmax= 2.6e-02 nm, Epot= -6.06932e+04 Fmax= 6.74370e+01, atom= 1037\n", + "Step= 425, Dmax= 3.1e-02 nm, Epot= -6.06943e+04 Fmax= 4.36958e+02, atom= 1037\n", + "Step= 426, Dmax= 3.7e-02 nm, Epot= -6.07107e+04 Fmax= 1.81910e+02, atom= 1037\n", + "Step= 428, Dmax= 2.2e-02 nm, Epot= -6.07146e+04 Fmax= 1.91709e+02, atom= 1037\n", + "Step= 429, Dmax= 2.7e-02 nm, Epot= -6.07168e+04 Fmax= 2.64640e+02, atom= 1037\n", + "Step= 430, Dmax= 3.2e-02 nm, Epot= -6.07201e+04 Fmax= 2.73523e+02, atom= 1037\n", + "Step= 432, Dmax= 1.9e-02 nm, Epot= -6.07298e+04 Fmax= 4.56656e+01, atom= 1037\n", + "Step= 433, Dmax= 2.3e-02 nm, Epot= -6.07352e+04 Fmax= 3.31970e+02, atom= 1037\n", + "Step= 434, Dmax= 2.8e-02 nm, Epot= -6.07491e+04 Fmax= 1.31192e+02, atom= 1037\n", + "Step= 436, Dmax= 1.7e-02 nm, Epot= -6.07529e+04 Fmax= 1.47563e+02, atom= 1037\n", + "Step= 437, Dmax= 2.0e-02 nm, Epot= -6.07555e+04 Fmax= 1.93043e+02, atom= 1037\n", + "Step= 438, Dmax= 2.4e-02 nm, Epot= -6.07585e+04 Fmax= 2.08789e+02, atom= 1037\n", + "Step= 440, Dmax= 1.4e-02 nm, Epot= -6.07676e+04 Fmax= 3.43850e+01, atom= 1223\n", + "Step= 441, Dmax= 1.7e-02 nm, Epot= -6.07744e+04 Fmax= 2.64587e+02, atom= 1223\n", + "Step= 442, Dmax= 2.1e-02 nm, Epot= -6.07872e+04 Fmax= 1.03972e+02, atom= 1223\n", + "Step= 444, Dmax= 1.3e-02 nm, Epot= -6.07913e+04 Fmax= 1.04103e+02, atom= 1223\n", + "Step= 445, Dmax= 1.5e-02 nm, Epot= -6.07947e+04 Fmax= 1.53758e+02, atom= 1223\n", + "Step= 446, Dmax= 1.8e-02 nm, Epot= -6.07989e+04 Fmax= 1.50513e+02, atom= 1223\n", + "Step= 447, Dmax= 2.2e-02 nm, Epot= -6.08002e+04 Fmax= 2.19039e+02, atom= 1223\n", + "Step= 448, Dmax= 2.6e-02 nm, Epot= -6.08041e+04 Fmax= 2.22060e+02, atom= 1223\n", + "Step= 450, Dmax= 1.6e-02 nm, Epot= -6.08135e+04 Fmax= 4.75881e+01, atom= 1223\n", + "Step= 451, Dmax= 1.9e-02 nm, Epot= -6.08187e+04 Fmax= 2.76175e+02, atom= 1223\n", + "Step= 452, Dmax= 2.2e-02 nm, Epot= -6.08289e+04 Fmax= 1.20156e+02, atom= 1223\n", + "Step= 454, Dmax= 1.3e-02 nm, Epot= -6.08331e+04 Fmax= 1.02000e+02, atom= 1223\n", + "Step= 455, Dmax= 1.6e-02 nm, Epot= -6.08363e+04 Fmax= 1.75351e+02, atom= 1223\n", + "Step= 456, Dmax= 1.9e-02 nm, Epot= -6.08409e+04 Fmax= 1.50898e+02, atom= 1223\n", + "Step= 457, Dmax= 2.3e-02 nm, Epot= -6.08416e+04 Fmax= 2.46299e+02, atom= 1223\n", + "Step= 458, Dmax= 2.8e-02 nm, Epot= -6.08464e+04 Fmax= 2.26878e+02, atom= 1223\n", + "Step= 460, Dmax= 1.7e-02 nm, Epot= -6.08549e+04 Fmax= 6.13702e+01, atom= 1223\n", + "Step= 461, Dmax= 2.0e-02 nm, Epot= -6.08577e+04 Fmax= 2.86679e+02, atom= 1223\n", + "Step= 462, Dmax= 2.4e-02 nm, Epot= -6.08675e+04 Fmax= 1.36801e+02, atom= 1223\n", + "Step= 464, Dmax= 1.4e-02 nm, Epot= -6.08718e+04 Fmax= 1.01521e+02, atom= 1223\n", + "Step= 465, Dmax= 1.7e-02 nm, Epot= -6.08744e+04 Fmax= 1.97236e+02, atom= 1223\n", + "Step= 466, Dmax= 2.1e-02 nm, Epot= -6.08796e+04 Fmax= 1.53329e+02, atom= 1223\n", + "Step= 468, Dmax= 1.3e-02 nm, Epot= -6.08847e+04 Fmax= 6.19772e+01, atom= 1223\n", + "Step= 469, Dmax= 1.5e-02 nm, Epot= -6.08891e+04 Fmax= 1.90634e+02, atom= 1223\n", + "Step= 470, Dmax= 1.8e-02 nm, Epot= -6.08948e+04 Fmax= 1.21095e+02, atom= 1223\n", + "Step= 471, Dmax= 2.2e-02 nm, Epot= -6.08957e+04 Fmax= 2.47276e+02, atom= 1223\n", + "Step= 472, Dmax= 2.6e-02 nm, Epot= -6.09016e+04 Fmax= 1.96336e+02, atom= 1223\n", + "Step= 474, Dmax= 1.6e-02 nm, Epot= -6.09080e+04 Fmax= 6.02448e+01, atom= 1223\n", + "Step= 475, Dmax= 1.9e-02 nm, Epot= -6.09096e+04 Fmax= 2.75479e+02, atom= 1223\n", + "Step= 476, Dmax= 2.2e-02 nm, Epot= -6.09199e+04 Fmax= 1.08913e+02, atom= 1223\n", + "Step= 478, Dmax= 1.3e-02 nm, Epot= -6.09237e+04 Fmax= 1.19632e+02, atom= 1223\n", + "Step= 479, Dmax= 1.6e-02 nm, Epot= -6.09268e+04 Fmax= 1.52513e+02, atom= 1223\n", + "Step= 480, Dmax= 1.9e-02 nm, Epot= -6.09299e+04 Fmax= 1.80940e+02, atom= 1223\n", + "Step= 481, Dmax= 2.3e-02 nm, Epot= -6.09323e+04 Fmax= 2.13340e+02, atom= 1223\n", + "Step= 482, Dmax= 2.8e-02 nm, Epot= -6.09336e+04 Fmax= 2.63215e+02, atom= 1223\n", + "Step= 483, Dmax= 3.3e-02 nm, Epot= -6.09343e+04 Fmax= 3.06582e+02, atom= 1223\n", + "Step= 485, Dmax= 2.0e-02 nm, Epot= -6.09489e+04 Fmax= 4.04548e+01, atom= 1223\n", + "Step= 486, Dmax= 2.4e-02 nm, Epot= -6.09537e+04 Fmax= 3.76858e+02, atom= 1223\n", + "Step= 487, Dmax= 2.9e-02 nm, Epot= -6.09692e+04 Fmax= 1.55120e+02, atom= 1223\n", + "Step= 489, Dmax= 1.7e-02 nm, Epot= -6.09732e+04 Fmax= 1.25488e+02, atom= 1223\n", + "Step= 490, Dmax= 2.1e-02 nm, Epot= -6.09748e+04 Fmax= 2.29167e+02, atom= 1223\n", + "Step= 491, Dmax= 2.5e-02 nm, Epot= -6.09798e+04 Fmax= 1.88647e+02, atom= 1223\n", + "Step= 493, Dmax= 1.5e-02 nm, Epot= -6.09860e+04 Fmax= 6.73851e+01, atom= 1223\n", + "Step= 494, Dmax= 1.8e-02 nm, Epot= -6.09887e+04 Fmax= 2.36720e+02, atom= 1223\n", + "Step= 495, Dmax= 2.2e-02 nm, Epot= -6.09961e+04 Fmax= 1.36557e+02, atom= 1223\n", + "Step= 497, Dmax= 1.3e-02 nm, Epot= -6.10005e+04 Fmax= 7.65016e+01, atom= 1223\n", + "Step= 498, Dmax= 1.6e-02 nm, Epot= -6.10031e+04 Fmax= 1.94286e+02, atom= 1223\n", + "Step= 499, Dmax= 1.9e-02 nm, Epot= -6.10091e+04 Fmax= 1.19070e+02, atom= 1223\n", + "Step= 501, Dmax= 1.1e-02 nm, Epot= -6.10134e+04 Fmax= 7.30174e+01, atom= 1223\n", + "Step= 502, Dmax= 1.3e-02 nm, Epot= -6.10168e+04 Fmax= 1.51189e+02, atom= 1223\n", + "Step= 503, Dmax= 1.6e-02 nm, Epot= -6.10214e+04 Fmax= 1.26629e+02, atom= 1223\n", + "Step= 504, Dmax= 1.9e-02 nm, Epot= -6.10226e+04 Fmax= 1.99469e+02, atom= 1223\n", + "Step= 505, Dmax= 2.3e-02 nm, Epot= -6.10264e+04 Fmax= 1.97282e+02, atom= 1223\n", + "Step= 507, Dmax= 1.4e-02 nm, Epot= -6.10345e+04 Fmax= 3.68117e+01, atom= 2326\n", + "Step= 508, Dmax= 1.7e-02 nm, Epot= -6.10375e+04 Fmax= 2.67975e+02, atom= 1223\n", + "Step= 509, Dmax= 2.0e-02 nm, Epot= -6.10507e+04 Fmax= 8.53279e+01, atom= 1223\n", + "Step= 511, Dmax= 1.2e-02 nm, Epot= -6.10542e+04 Fmax= 1.17067e+02, atom= 1223\n", + "Step= 512, Dmax= 1.4e-02 nm, Epot= -6.10576e+04 Fmax= 1.24958e+02, atom= 1223\n", + "Step= 513, Dmax= 1.7e-02 nm, Epot= -6.10595e+04 Fmax= 1.74918e+02, atom= 1223\n", + "Step= 514, Dmax= 2.1e-02 nm, Epot= -6.10629e+04 Fmax= 1.76175e+02, atom= 1223\n", + "Step= 516, Dmax= 1.2e-02 nm, Epot= -6.10707e+04 Fmax= 3.64384e+01, atom= 1223\n", + "Step= 517, Dmax= 1.5e-02 nm, Epot= -6.10747e+04 Fmax= 2.13923e+02, atom= 1223\n", + "Step= 518, Dmax= 1.8e-02 nm, Epot= -6.10846e+04 Fmax= 1.01816e+02, atom= 1223\n", + "Step= 520, Dmax= 1.1e-02 nm, Epot= -6.10887e+04 Fmax= 8.20037e+01, atom= 3536\n", + "Step= 521, Dmax= 1.3e-02 nm, Epot= -6.10910e+04 Fmax= 1.41798e+02, atom= 3536\n", + "Step= 522, Dmax= 1.6e-02 nm, Epot= -6.10953e+04 Fmax= 1.25890e+02, atom= 3536\n", + "Step= 523, Dmax= 1.9e-02 nm, Epot= -6.10957e+04 Fmax= 1.95616e+02, atom= 3536\n", + "Step= 524, Dmax= 2.2e-02 nm, Epot= -6.10998e+04 Fmax= 1.90703e+02, atom= 3536\n", + "Step= 526, Dmax= 1.3e-02 nm, Epot= -6.11084e+04 Fmax= 4.56537e+01, atom= 3536\n", + "Step= 527, Dmax= 1.6e-02 nm, Epot= -6.11114e+04 Fmax= 2.35867e+02, atom= 3536\n", + "Step= 528, Dmax= 1.9e-02 nm, Epot= -6.11206e+04 Fmax= 1.05585e+02, atom= 3536\n", + "Step= 530, Dmax= 1.2e-02 nm, Epot= -6.11243e+04 Fmax= 9.42027e+01, atom= 3536\n", + "Step= 531, Dmax= 1.4e-02 nm, Epot= -6.11271e+04 Fmax= 1.46164e+02, atom= 3536\n", + "Step= 532, Dmax= 1.7e-02 nm, Epot= -6.11308e+04 Fmax= 1.41635e+02, atom= 3536\n", + "Step= 533, Dmax= 2.0e-02 nm, Epot= -6.11321e+04 Fmax= 2.03785e+02, atom= 3536\n", + "Step= 534, Dmax= 2.4e-02 nm, Epot= -6.11353e+04 Fmax= 2.11627e+02, atom= 3536\n", + "Step= 536, Dmax= 1.4e-02 nm, Epot= -6.11433e+04 Fmax= 4.28999e+01, atom= 3536\n", + "Step= 537, Dmax= 1.7e-02 nm, Epot= -6.11476e+04 Fmax= 2.60986e+02, atom= 3536\n", + "Step= 538, Dmax= 2.1e-02 nm, Epot= -6.11565e+04 Fmax= 1.08001e+02, atom= 3536\n", + "Step= 540, Dmax= 1.2e-02 nm, Epot= -6.11600e+04 Fmax= 1.07247e+02, atom= 3536\n", + "Step= 541, Dmax= 1.5e-02 nm, Epot= -6.11628e+04 Fmax= 1.50989e+02, atom= 3536\n", + "Step= 542, Dmax= 1.8e-02 nm, Epot= -6.11661e+04 Fmax= 1.58614e+02, atom= 3536\n", + "Step= 543, Dmax= 2.2e-02 nm, Epot= -6.11676e+04 Fmax= 2.12372e+02, atom= 3536\n", + "Step= 544, Dmax= 2.6e-02 nm, Epot= -6.11702e+04 Fmax= 2.34395e+02, atom= 3536\n", + "Step= 546, Dmax= 1.5e-02 nm, Epot= -6.11784e+04 Fmax= 3.97968e+01, atom= 3536\n", + "Step= 547, Dmax= 1.9e-02 nm, Epot= -6.11834e+04 Fmax= 2.88808e+02, atom= 3536\n", + "Step= 548, Dmax= 2.2e-02 nm, Epot= -6.11931e+04 Fmax= 1.10823e+02, atom= 3536\n", + "Step= 550, Dmax= 1.3e-02 nm, Epot= -6.11964e+04 Fmax= 1.21323e+02, atom= 3536\n", + "Step= 551, Dmax= 1.6e-02 nm, Epot= -6.11991e+04 Fmax= 1.56086e+02, atom= 3536\n", + "Step= 552, Dmax= 1.9e-02 nm, Epot= -6.12021e+04 Fmax= 1.77007e+02, atom= 3536\n", + "Step= 553, Dmax= 2.3e-02 nm, Epot= -6.12037e+04 Fmax= 2.21460e+02, atom= 3536\n", + "Step= 554, Dmax= 2.8e-02 nm, Epot= -6.12055e+04 Fmax= 2.59053e+02, atom= 3536\n", + "Step= 556, Dmax= 1.7e-02 nm, Epot= -6.12147e+04 Fmax= 3.63356e+01, atom= 3536\n", + "Step= 557, Dmax= 2.0e-02 nm, Epot= -6.12201e+04 Fmax= 3.20579e+02, atom= 3536\n", + "Step= 558, Dmax= 2.4e-02 nm, Epot= -6.12315e+04 Fmax= 1.14052e+02, atom= 3536\n", + "Step= 560, Dmax= 1.4e-02 nm, Epot= -6.12346e+04 Fmax= 1.36861e+02, atom= 3536\n", + "Step= 561, Dmax= 1.7e-02 nm, Epot= -6.12374e+04 Fmax= 1.61623e+02, atom= 3536\n", + "Step= 562, Dmax= 2.1e-02 nm, Epot= -6.12398e+04 Fmax= 1.96946e+02, atom= 3536\n", + "Step= 563, Dmax= 2.5e-02 nm, Epot= -6.12415e+04 Fmax= 2.30953e+02, atom= 3536\n", + "Step= 564, Dmax= 3.0e-02 nm, Epot= -6.12423e+04 Fmax= 2.85884e+02, atom= 3536\n", + "Step= 566, Dmax= 1.8e-02 nm, Epot= -6.12531e+04 Fmax= 3.24288e+01, atom= 3536\n", + "Step= 567, Dmax= 2.1e-02 nm, Epot= -6.12590e+04 Fmax= 3.56015e+02, atom= 3536\n", + "Step= 568, Dmax= 2.6e-02 nm, Epot= -6.12726e+04 Fmax= 1.30569e+02, atom= 3535\n", + "Step= 570, Dmax= 1.5e-02 nm, Epot= -6.12759e+04 Fmax= 1.28331e+02, atom= 3536\n", + "Step= 571, Dmax= 1.9e-02 nm, Epot= -6.12777e+04 Fmax= 1.91110e+02, atom= 3536\n", + "Step= 572, Dmax= 2.2e-02 nm, Epot= -6.12810e+04 Fmax= 1.93296e+02, atom= 3536\n", + "Step= 574, Dmax= 1.3e-02 nm, Epot= -6.12870e+04 Fmax= 4.14069e+01, atom= 3536\n", + "Step= 575, Dmax= 1.6e-02 nm, Epot= -6.12918e+04 Fmax= 2.40806e+02, atom= 3536\n", + "Step= 576, Dmax= 1.9e-02 nm, Epot= -6.12992e+04 Fmax= 9.95260e+01, atom= 3536\n", + "Step= 578, Dmax= 1.2e-02 nm, Epot= -6.13025e+04 Fmax= 1.00033e+02, atom= 3536\n", + "Step= 579, Dmax= 1.4e-02 nm, Epot= -6.13053e+04 Fmax= 1.38688e+02, atom= 3536\n", + "Step= 580, Dmax= 1.7e-02 nm, Epot= -6.13084e+04 Fmax= 1.48428e+02, atom= 3536\n", + "Step= 581, Dmax= 2.0e-02 nm, Epot= -6.13101e+04 Fmax= 1.94908e+02, atom= 3536\n", + "Step= 582, Dmax= 2.4e-02 nm, Epot= -6.13125e+04 Fmax= 2.19067e+02, atom= 3536\n", + "Step= 584, Dmax= 1.4e-02 nm, Epot= -6.13201e+04 Fmax= 3.48821e+01, atom= 3536\n", + "Step= 585, Dmax= 1.7e-02 nm, Epot= -6.13257e+04 Fmax= 2.71266e+02, atom= 3536\n", + "Step= 586, Dmax= 2.1e-02 nm, Epot= -6.13351e+04 Fmax= 1.01484e+02, atom= 3535\n", + "Step= 588, Dmax= 1.2e-02 nm, Epot= -6.13383e+04 Fmax= 1.12499e+02, atom= 3536\n", + "Step= 589, Dmax= 1.5e-02 nm, Epot= -6.13410e+04 Fmax= 1.44481e+02, atom= 3536\n", + "Step= 590, Dmax= 1.8e-02 nm, Epot= -6.13438e+04 Fmax= 1.64689e+02, atom= 3536\n", + "Step= 591, Dmax= 2.1e-02 nm, Epot= -6.13454e+04 Fmax= 2.04446e+02, atom= 3536\n", + "Step= 592, Dmax= 2.6e-02 nm, Epot= -6.13470e+04 Fmax= 2.40872e+02, atom= 3536\n", + "Step= 594, Dmax= 1.5e-02 nm, Epot= -6.13561e+04 Fmax= 3.26409e+01, atom= 3536\n", + "Step= 595, Dmax= 1.9e-02 nm, Epot= -6.13617e+04 Fmax= 2.99428e+02, atom= 3536\n", + "Step= 596, Dmax= 2.2e-02 nm, Epot= -6.13730e+04 Fmax= 1.16821e+02, atom= 3535\n", + "Step= 598, Dmax= 1.3e-02 nm, Epot= -6.13765e+04 Fmax= 1.02805e+02, atom= 3536\n", + "Step= 599, Dmax= 1.6e-02 nm, Epot= -6.13782e+04 Fmax= 1.72226e+02, atom= 3536\n", + "Step= 600, Dmax= 1.9e-02 nm, Epot= -6.13820e+04 Fmax= 1.59228e+02, atom= 3536\n", + "Step= 602, Dmax= 1.2e-02 nm, Epot= -6.13872e+04 Fmax= 4.27717e+01, atom= 3536\n", + "Step= 603, Dmax= 1.4e-02 nm, Epot= -6.13915e+04 Fmax= 1.99919e+02, atom= 3536\n", + "Step= 604, Dmax= 1.7e-02 nm, Epot= -6.13979e+04 Fmax= 9.18379e+01, atom= 3536\n", + "Step= 606, Dmax= 1.0e-02 nm, Epot= -6.14012e+04 Fmax= 8.02773e+01, atom= 3536\n", + "Step= 607, Dmax= 1.2e-02 nm, Epot= -6.14041e+04 Fmax= 1.25358e+02, atom= 3536\n", + "Step= 608, Dmax= 1.4e-02 nm, Epot= -6.14075e+04 Fmax= 1.22421e+02, atom= 3536\n", + "Step= 609, Dmax= 1.7e-02 nm, Epot= -6.14092e+04 Fmax= 1.76739e+02, atom= 1040\n", + "Step= 610, Dmax= 2.1e-02 nm, Epot= -6.14124e+04 Fmax= 1.79814e+02, atom= 1040\n", + "Step= 612, Dmax= 1.2e-02 nm, Epot= -6.14186e+04 Fmax= 3.79408e+01, atom= 3536\n", + "Step= 613, Dmax= 1.5e-02 nm, Epot= -6.14233e+04 Fmax= 2.24755e+02, atom= 3536\n", + "Step= 614, Dmax= 1.8e-02 nm, Epot= -6.14311e+04 Fmax= 9.76453e+01, atom= 3535\n", + "Step= 616, Dmax= 1.1e-02 nm, Epot= -6.14345e+04 Fmax= 8.28804e+01, atom= 3536\n", + "Step= 617, Dmax= 1.3e-02 nm, Epot= -6.14371e+04 Fmax= 1.39041e+02, atom= 1040\n", + "Step= 618, Dmax= 1.5e-02 nm, Epot= -6.14408e+04 Fmax= 1.27000e+02, atom= 1040\n", + "Step= 619, Dmax= 1.8e-02 nm, Epot= -6.14418e+04 Fmax= 1.95549e+02, atom= 1040\n", + "Step= 620, Dmax= 2.2e-02 nm, Epot= -6.14455e+04 Fmax= 1.87765e+02, atom= 1040\n", + "Step= 622, Dmax= 1.3e-02 nm, Epot= -6.14524e+04 Fmax= 4.56862e+01, atom= 3536\n", + "Step= 623, Dmax= 1.6e-02 nm, Epot= -6.14549e+04 Fmax= 2.36901e+02, atom= 3536\n", + "Step= 624, Dmax= 1.9e-02 nm, Epot= -6.14635e+04 Fmax= 1.11614e+02, atom= 3535\n", + "Step= 626, Dmax= 1.2e-02 nm, Epot= -6.14672e+04 Fmax= 8.07026e+01, atom= 3536\n", + "Step= 627, Dmax= 1.4e-02 nm, Epot= -6.14694e+04 Fmax= 1.59835e+02, atom= 3535\n", + "Step= 628, Dmax= 1.7e-02 nm, Epot= -6.14738e+04 Fmax= 1.25099e+02, atom= 1040\n", + "Step= 630, Dmax= 9.9e-03 nm, Epot= -6.14782e+04 Fmax= 4.88771e+01, atom= 1040\n", + "Step= 631, Dmax= 1.2e-02 nm, Epot= -6.14820e+04 Fmax= 1.57882e+02, atom= 1040\n", + "Step= 632, Dmax= 1.4e-02 nm, Epot= -6.14870e+04 Fmax= 9.52265e+01, atom= 3535\n", + "Step= 633, Dmax= 1.7e-02 nm, Epot= -6.14876e+04 Fmax= 2.02487e+02, atom= 3535\n", + "Step= 634, Dmax= 2.1e-02 nm, Epot= -6.14928e+04 Fmax= 1.59548e+02, atom= 3535\n", + "Step= 636, Dmax= 1.2e-02 nm, Epot= -6.14985e+04 Fmax= 5.32573e+01, atom= 1040\n", + "Step= 637, Dmax= 1.5e-02 nm, Epot= -6.15012e+04 Fmax= 2.01872e+02, atom= 1040\n", + "Step= 638, Dmax= 1.8e-02 nm, Epot= -6.15081e+04 Fmax= 1.09783e+02, atom= 3535\n", + "Step= 640, Dmax= 1.1e-02 nm, Epot= -6.15119e+04 Fmax= 7.39377e+01, atom= 3535\n", + "Step= 641, Dmax= 1.3e-02 nm, Epot= -6.15145e+04 Fmax= 1.46850e+02, atom= 3535\n", + "Step= 642, Dmax= 1.5e-02 nm, Epot= -6.15186e+04 Fmax= 1.24426e+02, atom= 3535\n", + "Step= 643, Dmax= 1.8e-02 nm, Epot= -6.15197e+04 Fmax= 1.94596e+02, atom= 3535\n", + "Step= 644, Dmax= 2.2e-02 nm, Epot= -6.15230e+04 Fmax= 1.94441e+02, atom= 3535\n", + "Step= 646, Dmax= 1.3e-02 nm, Epot= -6.15306e+04 Fmax= 3.85532e+01, atom= 3152\n", + "Step= 647, Dmax= 1.6e-02 nm, Epot= -6.15364e+04 Fmax= 2.25046e+02, atom= 3535\n", + "Step= 648, Dmax= 1.9e-02 nm, Epot= -6.15440e+04 Fmax= 1.18780e+02, atom= 3535\n", + "Step= 650, Dmax= 1.1e-02 nm, Epot= -6.15479e+04 Fmax= 7.42152e+01, atom= 3535\n", + "Step= 651, Dmax= 1.4e-02 nm, Epot= -6.15502e+04 Fmax= 1.63515e+02, atom= 3535\n", + "Step= 652, Dmax= 1.7e-02 nm, Epot= -6.15549e+04 Fmax= 1.27170e+02, atom= 3535\n", + "Step= 653, Dmax= 2.0e-02 nm, Epot= -6.15549e+04 Fmax= 2.15525e+02, atom= 3535\n", + "Step= 654, Dmax= 2.4e-02 nm, Epot= -6.15589e+04 Fmax= 2.02478e+02, atom= 3535\n", + "Step= 656, Dmax= 1.4e-02 nm, Epot= -6.15670e+04 Fmax= 4.80192e+01, atom= 3152\n", + "Step= 657, Dmax= 1.7e-02 nm, Epot= -6.15703e+04 Fmax= 2.35520e+02, atom= 3535\n", + "Step= 658, Dmax= 2.1e-02 nm, Epot= -6.15783e+04 Fmax= 1.31697e+02, atom= 3535\n", + "Step= 660, Dmax= 1.2e-02 nm, Epot= -6.15824e+04 Fmax= 7.52233e+01, atom= 3535\n", + "Step= 661, Dmax= 1.5e-02 nm, Epot= -6.15840e+04 Fmax= 1.82022e+02, atom= 3535\n", + "Step= 662, Dmax= 1.8e-02 nm, Epot= -6.15894e+04 Fmax= 1.31556e+02, atom= 3535\n", + "Step= 664, Dmax= 1.1e-02 nm, Epot= -6.15939e+04 Fmax= 5.10321e+01, atom= 3152\n", + "Step= 665, Dmax= 1.3e-02 nm, Epot= -6.15972e+04 Fmax= 1.74469e+02, atom= 3535\n", + "Step= 666, Dmax= 1.5e-02 nm, Epot= -6.16031e+04 Fmax= 9.24820e+01, atom= 3535\n", + "Step= 668, Dmax= 9.2e-03 nm, Epot= -6.16065e+04 Fmax= 6.65004e+01, atom= 3535\n", + "Step= 669, Dmax= 1.1e-02 nm, Epot= -6.16097e+04 Fmax= 1.22253e+02, atom= 3535\n", + "Step= 670, Dmax= 1.3e-02 nm, Epot= -6.16133e+04 Fmax= 1.12178e+02, atom= 3535\n", + "Step= 671, Dmax= 1.6e-02 nm, Epot= -6.16153e+04 Fmax= 1.61177e+02, atom= 3535\n", + "Step= 672, Dmax= 1.9e-02 nm, Epot= -6.16182e+04 Fmax= 1.75494e+02, atom= 3535\n", + "Step= 673, Dmax= 2.3e-02 nm, Epot= -6.16192e+04 Fmax= 2.19201e+02, atom= 3535\n", + "Step= 674, Dmax= 2.8e-02 nm, Epot= -6.16196e+04 Fmax= 2.65133e+02, atom= 3535\n", + "Step= 675, Dmax= 3.3e-02 nm, Epot= -6.16197e+04 Fmax= 3.02379e+02, atom= 3535\n", + "Step= 677, Dmax= 2.0e-02 nm, Epot= -6.16353e+04 Fmax= 5.31556e+01, atom= 1039\n", + "Step= 679, Dmax= 1.2e-02 nm, Epot= -6.16397e+04 Fmax= 1.29421e+02, atom= 1040\n", + "Step= 680, Dmax= 1.4e-02 nm, Epot= -6.16433e+04 Fmax= 1.18995e+02, atom= 1040\n", + "Step= 681, Dmax= 1.7e-02 nm, Epot= -6.16449e+04 Fmax= 1.73260e+02, atom= 1040\n", + "Step= 682, Dmax= 2.1e-02 nm, Epot= -6.16476e+04 Fmax= 1.83415e+02, atom= 3535\n", + "Step= 684, Dmax= 1.2e-02 nm, Epot= -6.16548e+04 Fmax= 3.27409e+01, atom= 3152\n", + "Step= 685, Dmax= 1.5e-02 nm, Epot= -6.16621e+04 Fmax= 2.04349e+02, atom= 3535\n", + "Step= 686, Dmax= 1.8e-02 nm, Epot= -6.16687e+04 Fmax= 1.11196e+02, atom= 3535\n", + "Step= 688, Dmax= 1.1e-02 nm, Epot= -6.16724e+04 Fmax= 6.89311e+01, atom= 3535\n", + "Step= 689, Dmax= 1.3e-02 nm, Epot= -6.16748e+04 Fmax= 1.49800e+02, atom= 3535\n", + "Step= 690, Dmax= 1.5e-02 nm, Epot= -6.16790e+04 Fmax= 1.19317e+02, atom= 3535\n", + "Step= 691, Dmax= 1.8e-02 nm, Epot= -6.16796e+04 Fmax= 1.96283e+02, atom= 3535\n", + "Step= 692, Dmax= 2.2e-02 nm, Epot= -6.16831e+04 Fmax= 1.90789e+02, atom= 3535\n", + "Step= 694, Dmax= 1.3e-02 nm, Epot= -6.16906e+04 Fmax= 4.29290e+01, atom= 3152\n", + "Step= 695, Dmax= 1.6e-02 nm, Epot= -6.16950e+04 Fmax= 2.15578e+02, atom= 3152\n", + "Step= 696, Dmax= 1.9e-02 nm, Epot= -6.17018e+04 Fmax= 1.18125e+02, atom= 3535\n", + "Step= 698, Dmax= 1.1e-02 nm, Epot= -6.17055e+04 Fmax= 7.49041e+01, atom= 3535\n", + "Step= 699, Dmax= 1.4e-02 nm, Epot= -6.17074e+04 Fmax= 1.60538e+02, atom= 3535\n", + "Step= 700, Dmax= 1.6e-02 nm, Epot= -6.17118e+04 Fmax= 1.28790e+02, atom= 3535\n", + "Step= 702, Dmax= 9.9e-03 nm, Epot= -6.17163e+04 Fmax= 4.33085e+01, atom= 3152\n", + "Step= 703, Dmax= 1.2e-02 nm, Epot= -6.17206e+04 Fmax= 1.55624e+02, atom= 3535\n", + "Step= 704, Dmax= 1.4e-02 nm, Epot= -6.17256e+04 Fmax= 9.05495e+01, atom= 3535\n", + "Step= 706, Dmax= 8.5e-03 nm, Epot= -6.17289e+04 Fmax= 5.71328e+01, atom= 3535\n", + "Step= 707, Dmax= 1.0e-02 nm, Epot= -6.17322e+04 Fmax= 1.16949e+02, atom= 3535\n", + "Step= 708, Dmax= 1.2e-02 nm, Epot= -6.17359e+04 Fmax= 1.00195e+02, atom= 3535\n", + "Step= 709, Dmax= 1.5e-02 nm, Epot= -6.17378e+04 Fmax= 1.51963e+02, atom= 3535\n", + "Step= 710, Dmax= 1.8e-02 nm, Epot= -6.17408e+04 Fmax= 1.59449e+02, atom= 3535\n", + "Step= 711, Dmax= 2.1e-02 nm, Epot= -6.17417e+04 Fmax= 2.04817e+02, atom= 3535\n", + "Step= 712, Dmax= 2.6e-02 nm, Epot= -6.17427e+04 Fmax= 2.43150e+02, atom= 3535\n", + "Step= 714, Dmax= 1.5e-02 nm, Epot= -6.17536e+04 Fmax= 3.42329e+01, atom= 4321\n", + "Step= 715, Dmax= 1.8e-02 nm, Epot= -6.17636e+04 Fmax= 2.31897e+02, atom= 3152\n", + "Step= 716, Dmax= 2.2e-02 nm, Epot= -6.17686e+04 Fmax= 1.42026e+02, atom= 3535\n", + "Step= 718, Dmax= 1.3e-02 nm, Epot= -6.17727e+04 Fmax= 8.02666e+01, atom= 3152\n", + "Step= 719, Dmax= 1.6e-02 nm, Epot= -6.17736e+04 Fmax= 1.90428e+02, atom= 3152\n", + "Step= 720, Dmax= 1.9e-02 nm, Epot= -6.17787e+04 Fmax= 1.39559e+02, atom= 3152\n", + "Step= 722, Dmax= 1.1e-02 nm, Epot= -6.17833e+04 Fmax= 6.06141e+01, atom= 3152\n", + "Step= 723, Dmax= 1.4e-02 nm, Epot= -6.17858e+04 Fmax= 1.69710e+02, atom= 3152\n", + "Step= 724, Dmax= 1.6e-02 nm, Epot= -6.17906e+04 Fmax= 1.12501e+02, atom= 3152\n", + "Step= 726, Dmax= 9.9e-03 nm, Epot= -6.17943e+04 Fmax= 5.36911e+01, atom= 3535\n", + "Step= 727, Dmax= 1.2e-02 nm, Epot= -6.17967e+04 Fmax= 1.49719e+02, atom= 3535\n", + "Step= 728, Dmax= 1.4e-02 nm, Epot= -6.18015e+04 Fmax= 1.01397e+02, atom= 3535\n", + "Step= 729, Dmax= 1.7e-02 nm, Epot= -6.18016e+04 Fmax= 1.90520e+02, atom= 3535\n", + "Step= 730, Dmax= 2.0e-02 nm, Epot= -6.18058e+04 Fmax= 1.67668e+02, atom= 3535\n", + "Step= 732, Dmax= 1.2e-02 nm, Epot= -6.18119e+04 Fmax= 4.75691e+01, atom= 3152\n", + "Step= 733, Dmax= 1.5e-02 nm, Epot= -6.18147e+04 Fmax= 1.96121e+02, atom= 3152\n", + "Step= 734, Dmax= 1.8e-02 nm, Epot= -6.18208e+04 Fmax= 1.07648e+02, atom= 3152\n", + "Step= 736, Dmax= 1.1e-02 nm, Epot= -6.18243e+04 Fmax= 7.27536e+01, atom= 3535\n", + "Step= 737, Dmax= 1.3e-02 nm, Epot= -6.18262e+04 Fmax= 1.44440e+02, atom= 3535\n", + "Step= 738, Dmax= 1.5e-02 nm, Epot= -6.18300e+04 Fmax= 1.23070e+02, atom= 3535\n", + "Step= 739, Dmax= 1.8e-02 nm, Epot= -6.18303e+04 Fmax= 1.90369e+02, atom= 3535\n", + "Step= 740, Dmax= 2.2e-02 nm, Epot= -6.18331e+04 Fmax= 1.93885e+02, atom= 3535\n", + "Step= 742, Dmax= 1.3e-02 nm, Epot= -6.18408e+04 Fmax= 3.97379e+01, atom= 3152\n", + "Step= 743, Dmax= 1.6e-02 nm, Epot= -6.18453e+04 Fmax= 2.14565e+02, atom= 3152\n", + "Step= 744, Dmax= 1.9e-02 nm, Epot= -6.18517e+04 Fmax= 1.10914e+02, atom= 3535\n", + "Step= 746, Dmax= 1.1e-02 nm, Epot= -6.18550e+04 Fmax= 8.17804e+01, atom= 3152\n", + "Step= 747, Dmax= 1.4e-02 nm, Epot= -6.18565e+04 Fmax= 1.51966e+02, atom= 3152\n", + "Step= 748, Dmax= 1.6e-02 nm, Epot= -6.18602e+04 Fmax= 1.31997e+02, atom= 3535\n", + "Step= 750, Dmax= 9.9e-03 nm, Epot= -6.18648e+04 Fmax= 4.06369e+01, atom= 3152\n", + "Step= 751, Dmax= 1.2e-02 nm, Epot= -6.18686e+04 Fmax= 1.55739e+02, atom= 3152\n", + "Step= 752, Dmax= 1.4e-02 nm, Epot= -6.18733e+04 Fmax= 8.78158e+01, atom= 3152\n", + "Step= 754, Dmax= 8.5e-03 nm, Epot= -6.18764e+04 Fmax= 5.63439e+01, atom= 3535\n", + "Step= 755, Dmax= 1.0e-02 nm, Epot= -6.18791e+04 Fmax= 1.17904e+02, atom= 3152\n", + "Step= 756, Dmax= 1.2e-02 nm, Epot= -6.18825e+04 Fmax= 9.56329e+01, atom= 3535\n", + "Step= 757, Dmax= 1.5e-02 nm, Epot= -6.18836e+04 Fmax= 1.54804e+02, atom= 3535\n", + "Step= 758, Dmax= 1.8e-02 nm, Epot= -6.18867e+04 Fmax= 1.53237e+02, atom= 3535\n", + "Step= 760, Dmax= 1.1e-02 nm, Epot= -6.18922e+04 Fmax= 3.31460e+01, atom= 3152\n", + "Step= 761, Dmax= 1.3e-02 nm, Epot= -6.18975e+04 Fmax= 1.73636e+02, atom= 3152\n", + "Step= 762, Dmax= 1.5e-02 nm, Epot= -6.19028e+04 Fmax= 8.76914e+01, atom= 3152\n", + "Step= 764, Dmax= 9.2e-03 nm, Epot= -6.19058e+04 Fmax= 6.73964e+01, atom= 3152\n", + "Step= 765, Dmax= 1.1e-02 nm, Epot= -6.19080e+04 Fmax= 1.20765e+02, atom= 3152\n", + "Step= 766, Dmax= 1.3e-02 nm, Epot= -6.19113e+04 Fmax= 1.05827e+02, atom= 3152\n", + "Step= 767, Dmax= 1.6e-02 nm, Epot= -6.19121e+04 Fmax= 1.64467e+02, atom= 3152\n", + "Step= 768, Dmax= 1.9e-02 nm, Epot= -6.19149e+04 Fmax= 1.64561e+02, atom= 3535\n", + "Step= 770, Dmax= 1.1e-02 nm, Epot= -6.19211e+04 Fmax= 3.64448e+01, atom= 3152\n", + "Step= 771, Dmax= 1.4e-02 nm, Epot= -6.19256e+04 Fmax= 1.85661e+02, atom= 3152\n", + "Step= 772, Dmax= 1.6e-02 nm, Epot= -6.19312e+04 Fmax= 9.48668e+01, atom= 3152\n", + "Step= 774, Dmax= 9.8e-03 nm, Epot= -6.19342e+04 Fmax= 7.16065e+01, atom= 3152\n", + "Step= 775, Dmax= 1.2e-02 nm, Epot= -6.19363e+04 Fmax= 1.30276e+02, atom= 3152\n", + "Step= 776, Dmax= 1.4e-02 nm, Epot= -6.19396e+04 Fmax= 1.12993e+02, atom= 3152\n", + "Step= 777, Dmax= 1.7e-02 nm, Epot= -6.19399e+04 Fmax= 1.76969e+02, atom= 3152\n", + "Step= 778, Dmax= 2.0e-02 nm, Epot= -6.19428e+04 Fmax= 1.76224e+02, atom= 3152\n", + "Step= 780, Dmax= 1.2e-02 nm, Epot= -6.19497e+04 Fmax= 3.93834e+01, atom= 3152\n", + "Step= 781, Dmax= 1.5e-02 nm, Epot= -6.19534e+04 Fmax= 2.00393e+02, atom= 3152\n", + "Step= 782, Dmax= 1.8e-02 nm, Epot= -6.19595e+04 Fmax= 1.01110e+02, atom= 3152\n", + "Step= 784, Dmax= 1.1e-02 nm, Epot= -6.19627e+04 Fmax= 7.74010e+01, atom= 3152\n", + "Step= 785, Dmax= 1.3e-02 nm, Epot= -6.19644e+04 Fmax= 1.39127e+02, atom= 3152\n", + "Step= 786, Dmax= 1.5e-02 nm, Epot= -6.19678e+04 Fmax= 1.22153e+02, atom= 3152\n", + "Step= 788, Dmax= 9.1e-03 nm, Epot= -6.19720e+04 Fmax= 3.89169e+01, atom= 4122\n", + "Step= 789, Dmax= 1.1e-02 nm, Epot= -6.19761e+04 Fmax= 1.36355e+02, atom= 3152\n", + "Step= 790, Dmax= 1.3e-02 nm, Epot= -6.19800e+04 Fmax= 8.85624e+01, atom= 3152\n", + "Step= 791, Dmax= 1.6e-02 nm, Epot= -6.19801e+04 Fmax= 1.86158e+02, atom= 3152\n", + "Step= 792, Dmax= 1.9e-02 nm, Epot= -6.19849e+04 Fmax= 1.38396e+02, atom= 3152\n", + "Step= 794, Dmax= 1.1e-02 nm, Epot= -6.19895e+04 Fmax= 5.09696e+01, atom= 1040\n", + "Step= 795, Dmax= 1.4e-02 nm, Epot= -6.19897e+04 Fmax= 1.86002e+02, atom= 3152\n", + "Step= 796, Dmax= 1.6e-02 nm, Epot= -6.19966e+04 Fmax= 1.01536e+02, atom= 3535\n", + "Step= 798, Dmax= 9.8e-03 nm, Epot= -6.20000e+04 Fmax= 6.64572e+01, atom= 3152\n", + "Step= 799, Dmax= 1.2e-02 nm, Epot= -6.20016e+04 Fmax= 1.33691e+02, atom= 3152\n", + "Step= 800, Dmax= 1.4e-02 nm, Epot= -6.20052e+04 Fmax= 1.08370e+02, atom= 3152\n", + "Step= 802, Dmax= 8.5e-03 nm, Epot= -6.20089e+04 Fmax= 3.70154e+01, atom= 1040\n", + "Step= 803, Dmax= 1.0e-02 nm, Epot= -6.20119e+04 Fmax= 1.35100e+02, atom= 1040\n", + "Step= 804, Dmax= 1.2e-02 nm, Epot= -6.20164e+04 Fmax= 7.73837e+01, atom= 3535\n", + "Step= 806, Dmax= 7.3e-03 nm, Epot= -6.20193e+04 Fmax= 4.72407e+01, atom= 3152\n", + "Step= 807, Dmax= 8.8e-03 nm, Epot= -6.20219e+04 Fmax= 1.05023e+02, atom= 1040\n", + "Step= 808, Dmax= 1.1e-02 nm, Epot= -6.20252e+04 Fmax= 7.44326e+01, atom= 3152\n", + "Step= 809, Dmax= 1.3e-02 nm, Epot= -6.20261e+04 Fmax= 1.44141e+02, atom= 3152\n", + "Step= 810, Dmax= 1.5e-02 nm, Epot= -6.20299e+04 Fmax= 1.16531e+02, atom= 3152\n", + "Step= 812, Dmax= 9.1e-03 nm, Epot= -6.20341e+04 Fmax= 4.05647e+01, atom= 1040\n", + "Step= 813, Dmax= 1.1e-02 nm, Epot= -6.20362e+04 Fmax= 1.44984e+02, atom= 1040\n", + "Step= 814, Dmax= 1.3e-02 nm, Epot= -6.20412e+04 Fmax= 8.27354e+01, atom= 1040\n", + "Step= 816, Dmax= 7.9e-03 nm, Epot= -6.20442e+04 Fmax= 5.09708e+01, atom= 1040\n", + "Step= 817, Dmax= 9.5e-03 nm, Epot= -6.20462e+04 Fmax= 1.13030e+02, atom= 1040\n", + "Step= 818, Dmax= 1.1e-02 nm, Epot= -6.20498e+04 Fmax= 7.92451e+01, atom= 1040\n", + "Step= 820, Dmax= 6.8e-03 nm, Epot= -6.20529e+04 Fmax= 3.87388e+01, atom= 1040\n", + "Step= 821, Dmax= 8.2e-03 nm, Epot= -6.20556e+04 Fmax= 9.87226e+01, atom= 1040\n", + "Step= 822, Dmax= 9.8e-03 nm, Epot= -6.20590e+04 Fmax= 7.10804e+01, atom= 1040\n", + "Step= 823, Dmax= 1.2e-02 nm, Epot= -6.20598e+04 Fmax= 1.28394e+02, atom= 1040\n", + "Step= 824, Dmax= 1.4e-02 nm, Epot= -6.20629e+04 Fmax= 1.15790e+02, atom= 1040\n", + "Step= 826, Dmax= 8.5e-03 nm, Epot= -6.20679e+04 Fmax= 2.99533e+01, atom= 3152\n", + "Step= 827, Dmax= 1.0e-02 nm, Epot= -6.20707e+04 Fmax= 1.38865e+02, atom= 4937\n", + "Step= 828, Dmax= 1.2e-02 nm, Epot= -6.20765e+04 Fmax= 7.09483e+01, atom= 4937\n", + "Step= 830, Dmax= 7.3e-03 nm, Epot= -6.20792e+04 Fmax= 5.78147e+01, atom= 4937\n", + "Step= 831, Dmax= 8.8e-03 nm, Epot= -6.20813e+04 Fmax= 9.70556e+01, atom= 4937\n", + "Step= 832, Dmax= 1.1e-02 nm, Epot= -6.20842e+04 Fmax= 8.95919e+01, atom= 4937\n", + "Step= 833, Dmax= 1.3e-02 nm, Epot= -6.20856e+04 Fmax= 1.33092e+02, atom= 4937\n", + "Step= 834, Dmax= 1.5e-02 nm, Epot= -6.20881e+04 Fmax= 1.36257e+02, atom= 4937\n", + "Step= 835, Dmax= 1.8e-02 nm, Epot= -6.20887e+04 Fmax= 1.83325e+02, atom= 4937\n", + "Step= 836, Dmax= 2.2e-02 nm, Epot= -6.20901e+04 Fmax= 2.04424e+02, atom= 4937\n", + "Step= 838, Dmax= 1.3e-02 nm, Epot= -6.20986e+04 Fmax= 2.09576e+01, atom= 4957\n", + "Step= 839, Dmax= 1.6e-02 nm, Epot= -6.21079e+04 Fmax= 2.04645e+02, atom= 4937\n", + "Step= 840, Dmax= 1.9e-02 nm, Epot= -6.21149e+04 Fmax= 1.09620e+02, atom= 4937\n", + "Step= 842, Dmax= 1.1e-02 nm, Epot= -6.21180e+04 Fmax= 9.83847e+01, atom= 4937\n", + "Step= 843, Dmax= 1.4e-02 nm, Epot= -6.21195e+04 Fmax= 1.38212e+02, atom= 4937\n", + "Step= 844, Dmax= 1.6e-02 nm, Epot= -6.21216e+04 Fmax= 1.52302e+02, atom= 4937\n", + "Step= 845, Dmax= 2.0e-02 nm, Epot= -6.21227e+04 Fmax= 1.89961e+02, atom= 4937\n", + "Step= 846, Dmax= 2.4e-02 nm, Epot= -6.21232e+04 Fmax= 2.26308e+02, atom= 4937\n", + "Step= 847, Dmax= 2.8e-02 nm, Epot= -6.21239e+04 Fmax= 2.63974e+02, atom= 4937\n", + "Step= 849, Dmax= 1.7e-02 nm, Epot= -6.21349e+04 Fmax= 5.16396e+01, atom= 4938\n", + "Step= 851, Dmax= 1.0e-02 nm, Epot= -6.21380e+04 Fmax= 1.14491e+02, atom= 4232\n", + "Step= 852, Dmax= 1.2e-02 nm, Epot= -6.21406e+04 Fmax= 1.03019e+02, atom= 4937\n", + "Step= 853, Dmax= 1.5e-02 nm, Epot= -6.21424e+04 Fmax= 1.56752e+02, atom= 4937\n", + "Step= 854, Dmax= 1.8e-02 nm, Epot= -6.21448e+04 Fmax= 1.55059e+02, atom= 4937\n", + "Step= 855, Dmax= 2.1e-02 nm, Epot= -6.21458e+04 Fmax= 2.15500e+02, atom= 4937\n", + "Step= 856, Dmax= 2.5e-02 nm, Epot= -6.21471e+04 Fmax= 2.33906e+02, atom= 4937\n", + "Step= 857, Dmax= 3.0e-02 nm, Epot= -6.21476e+04 Fmax= 2.95153e+02, atom= 4937\n", + "Step= 859, Dmax= 1.8e-02 nm, Epot= -6.21568e+04 Fmax= 5.16491e+01, atom= 4938\n", + "Step= 860, Dmax= 2.2e-02 nm, Epot= -6.21577e+04 Fmax= 3.69765e+02, atom= 4938\n", + "Step= 861, Dmax= 2.6e-02 nm, Epot= -6.21660e+04 Fmax= 1.30235e+02, atom= 4232\n", + "Step= 863, Dmax= 1.6e-02 nm, Epot= -6.21685e+04 Fmax= 1.33596e+02, atom= 4937\n", + "Step= 864, Dmax= 1.9e-02 nm, Epot= -6.21693e+04 Fmax= 1.92062e+02, atom= 4937\n", + "Step= 865, Dmax= 2.3e-02 nm, Epot= -6.21719e+04 Fmax= 2.03022e+02, atom= 4937\n", + "Step= 867, Dmax= 1.4e-02 nm, Epot= -6.21768e+04 Fmax= 4.63918e+01, atom= 4938\n", + "Step= 868, Dmax= 1.6e-02 nm, Epot= -6.21792e+04 Fmax= 2.57323e+02, atom= 4232\n", + "Step= 869, Dmax= 2.0e-02 nm, Epot= -6.21849e+04 Fmax= 1.05312e+02, atom= 4232\n", + "Step= 871, Dmax= 1.2e-02 nm, Epot= -6.21875e+04 Fmax= 9.94924e+01, atom= 4937\n", + "Step= 872, Dmax= 1.4e-02 nm, Epot= -6.21893e+04 Fmax= 1.43631e+02, atom= 4937\n", + "Step= 873, Dmax= 1.7e-02 nm, Epot= -6.21916e+04 Fmax= 1.52428e+02, atom= 4937\n", + "Step= 874, Dmax= 2.0e-02 nm, Epot= -6.21925e+04 Fmax= 2.03846e+02, atom= 4937\n", + "Step= 875, Dmax= 2.4e-02 nm, Epot= -6.21947e+04 Fmax= 2.19780e+02, atom= 4937\n", + "Step= 877, Dmax= 1.5e-02 nm, Epot= -6.22001e+04 Fmax= 4.90004e+01, atom= 4938\n", + "Step= 878, Dmax= 1.8e-02 nm, Epot= -6.22015e+04 Fmax= 2.84363e+02, atom= 4938\n", + "Step= 879, Dmax= 2.1e-02 nm, Epot= -6.22080e+04 Fmax= 1.09517e+02, atom= 4232\n", + "Step= 881, Dmax= 1.3e-02 nm, Epot= -6.22105e+04 Fmax= 1.08670e+02, atom= 4937\n", + "Step= 882, Dmax= 1.5e-02 nm, Epot= -6.22121e+04 Fmax= 1.53289e+02, atom= 4937\n", + "Step= 883, Dmax= 1.8e-02 nm, Epot= -6.22145e+04 Fmax= 1.64962e+02, atom= 4937\n", + "Step= 884, Dmax= 2.2e-02 nm, Epot= -6.22149e+04 Fmax= 2.18569e+02, atom= 4937\n", + "Step= 885, Dmax= 2.6e-02 nm, Epot= -6.22171e+04 Fmax= 2.36531e+02, atom= 4937\n", + "Step= 887, Dmax= 1.6e-02 nm, Epot= -6.22231e+04 Fmax= 5.39146e+01, atom= 4938\n", + "Step= 888, Dmax= 1.9e-02 nm, Epot= -6.22235e+04 Fmax= 3.07840e+02, atom= 4938\n", + "Step= 889, Dmax= 2.3e-02 nm, Epot= -6.22306e+04 Fmax= 1.17751e+02, atom= 4232\n", + "Step= 891, Dmax= 1.4e-02 nm, Epot= -6.22331e+04 Fmax= 1.15136e+02, atom= 4937\n", + "Step= 892, Dmax= 1.6e-02 nm, Epot= -6.22345e+04 Fmax= 1.65697e+02, atom= 4937\n", + "Step= 893, Dmax= 2.0e-02 nm, Epot= -6.22368e+04 Fmax= 1.75996e+02, atom= 4937\n", + "Step= 894, Dmax= 2.3e-02 nm, Epot= -6.22368e+04 Fmax= 2.36080e+02, atom= 4937\n", + "Step= 895, Dmax= 2.8e-02 nm, Epot= -6.22392e+04 Fmax= 2.52428e+02, atom= 4937\n", + "Step= 897, Dmax= 1.7e-02 nm, Epot= -6.22458e+04 Fmax= 6.01755e+01, atom= 4938\n", + "Step= 899, Dmax= 1.0e-02 nm, Epot= -6.22484e+04 Fmax= 1.10379e+02, atom= 4937\n", + "Step= 900, Dmax= 1.2e-02 nm, Epot= -6.22507e+04 Fmax= 1.04268e+02, atom= 4937\n", + "Step= 901, Dmax= 1.5e-02 nm, Epot= -6.22525e+04 Fmax= 1.54957e+02, atom= 4937\n", + "Step= 902, Dmax= 1.7e-02 nm, Epot= -6.22546e+04 Fmax= 1.55216e+02, atom= 4937\n", + "Step= 903, Dmax= 2.1e-02 nm, Epot= -6.22555e+04 Fmax= 2.14527e+02, atom= 4937\n", + "Step= 904, Dmax= 2.5e-02 nm, Epot= -6.22567e+04 Fmax= 2.33947e+02, atom= 4937\n", + "Step= 905, Dmax= 3.0e-02 nm, Epot= -6.22571e+04 Fmax= 2.94030e+02, atom= 4937\n", + "Step= 907, Dmax= 1.8e-02 nm, Epot= -6.22658e+04 Fmax= 5.29294e+01, atom= 4938\n", + "Step= 908, Dmax= 2.2e-02 nm, Epot= -6.22661e+04 Fmax= 3.67976e+02, atom= 4938\n", + "Step= 909, Dmax= 2.6e-02 nm, Epot= -6.22742e+04 Fmax= 1.31871e+02, atom= 4232\n", + "Step= 911, Dmax= 1.6e-02 nm, Epot= -6.22766e+04 Fmax= 1.29504e+02, atom= 4937\n", + "Step= 912, Dmax= 1.9e-02 nm, Epot= -6.22773e+04 Fmax= 1.94701e+02, atom= 4937\n", + "Step= 913, Dmax= 2.3e-02 nm, Epot= -6.22799e+04 Fmax= 1.98946e+02, atom= 4937\n", + "Step= 915, Dmax= 1.4e-02 nm, Epot= -6.22847e+04 Fmax= 4.96305e+01, atom= 4232\n", + "Step= 916, Dmax= 1.6e-02 nm, Epot= -6.22864e+04 Fmax= 2.57197e+02, atom= 4232\n", + "Step= 917, Dmax= 1.9e-02 nm, Epot= -6.22921e+04 Fmax= 1.04687e+02, atom= 4232\n", + "Step= 919, Dmax= 1.2e-02 nm, Epot= -6.22946e+04 Fmax= 9.76861e+01, atom= 4937\n", + "Step= 920, Dmax= 1.4e-02 nm, Epot= -6.22963e+04 Fmax= 1.44921e+02, atom= 4937\n", + "Step= 921, Dmax= 1.7e-02 nm, Epot= -6.22986e+04 Fmax= 1.50378e+02, atom= 4937\n", + "Step= 922, Dmax= 2.0e-02 nm, Epot= -6.22993e+04 Fmax= 2.05034e+02, atom= 4937\n", + "Step= 923, Dmax= 2.4e-02 nm, Epot= -6.23016e+04 Fmax= 2.17295e+02, atom= 4937\n", + "Step= 925, Dmax= 1.5e-02 nm, Epot= -6.23069e+04 Fmax= 5.08132e+01, atom= 4938\n", + "Step= 926, Dmax= 1.7e-02 nm, Epot= -6.23079e+04 Fmax= 2.83090e+02, atom= 4232\n", + "Step= 927, Dmax= 2.1e-02 nm, Epot= -6.23144e+04 Fmax= 1.09743e+02, atom= 4232\n", + "Step= 929, Dmax= 1.3e-02 nm, Epot= -6.23168e+04 Fmax= 1.06751e+02, atom= 4937\n", + "Step= 930, Dmax= 1.5e-02 nm, Epot= -6.23184e+04 Fmax= 1.54097e+02, atom= 4937\n", + "Step= 931, Dmax= 1.8e-02 nm, Epot= -6.23207e+04 Fmax= 1.63148e+02, atom= 4937\n", + "Step= 932, Dmax= 2.2e-02 nm, Epot= -6.23211e+04 Fmax= 2.18825e+02, atom= 4937\n", + "Step= 933, Dmax= 2.6e-02 nm, Epot= -6.23234e+04 Fmax= 2.35013e+02, atom= 4937\n", + "Step= 935, Dmax= 1.6e-02 nm, Epot= -6.23294e+04 Fmax= 5.38731e+01, atom= 4938\n", + "Step= 936, Dmax= 1.9e-02 nm, Epot= -6.23296e+04 Fmax= 3.05935e+02, atom= 4938\n", + "Step= 937, Dmax= 2.3e-02 nm, Epot= -6.23368e+04 Fmax= 1.17233e+02, atom= 4232\n", + "Step= 939, Dmax= 1.4e-02 nm, Epot= -6.23394e+04 Fmax= 1.15950e+02, atom= 4937\n", + "Step= 940, Dmax= 1.6e-02 nm, Epot= -6.23408e+04 Fmax= 1.63323e+02, atom= 4937\n", + "Step= 941, Dmax= 1.9e-02 nm, Epot= -6.23431e+04 Fmax= 1.77603e+02, atom= 4937\n", + "Step= 942, Dmax= 2.3e-02 nm, Epot= -6.23434e+04 Fmax= 2.32006e+02, atom= 4937\n", + "Step= 943, Dmax= 2.8e-02 nm, Epot= -6.23454e+04 Fmax= 2.55754e+02, atom= 4937\n", + "Step= 945, Dmax= 1.7e-02 nm, Epot= -6.23523e+04 Fmax= 5.46636e+01, atom= 4938\n", + "Step= 947, Dmax= 1.0e-02 nm, Epot= -6.23551e+04 Fmax= 1.16453e+02, atom= 4937\n", + "Step= 948, Dmax= 1.2e-02 nm, Epot= -6.23577e+04 Fmax= 9.75498e+01, atom= 4937\n", + "Step= 949, Dmax= 1.5e-02 nm, Epot= -6.23594e+04 Fmax= 1.61479e+02, atom= 4937\n", + "Step= 950, Dmax= 1.7e-02 nm, Epot= -6.23620e+04 Fmax= 1.46492e+02, atom= 4937\n", + "Step= 951, Dmax= 2.1e-02 nm, Epot= -6.23628e+04 Fmax= 2.23226e+02, atom= 4937\n", + "Step= 952, Dmax= 2.5e-02 nm, Epot= -6.23647e+04 Fmax= 2.21822e+02, atom= 4937\n", + "Step= 954, Dmax= 1.5e-02 nm, Epot= -6.23709e+04 Fmax= 3.62247e+01, atom= 4937\n", + "Step= 955, Dmax= 1.8e-02 nm, Epot= -6.23769e+04 Fmax= 2.36117e+02, atom= 4937\n", + "Step= 956, Dmax= 2.2e-02 nm, Epot= -6.23821e+04 Fmax= 1.31344e+02, atom= 4937\n", + "Step= 958, Dmax= 1.3e-02 nm, Epot= -6.23848e+04 Fmax= 1.01966e+02, atom= 4937\n", + "Step= 959, Dmax= 1.6e-02 nm, Epot= -6.23866e+04 Fmax= 1.73325e+02, atom= 4937\n", + "Step= 960, Dmax= 1.9e-02 nm, Epot= -6.23892e+04 Fmax= 1.58116e+02, atom= 4937\n", + "Step= 961, Dmax= 2.2e-02 nm, Epot= -6.23898e+04 Fmax= 2.38437e+02, atom= 4937\n", + "Step= 962, Dmax= 2.7e-02 nm, Epot= -6.23918e+04 Fmax= 2.37452e+02, atom= 4937\n", + "Step= 964, Dmax= 1.6e-02 nm, Epot= -6.23984e+04 Fmax= 3.79664e+01, atom= 4937\n", + "Step= 965, Dmax= 1.9e-02 nm, Epot= -6.24038e+04 Fmax= 2.57519e+02, atom= 4937\n", + "Step= 966, Dmax= 2.3e-02 nm, Epot= -6.24099e+04 Fmax= 1.38387e+02, atom= 4937\n", + "Step= 968, Dmax= 1.4e-02 nm, Epot= -6.24127e+04 Fmax= 1.11199e+02, atom= 4937\n", + "Step= 969, Dmax= 1.7e-02 nm, Epot= -6.24143e+04 Fmax= 1.84605e+02, atom= 4937\n", + "Step= 970, Dmax= 2.0e-02 nm, Epot= -6.24169e+04 Fmax= 1.70377e+02, atom= 4937\n", + "Step= 971, Dmax= 2.4e-02 nm, Epot= -6.24173e+04 Fmax= 2.55060e+02, atom= 4937\n", + "Step= 972, Dmax= 2.9e-02 nm, Epot= -6.24192e+04 Fmax= 2.54829e+02, atom= 4937\n", + "Step= 974, Dmax= 1.7e-02 nm, Epot= -6.24265e+04 Fmax= 3.89337e+01, atom= 4937\n", + "Step= 975, Dmax= 2.1e-02 nm, Epot= -6.24311e+04 Fmax= 2.82097e+02, atom= 4937\n", + "Step= 976, Dmax= 2.5e-02 nm, Epot= -6.24384e+04 Fmax= 1.42949e+02, atom= 4937\n", + "Step= 978, Dmax= 1.5e-02 nm, Epot= -6.24412e+04 Fmax= 1.25817e+02, atom= 4937\n", + "Step= 979, Dmax= 1.8e-02 nm, Epot= -6.24426e+04 Fmax= 1.90537e+02, atom= 4937\n", + "Step= 980, Dmax= 2.2e-02 nm, Epot= -6.24449e+04 Fmax= 1.90014e+02, atom= 4937\n", + "Step= 981, Dmax= 2.6e-02 nm, Epot= -6.24452e+04 Fmax= 2.65050e+02, atom= 4937\n", + "Step= 982, Dmax= 3.1e-02 nm, Epot= -6.24462e+04 Fmax= 2.81059e+02, atom= 4937\n", + "Step= 984, Dmax= 1.9e-02 nm, Epot= -6.24552e+04 Fmax= 3.23257e+01, atom= 4937\n", + "Step= 985, Dmax= 2.2e-02 nm, Epot= -6.24587e+04 Fmax= 3.07773e+02, atom= 4937\n", + "Step= 986, Dmax= 2.7e-02 nm, Epot= -6.24693e+04 Fmax= 1.49570e+02, atom= 4937\n", + "Step= 988, Dmax= 1.6e-02 nm, Epot= -6.24721e+04 Fmax= 1.44218e+02, atom= 4937\n", + "Step= 989, Dmax= 1.9e-02 nm, Epot= -6.24728e+04 Fmax= 1.93622e+02, atom= 4937\n", + "Step= 990, Dmax= 2.3e-02 nm, Epot= -6.24739e+04 Fmax= 2.15334e+02, atom= 4937\n", + "Step= 992, Dmax= 1.4e-02 nm, Epot= -6.24818e+04 Fmax= 3.12608e+01, atom= 4100\n", + "Step= 993, Dmax= 1.7e-02 nm, Epot= -6.24872e+04 Fmax= 2.83895e+02, atom= 4100\n", + "Step= 994, Dmax= 2.0e-02 nm, Epot= -6.24945e+04 Fmax= 8.68751e+01, atom= 4100\n", + "Step= 996, Dmax= 1.2e-02 nm, Epot= -6.24970e+04 Fmax= 1.27709e+02, atom= 4100\n", + "Step= 997, Dmax= 1.4e-02 nm, Epot= -6.24995e+04 Fmax= 1.28375e+02, atom= 4100\n", + "Step= 998, Dmax= 1.7e-02 nm, Epot= -6.25014e+04 Fmax= 1.81174e+02, atom= 4100\n", + "Step= 999, Dmax= 2.1e-02 nm, Epot= -6.25038e+04 Fmax= 1.87428e+02, atom= 4100\n", + "Step= 1000, Dmax= 2.5e-02 nm, Epot= -6.25048e+04 Fmax= 2.56882e+02, atom= 4100\n", + "\n", + "Energy minimization reached the maximum number of steps before the forces\n", + "reached the requested precision Fmax < 10.\n", + "\n", + "writing lowest energy coordinates.\n", + "\n", + "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n", + "Potential Energy = -6.2504758e+04\n", + "Maximum force = 2.5688226e+02 on atom 4100\n", + "Norm of force = 5.8315262e+00\n", + "\n", + "GROMACS reminds you: \"Furious activity is no substitute for understanding.\" (H.H. Williams)\n", + "\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top\n", + "\n", + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", + "\n", + "GROMACS reminds you: \"Way to Go Dude\" (Beavis and Butthead)\n", + "\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] All files set up for a run time of 1000 ps (dt=0.01, nsteps=100000)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to 936892543\n", + "\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", + "\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", + "\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", + "\n", + "Calculated rlist for 1x1 atom pair-list as 1.125 nm, buffer size 0.025 nm\n", + "\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.100 nm, buffer size 0.000 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 3 Mb of data\n" + ] + }, + { + "data": { + "text/plain": [ + "{'struct': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro',\n", + " 'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top',\n", + " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx',\n", + " 'qscript': ['./local.sh'],\n", + " 'mainselection': None,\n", + " 'deffnm': 'md',\n", + " 'includes': ['/home/awsm/MDPOW/mdpow/top',\n", + " '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top']}" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from mdpow.equil import OctanolSimulation\n", + "\n", + "oct_sim = OctanolSimulation(\n", + " molecule=\"BENZ\",\n", + " ff_class=MARTINI,\n", + " mdp={\n", + " \"energy_minimize\": str(EM_FILE.absolute()),\n", + " \"MD_relaxed\": str(EQ_FILE.absolute()),\n", + " \"MD_NPT\": str(EQ_FILE.absolute()),\n", + " \"MD_restrained\": str(RUN_FILE.absolute()),\n", + " },\n", + " distance=4.0,\n", + ")\n", + "oct_sim.topology(str(BENZENE_ITP))\n", + "oct_sim.solvate(struct=MARTINI_BENZENE, maxwarn=1)\n", + "oct_sim.energy_minimize(maxwarn=1)\n", + "oct_sim.MD_relaxed(runtime=1e3, dt=0.01)" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 10 to 50, rlist from 1.1 to 1.233\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the GPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "100000 steps, 1000.0 ps.\n", + "\n", + "Step 0 Warning: pressure scaling more than 1%, mu: 0.972666 0.972666 0.972666\n", + "step 99900, remaining wall clock time: 0 s \n", + "Writing final coordinates.\n", + "step 100000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 316.146 79.037 400.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 1093.175 0.022\n", + "\n", + "GROMACS reminds you: \"Why Do *You* Use Constraints ?\" (H.J.C. Berendsen)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + }, + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "r = gromacs.run.MDrunner(\n", + " dirname=oct_sim.dirs[\"MD_relaxed\"],\n", + " deffnm=\"md\",\n", + " c=\"md.pdb\",\n", + " cpi=True,\n", + " v=True,\n", + ")\n", + "r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.equil : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro').\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 't']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt'}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt'}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", " :-) GROMACS - gmx grompp, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", @@ -6062,7 +6337,7 @@ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "Last frame -1 time 1000.000 \n", "\n", - "GROMACS reminds you: \"I was told I'd never make it to VP rank because I was too outspoken. Maybe so, but I think men will always find an excuse for keeping women in their 'place.' So, let's make that place the executive suite and start more of our own companies.\" (Jean Bartik, ENIAC developer)\n", + "GROMACS reminds you: \"Why Do *You* Use Constraints ?\" (H.J.C. Berendsen)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -6087,7 +6362,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -989987098\n", + "Setting the LD random seed to -1163133461\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -6097,9 +6372,9 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.168 nm, buffer size 0.068 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.167 nm, buffer size 0.067 nm\n", "\n", - "Set rlist, assuming 4x4 atom pair-list, to 1.109 nm, buffer size 0.009 nm\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.108 nm, buffer size 0.008 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", @@ -6119,7 +6394,7 @@ "output_type": "stream", "text": [ "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 10 to 25, rlist from 1.108 to 1.223\n", + "Changing nstlist from 10 to 25, rlist from 1.108 to 1.222\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -6131,15 +6406,15 @@ "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", "500000 steps, 10000.0 ps.\n", - "step 499900, remaining wall clock time: 0 s \n", + "step 499900, remaining wall clock time: 0 s ll finish Mon Sep 4 21:46:53 202388600, will finish Mon Sep 4 21:46:52 2023248000, remaining wall clock time: 219 s 370400, remaining wall clock time: 113 s , remaining wall clock time: 9 s \n", "Writing final coordinates.\n", "step 500000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 1247.510 311.878 400.0\n", + " Time: 1881.626 470.407 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2770.319 0.009\n", + "Performance: 1836.712 0.013\n", "\n", - "GROMACS reminds you: \"Garbage Collecting...\" (GNU Emacs)\n", + "GROMACS reminds you: \"These are Ideas, They are Not Lies\" (Magnapop)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n" ] @@ -6150,14 +6425,14 @@ "0" ] }, - "execution_count": 18, + "execution_count": 21, "metadata": {}, "output_type": "execute_result" } ], "source": [ "oct_sim.MD(\n", - " runtime=10e3, qscript=[\"local.sh\"], dt=0.02\n", + " runtime=1e4, qscript=[\"local.sh\"], dt=0.02\n", ")\n", "\n", "r = gromacs.run.MDrunner(\n", @@ -6168,7 +6443,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 22, "metadata": {}, "outputs": [ { @@ -6181,259 +6456,10 @@ "mdpow.fep : INFO Using setup directories under 'FEP/octanol': {'coulomb': 'FEP/octanol/Coulomb', 'vdw': 'FEP/octanol/VDW'}\n", "mdpow.fep : INFO Default checkpoint file is '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep'\n", "mdpow.fep : INFO Preparing coulomb for lambda=0\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000' (newly created)...\n", - "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", - "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", - "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", - "{'pp': 'processed.top', 'maxwarn': 1}\n", - "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", - "{'pp': 'processed.top', 'maxwarn': 1}\n", - " warnings.warn(wmsg, category=UsageWarning)\n", - " :-) GROMACS - gmx grompp, 2023.2 (-:\n", - "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000\n", - "Command line:\n", - " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", - "\n", - "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", - "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", - "\n", - "NOTE 1 [file md.mdp, line 109]:\n", - " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", - "\n", - "\n", - "\n", - "NOTE 2 [file md.mdp]:\n", - " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", - " implicitly. See the documentation for more information on which\n", - " parameters affect temperature for sd.\n", - "\n", - "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", - "WARNING 1 [file md.mdp]:\n", - " You are generating velocities so I am assuming you are equilibrating a\n", - " system. You are using Parrinello-Rahman pressure coupling, but this can\n", - " be unstable for equilibration. If your system crashes, try equilibrating\n", - " first with Berendsen pressure coupling. If you are not equilibrating the\n", - " system, you can probably ignore this warning.\n", - "\n", - "Number of degrees of freedom in T-Coupling group System is 15339.00\n", - "\n", - "There were 3 NOTEs\n", - "\n", - "There was 1 WARNING\n", - "\n", - "GROMACS reminds you: \"I had trouble with physics in college. When I signed up I thought it said psychics.\" (Greg Tamblyn)\n", - "\n", - "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", - "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", - "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing coulomb for lambda=0.25\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250' (newly created)...\n", - "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", - "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", - "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", - "{'pp': 'processed.top', 'maxwarn': 1}\n", - "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", - "{'pp': 'processed.top', 'maxwarn': 1}\n", - " warnings.warn(wmsg, category=UsageWarning)\n", - " :-) GROMACS - gmx grompp, 2023.2 (-:\n", - "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250\n", - "Command line:\n", - " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", - "\n", - "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", - "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", - "\n", - "NOTE 1 [file md.mdp, line 109]:\n", - " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", - "\n", - "\n", - "\n", - "NOTE 2 [file md.mdp]:\n", - " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", - " implicitly. See the documentation for more information on which\n", - " parameters affect temperature for sd.\n", - "\n", - "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", - "WARNING 1 [file md.mdp]:\n", - " You are generating velocities so I am assuming you are equilibrating a\n", - " system. You are using Parrinello-Rahman pressure coupling, but this can\n", - " be unstable for equilibration. If your system crashes, try equilibrating\n", - " first with Berendsen pressure coupling. If you are not equilibrating the\n", - " system, you can probably ignore this warning.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Setting the LD random seed to -1610694785\n", - "\n", - "Generated 844 of the 356590 non-bonded parameter combinations\n", - "\n", - "Excluding 1 bonded neighbours molecule type 'BENZ'\n", - "\n", - "Excluding 1 bonded neighbours molecule type 'OCO'\n", - "\n", - "Coupling 1 copies of molecule type 'BENZ'\n", - "\n", - "Velocities were taken from a Maxwell distribution at 300 K\n", - "\n", - "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", - "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", - "\n", - "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", - "\n", - "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", - "\n", - "This run will generate roughly 8 Mb of data\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Number of degrees of freedom in T-Coupling group System is 15339.00\n", - "\n", - "There were 3 NOTEs\n", - "\n", - "There was 1 WARNING\n", - "\n", - "GROMACS reminds you: \"Your theory is crazy, but it's not crazy enough to be true.\" (Niels Bohr)\n", - "\n", - "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", - "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", - "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing coulomb for lambda=0.5\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500' (newly created)...\n", - "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", - "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", - "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", - "{'pp': 'processed.top', 'maxwarn': 1}\n", - "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", - "{'pp': 'processed.top', 'maxwarn': 1}\n", - " warnings.warn(wmsg, category=UsageWarning)\n", - " :-) GROMACS - gmx grompp, 2023.2 (-:\n", - "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500\n", - "Command line:\n", - " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", - "\n", - "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", - "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", - "\n", - "NOTE 1 [file md.mdp, line 109]:\n", - " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", - "\n", - "\n", - "\n", - "NOTE 2 [file md.mdp]:\n", - " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", - " implicitly. See the documentation for more information on which\n", - " parameters affect temperature for sd.\n", - "\n", - "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", - "WARNING 1 [file md.mdp]:\n", - " You are generating velocities so I am assuming you are equilibrating a\n", - " system. You are using Parrinello-Rahman pressure coupling, but this can\n", - " be unstable for equilibration. If your system crashes, try equilibrating\n", - " first with Berendsen pressure coupling. If you are not equilibrating the\n", - " system, you can probably ignore this warning.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Setting the LD random seed to -102842532\n", - "\n", - "Generated 844 of the 356590 non-bonded parameter combinations\n", - "\n", - "Excluding 1 bonded neighbours molecule type 'BENZ'\n", - "\n", - "Excluding 1 bonded neighbours molecule type 'OCO'\n", - "\n", - "Coupling 1 copies of molecule type 'BENZ'\n", - "\n", - "Velocities were taken from a Maxwell distribution at 300 K\n", - "\n", - "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", - "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", - "\n", - "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", - "\n", - "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", - "\n", - "This run will generate roughly 8 Mb of data\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Number of degrees of freedom in T-Coupling group System is 15339.00\n", - "\n", - "There were 3 NOTEs\n", - "\n", - "There was 1 WARNING\n", - "\n", - "GROMACS reminds you: \"Your theory is crazy, but it's not crazy enough to be true.\" (Niels Bohr)\n", - "\n", - "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", - "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", - "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing coulomb for lambda=0.75\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750' (newly created)...\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6445,7 +6471,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -6463,71 +6489,34 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Setting the LD random seed to -16979715\n", - "\n", - "Generated 844 of the 356590 non-bonded parameter combinations\n", - "\n", - "Excluding 1 bonded neighbours molecule type 'BENZ'\n", "\n", - "Excluding 1 bonded neighbours molecule type 'OCO'\n", - "\n", - "Coupling 1 copies of molecule type 'BENZ'\n", - "\n", - "Velocities were taken from a Maxwell distribution at 300 K\n", - "\n", - "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", - "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", - "\n", - "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", - "\n", - "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", - "\n", - "This run will generate roughly 8 Mb of data\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"But I always say, one's company, two's a crowd, and three's a party.\" (Andy Warhol)\n", + "GROMACS reminds you: \"Hey Man You Know, I'm Really OK\" (Offspring)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing coulomb for lambda=1\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.25\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6539,7 +6528,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -6557,10 +6546,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -6574,7 +6559,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -322961413\n", + "Setting the LD random seed to 1006616575\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -6588,13 +6573,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -6603,28 +6588,26 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"No matter how important you are, you are not as important as lunch.\" (Randy Pausch)\n", + "GROMACS reminds you: \"Contemplating answers that could break my bonds.\" (Peter Hammill)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", - "mdpow.fep : INFO [coulomb] Wrote array job scripts [None]\n", - "mdpow.fep : INFO Preparing vdw for lambda=0\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000' (newly created)...\n", - "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.5\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", "{'pp': 'processed.top', 'maxwarn': 1}\n", @@ -6635,7 +6618,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -6653,10 +6636,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -6670,7 +6649,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -176234568\n", + "Setting the LD random seed to 1409249663\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -6684,13 +6663,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -6699,26 +6678,26 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"No matter how important you are, you are not as important as lunch.\" (Randy Pausch)\n", + "GROMACS reminds you: \"Contemplating answers that could break my bonds.\" (Peter Hammill)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.05\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050' (newly created)...\n", - "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=0.75\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", "{'pp': 'processed.top', 'maxwarn': 1}\n", @@ -6729,7 +6708,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -6747,10 +6726,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -6764,9 +6739,9 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1878318079\n", + "Setting the LD random seed to -271363881\n", "\n", - "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", "Excluding 1 bonded neighbours molecule type 'BENZ'\n", "\n", @@ -6778,13 +6753,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -6793,26 +6768,26 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Numbers have life; they’re not just symbols on paper.\" (Shakuntala Devi)\n", + "GROMACS reminds you: \"A computer once beat me at chess, but it was no match for me at kick boxing.\" (Emo Philips)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.1\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100' (newly created)...\n", - "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing coulomb for lambda=1\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", "{'pp': 'processed.top', 'maxwarn': 1}\n", @@ -6823,7 +6798,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -6841,10 +6816,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -6858,9 +6829,9 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1209184641\n", + "Setting the LD random seed to -939803669\n", "\n", - "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", "Excluding 1 bonded neighbours molecule type 'BENZ'\n", "\n", @@ -6872,13 +6843,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -6887,25 +6858,27 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Numbers have life; they’re not just symbols on paper.\" (Shakuntala Devi)\n", + "GROMACS reminds you: \"My Brothers are Protons (Protons!), My Sisters are Neurons (Neurons)\" (Gogol Bordello)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.2\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", + "mdpow.fep : INFO [coulomb] Wrote array job scripts [None]\n", + "mdpow.fep : INFO Preparing vdw for lambda=0\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6917,7 +6890,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -6935,10 +6908,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -6952,9 +6921,9 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -589374473\n", + "Setting the LD random seed to -1611204865\n", "\n", - "Generated 1689 of the 357435 non-bonded parameter combinations\n", + "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", "Excluding 1 bonded neighbours molecule type 'BENZ'\n", "\n", @@ -6966,13 +6935,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -6981,25 +6950,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"All Work and No Play Makes Jack a Dull Boy\" (The Shining)\n", + "GROMACS reminds you: \"My Brothers are Protons (Protons!), My Sisters are Neurons (Neurons)\" (Gogol Bordello)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.3\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.05\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7011,7 +6980,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7029,10 +6998,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7046,7 +7011,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -187252737\n", + "Setting the LD random seed to 800586729\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7060,13 +7025,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -7075,25 +7040,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"All Work and No Play Makes Jack a Dull Boy\" (The Shining)\n", + "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.4\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.1\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7105,7 +7070,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7123,10 +7088,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7140,7 +7101,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 331345371\n", + "Setting the LD random seed to -1243615521\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7154,13 +7115,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -7169,25 +7130,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"It is a cute toxin.\" (Rebecca Howard)\n", + "GROMACS reminds you: \"Royale With Cheese\" (Pulp Fiction)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.5\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.2\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7199,7 +7160,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7217,10 +7178,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7234,7 +7191,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 2006891771\n", + "Setting the LD random seed to -784465921\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7248,13 +7205,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -7263,25 +7220,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"It is a cute toxin.\" (Rebecca Howard)\n", + "GROMACS reminds you: \"Royale With Cheese\" (Pulp Fiction)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.6\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.3\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7293,7 +7250,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7311,10 +7268,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7328,7 +7281,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1110644929\n", + "Setting the LD random seed to -33784117\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7342,13 +7295,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -7357,25 +7310,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"It's So Fast It's Slow\" (F. Black)\n", + "GROMACS reminds you: \"Science is a way of thinking much more than it is a body of knowledge.\" (Carl Sagan)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.65\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.4\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7387,7 +7340,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7405,10 +7358,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7422,7 +7371,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -9461789\n", + "Setting the LD random seed to 1609039455\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7436,13 +7385,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -7451,25 +7400,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"It's So Fast It's Slow\" (F. Black)\n", + "GROMACS reminds you: \"Science is a way of thinking much more than it is a body of knowledge.\" (Carl Sagan)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.7\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.5\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7481,7 +7430,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7499,10 +7448,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7516,7 +7461,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -297900070\n", + "Setting the LD random seed to 1609899597\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7530,13 +7475,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -7545,25 +7490,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"It takes money to make money, they say\" (Lou Reed)\n", + "GROMACS reminds you: \"I think everybody should like everybody.\" (Andy Warhol)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.75\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.6\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7575,7 +7520,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7593,10 +7538,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7610,7 +7551,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1093150214\n", + "Setting the LD random seed to -1077948441\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7624,13 +7565,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -7639,25 +7580,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"It takes money to make money, they say\" (Lou Reed)\n", + "GROMACS reminds you: \"It Doesn't Have to Be Tip Top\" (Pulp Fiction)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.8\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.65\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7669,7 +7610,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7687,10 +7628,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7704,7 +7641,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -24248510\n", + "Setting the LD random seed to -14691763\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7718,13 +7655,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -7733,25 +7670,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Kissing You is Like Kissing Gravel\" (Throwing Muses)\n", + "GROMACS reminds you: \"It Doesn't Have to Be Tip Top\" (Pulp Fiction)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.85\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.7\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7763,7 +7700,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7781,10 +7718,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7798,7 +7731,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1256396671\n", + "Setting the LD random seed to 2096885113\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7812,13 +7745,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -7827,25 +7760,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Kissing You is Like Kissing Gravel\" (Throwing Muses)\n", + "GROMACS reminds you: \"I never see what has been done; I only see what remains to be done.\" (Marie Curie)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.9\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.75\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7857,7 +7790,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7875,10 +7808,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7892,7 +7821,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -6310919\n", + "Setting the LD random seed to 1864226270\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7906,13 +7835,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -7921,25 +7850,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Some of these pro-drug messages come from popular culture.\" (John Walters)\n", + "GROMACS reminds you: \"I never see what has been done; I only see what remains to be done.\" (Marie Curie)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=0.95\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.8\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7951,7 +7880,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -7969,10 +7898,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -7986,7 +7911,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1208987793\n", + "Setting the LD random seed to -10538113\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -8000,13 +7925,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -8015,25 +7940,25 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Some of these pro-drug messages come from popular culture.\" (John Walters)\n", + "GROMACS reminds you: \"Royale With Cheese\" (Pulp Fiction)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "mdpow.fep : INFO Preparing vdw for lambda=1\n", - "mdpow.fep : INFO Setting dhdl file to xvg format\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] Setting up MD...\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000' (newly created)...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.85\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -8045,7 +7970,7 @@ "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850\n", "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", @@ -8063,10 +7988,6 @@ " parameters affect temperature for sd.\n", "\n", "\n", - "NOTE 3 [file md.mdp]:\n", - " Setting nstcalcenergy (100) equal to nstdhdl (10)\n", - "\n", - "\n", "WARNING 1 [file md.mdp]:\n", " You are generating velocities so I am assuming you are equilibrating a\n", " system. You are using Parrinello-Rahman pressure coupling, but this can\n", @@ -8080,7 +8001,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -35661570\n", + "Setting the LD random seed to -394711249\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -8094,13 +8015,13 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, { @@ -8109,31 +8030,68 @@ "text": [ "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "There were 3 NOTEs\n", + "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Science and everyday life cannot and should not be separated.\" (Rosalind Franklin)\n", + "GROMACS reminds you: \"No great discovery was ever made without a bold guess.\" (Marie Curie)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", "gromacs.cbook: INFO edited txt = './local.sh'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output mdp = 'md.mdp'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output tpr = 'md.tpr'\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output runscripts = ['./local.sh']\n", - "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", - "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", - "mdpow.fep : INFO [vdw] Wrote array job scripts [None]\n", - "mdpow.fep : INFO Saved state information to '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep'; reload later with G = Goct(filename='/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep').\n", - "mdpow.fep : INFO Finished setting up all individual simulations. Now run them...\n" + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.9\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900\n", + "Command line:\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", + "\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", + "\n", + "\n", + "\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", + "\n", + "\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -109805585\n", + "Setting the LD random seed to -536871077\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -8147,435 +8105,305 @@ "\n", "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "Calculated rlist for 1x1 atom pair-list as 1.291 nm, buffer size 0.191 nm\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "This run will generate roughly 8 Mb of data\n" + "This run will generate roughly 6 Mb of data\n" ] }, - { - "data": { - "text/plain": [ - "{'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top',\n", - " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx',\n", - " 'qscript': ['./local.sh'],\n", - " 'mainselection': None,\n", - " 'deffnm': 'md',\n", - " 'includes': ['/home/awsm/MDPOW/mdpow/top'],\n", - " 'maxwarn': 1,\n", - " 'couple-intramol': 'no',\n", - " 'couple_lambda0': 'vdw',\n", - " 'couple_lambda1': 'none',\n", - " 'sc_alpha': 0.5,\n", - " 'sc_power': 1,\n", - " 'sc_sigma': 0.3,\n", - " 'separate-dhdl-file': 'yes',\n", - " 'ref_t': 300.0,\n", - " 'gen_temp': 300.0,\n", - " 'free_energy': 'yes',\n", - " 'couple_moltype': 'BENZ',\n", - " 'init_lambda_state': 15,\n", - " 'fep_lambdas': array([0. , 0.05, 0.1 , 0.2 , 0.3 , 0.4 , 0.5 , 0.6 , 0.65, 0.7 , 0.75,\n", - " 0.8 , 0.85, 0.9 , 0.95, 1. ]),\n", - " 'calc_lambda_neighbors': -1}" - ] - }, - "execution_count": 20, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "goct = mdpow.fep.Goct(simulation=oct_sim, runtime=1e+3, mdp=str(RUN_FILE.absolute()))\n", - "goct.setup(dt=0.02, edr=False)" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", - "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000\n", - "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", - "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", - "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 155.428 38.857 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 2223.565 0.011\n", - "\n", - "GROMACS reminds you: \"The greatest shortcoming of the human race is our inability to understand the exponential function.\" (Albert Bartlett)\n", - "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", - "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250\n", - "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + "There were 2 NOTEs\n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 115.908 28.977 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 2981.738 0.008\n", + "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Microsecond Here I Come\" (P.J. Van Maaren)\n", + "GROMACS reminds you: \"No great discovery was ever made without a bold guess.\" (Marie Curie)\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=0.95\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", - "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 147.410 36.853 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 2344.525 0.010\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", "\n", - "GROMACS reminds you: \"I see they found out the universe is 80 million years older than we thought. It's also been lying about its weight.\" (Bill Maher)\n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750\n", - "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s , remaining wall clock time: 15 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 177.267 44.317 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 1949.639 0.012\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1090605057\n", "\n", - "GROMACS reminds you: \"In the processing of models we must be especially cautious of the human weakness to think that models can be verified or validated. Especially one's own.\" (Roald Hoffmann)\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000\n", - "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Coupling 1 copies of molecule type 'BENZ'\n", "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + "Velocities were taken from a Maxwell distribution at 300 K\n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 119.299 29.825 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 2896.969 0.008\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "GROMACS reminds you: \"Here's Another Useful Quote\" (S. Boot)\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000\n", - "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + "There were 2 NOTEs\n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 179.663 44.916 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 1923.637 0.012\n", + "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"The historical meaning of QM/MM: Quanto Mangi, Mamma Mia!\" (Attilio Vittorio Vargiu, at BioExcel 2022 Summer School in Sardinia)\n", + "GROMACS reminds you: \"Yeah, uh uh, Neil's Head !\" (Neil)\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "mdpow.fep : INFO Preparing vdw for lambda=1\n", + "mdpow.fep : INFO Setting dhdl file to edr format\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] Setting up MD...\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", + "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000' (newly created)...\n", + "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", + "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", + "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n", + "{'pp': 'processed.top', 'maxwarn': 1}\n", + " warnings.warn(wmsg, category=UsageWarning)\n", + " :-) GROMACS - gmx grompp, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n", "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + "NOTE 1 [file md.mdp, line 109]:\n", + " Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 190.598 47.650 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 1813.274 0.013\n", "\n", - "GROMACS reminds you: \"I Am a Wonderful Thing\" (Kid Creole)\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "NOTE 2 [file md.mdp]:\n", + " Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n", + " implicitly. See the documentation for more information on which\n", + " parameters affect temperature for sd.\n", "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100\n", - "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "WARNING 1 [file md.mdp]:\n", + " You are generating velocities so I am assuming you are equilibrating a\n", + " system. You are using Parrinello-Rahman pressure coupling, but this can\n", + " be unstable for equilibration. If your system crashes, try equilibrating\n", + " first with Berendsen pressure coupling. If you are not equilibrating the\n", + " system, you can probably ignore this warning.\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -285245490\n", "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 120.687 30.172 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 2863.642 0.008\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", "\n", - "GROMACS reminds you: \"For the first time we can now mechanically simulate the cognitive process. We can make studies in artificial intelligence. Beyond that, this mechanism can be used to assist humans in learning. As we are going to have more mature students in greater numbers as time goes on, this type of teaching will probably be increasingly important.\" (Sister Mary Kenneth Keller)\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "Coupling 1 copies of molecule type 'BENZ'\n", "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200\n", - "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "Velocities were taken from a Maxwell distribution at 300 K\n", "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 125.666 31.417 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 2750.194 0.009\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", "\n", - "GROMACS reminds you: \"Try to calculate the numbers that have been\" (The Smoke Fairies)\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300\n", - "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "There were 2 NOTEs\n", "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "There was 1 WARNING\n", "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + "GROMACS reminds you: \"They don't have any beavers in India, so they have to simulate them\" (The Tubes)\n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 125.003 31.251 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 2764.782 0.009\n", + "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", + "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", + "gromacs.cbook: INFO edited txt = './local.sh'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output mdp = 'md.mdp'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output tpr = 'md.tpr'\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output runscripts = ['./local.sh']\n", + "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n", + "gromacs.qsub: WARNING Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n", + "mdpow.fep : INFO [vdw] Wrote array job scripts [None]\n", + "mdpow.fep : INFO Saved state information to '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep'; reload later with G = Goct(filename='/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep').\n", + "mdpow.fep : INFO Finished setting up all individual simulations. Now run them...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Setting the LD random seed to -1614840594\n", "\n", - "GROMACS reminds you: \"I see they found out the universe is 80 million years older than we thought. It's also been lying about its weight.\" (Bill Maher)\n", + "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", - " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "Excluding 1 bonded neighbours molecule type 'BENZ'\n", "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400\n", - "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "Excluding 1 bonded neighbours molecule type 'OCO'\n", "\n", - "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Coupling 1 copies of molecule type 'BENZ'\n", "\n", - "1 GPU selected for this run.\n", - "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", - " PP:0\n", - "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", - "PP task will update and constrain coordinates on the CPU\n", - "Using 1 MPI thread\n", - "Using 4 OpenMP threads \n", + "Velocities were taken from a Maxwell distribution at 300 K\n", "\n", - "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 124.501 31.125 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 2775.941 0.009\n", + "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n", "\n", - "GROMACS reminds you: \"Well, I am a dilettante. It's only in England that dilettantism is considered a bad thing. In other countries it's called interdisciplinary research.\" (Brian Eno)\n", + "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n", "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n", + "\n", + "Note that mdrun will redetermine rlist based on the actual pair-list setup\n", + "\n", + "This run will generate roughly 6 Mb of data\n" + ] + }, + { + "data": { + "text/plain": [ + "{'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top',\n", + " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx',\n", + " 'qscript': ['./local.sh'],\n", + " 'mainselection': None,\n", + " 'deffnm': 'md',\n", + " 'includes': ['/home/awsm/MDPOW/mdpow/top'],\n", + " 'maxwarn': 1,\n", + " 'couple-intramol': 'no',\n", + " 'couple_lambda0': 'vdw',\n", + " 'couple_lambda1': 'none',\n", + " 'sc_alpha': 0.5,\n", + " 'sc_power': 1,\n", + " 'sc_sigma': 0.3,\n", + " 'separate-dhdl-file': 'no',\n", + " 'ref_t': 300.0,\n", + " 'gen_temp': 300.0,\n", + " 'free_energy': 'yes',\n", + " 'couple_moltype': 'BENZ',\n", + " 'init_lambda_state': 15,\n", + " 'fep_lambdas': array([0. , 0.05, 0.1 , 0.2 , 0.3 , 0.4 , 0.5 , 0.6 , 0.65, 0.7 , 0.75,\n", + " 0.8 , 0.85, 0.9 , 0.95, 1. ]),\n", + " 'calc_lambda_neighbors': -1}" + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "goct = mdpow.fep.Goct(simulation=oct_sim, runtime=1e+3, mdp=str(RUN_FILE.absolute()))\n", + "goct.setup(dt=0.02)" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8591,24 +8419,24 @@ "Writing final coordinates.\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 125.453 31.363 400.0\n", + " Time: 182.577 45.644 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2754.873 0.009\n", + "Performance: 1892.938 0.013\n", "\n", - "GROMACS reminds you: \"Good Music Saves your Soul\" (Lemmy)\n", + "GROMACS reminds you: \"Why, how now, Claudio ! Whence Comes this Restraint ?\" (Lucio in Measure for measure, Act 1, Scene 4, William Shakespeare)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8624,24 +8452,24 @@ "Writing final coordinates.\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 125.507 31.377 400.0\n", + " Time: 250.913 62.728 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2753.682 0.009\n", + "Performance: 1377.395 0.017\n", "\n", - "GROMACS reminds you: \"Your assumptions are your windows on the world. Scrub them off every once in a while, or the light won't come in.\" (Isaac Asimov)\n", + "GROMACS reminds you: \"It Was My Pleasure\" (Pulp Fiction)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8657,24 +8485,24 @@ "Writing final coordinates.\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 127.829 31.957 400.0\n", + " Time: 205.528 51.382 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2703.654 0.009\n", + "Performance: 1681.555 0.014\n", "\n", - "GROMACS reminds you: \"Everybody's Good Enough For Some Change\" (LIVE)\n", + "GROMACS reminds you: \"There are three kinds of men. The one that learns by reading. The few who learn by observation. The rest of them have to pee on the electric fence for themselves.\" (Will Rogers)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8690,24 +8518,24 @@ "Writing final coordinates.\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 131.403 32.851 400.0\n", + " Time: 212.060 53.015 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2630.119 0.009\n", + "Performance: 1629.756 0.015\n", "\n", - "GROMACS reminds you: \"Would You Like to Be the Monster Tonight ?\" (Captain Beefheart)\n", + "GROMACS reminds you: \"A real scientist solves problems, not wails that they are unsolvable.\" (Anne McCaffrey)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8719,28 +8547,28 @@ "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "step 49900, remaining wall clock time: 0 s , remaining wall clock time: 24 s \n", "Writing final coordinates.\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 131.139 32.785 400.0\n", + " Time: 237.020 59.255 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2635.427 0.009\n", + "Performance: 1458.132 0.016\n", "\n", - "GROMACS reminds you: \"GROMACS First : Making MD Great Again\" (Vedran Miletic)\n", + "GROMACS reminds you: \"When doing HPC, don't communica\" (Jim Demmel)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8756,24 +8584,24 @@ "Writing final coordinates.\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 129.744 32.436 400.0\n", + " Time: 250.708 62.677 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2663.753 0.009\n", + "Performance: 1378.522 0.017\n", "\n", - "GROMACS reminds you: \"Erwin with his psi can do / Calculations quite a few. / But one thing has not been seen / Just what psi really mean.\" (Felix Bloch)\n", + "GROMACS reminds you: \"After a few talks we usually sit down to do some work... or drinking.\" (Mike Klein)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8789,24 +8617,24 @@ "Writing final coordinates.\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 130.443 32.611 400.0\n", + " Time: 188.780 47.195 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2649.482 0.009\n", + "Performance: 1830.737 0.013\n", "\n", - "GROMACS reminds you: \"The only place success comes before work is in the dictionary\" (Vince Lombardi)\n", + "GROMACS reminds you: \"Therefore, things must be learned only to be unlearned again or, more likely, to be corrected.\" (Richard Feynman)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8822,24 +8650,24 @@ "Writing final coordinates.\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 130.377 32.594 400.0\n", + " Time: 180.190 45.048 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2650.831 0.009\n", + "Performance: 1918.007 0.013\n", "\n", - "GROMACS reminds you: \"Here are all the 'gmx' tools... but no gmx writethesis\" (Christian Blau)\n", + "GROMACS reminds you: \"I can't help but think the model is ungrateful for all that nice data I gave it. Jerk.\" (Kate Stafford)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8855,24 +8683,24 @@ "Writing final coordinates.\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 136.588 34.147 400.0\n", + " Time: 202.058 50.514 400.0\n", " (ns/day) (hour/ns)\n", - "Performance: 2530.279 0.009\n", + "Performance: 1710.436 0.014\n", "\n", - "GROMACS reminds you: \"I was detained, I was restrained\" (The Smiths)\n", + "GROMACS reminds you: \"The biggest lie in science is 'data and code available upon request'\" (Michael Eisen)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300\n", "Command line:\n", - " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl md.xvg\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8884,31 +8712,21 @@ "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", - "Writing final coordinates.\n", - "step 50000, remaining wall clock time: 0 s \n", - " Core t (s) Wall t (s) (%)\n", - " Time: 129.204 32.301 400.0\n", - " (ns/day) (hour/ns)\n", - "Performance: 2674.882 0.009\n", - "\n", - "GROMACS reminds you: \"We ignore public understanding of science at our peril.\" (Eugenie Clark)\n", - "\n", - "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + "step 27300, remaining wall clock time: 32 s " ] } ], "source": [ "for dir_ in goct.fep_dirs():\n", " r = gromacs.run.MDrunner(\n", - " dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=\"md.xvg\"\n", + " dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=True\n", " )\n", " r.run() # runs mdrun in the python shell" ] }, { "cell_type": "code", - "execution_count": 22, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -8983,14 +8801,22 @@ } ], "source": [ - "goct.collect()\n", - "goct.analyze()\n", - "goct.plot()" + "goct.convert_edr()\n", + "goct.analyze_alchemlyb()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "plot_results(goct)" ] }, { "cell_type": "code", - "execution_count": 25, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/doc/examples/martini/run.mdp b/doc/examples/martini/run.mdp index 8802883e..ed84f749 100644 --- a/doc/examples/martini/run.mdp +++ b/doc/examples/martini/run.mdp @@ -73,8 +73,7 @@ init-lambda-state = sedstate ; What are the values of lambda at the intermediate states? ;------- -vdw-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 -; fep_lambdas = 0.0 0.25 0.5 0.75 1.0 +fep_lambdas = 0 ; This makes sure we print out the differences in Hamiltonians between all states, and not just the neighboring states ;-------- From a80ecb3a4b3ff38e2f0fc65f31c84dd78fd39536 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Mon, 4 Sep 2023 22:42:12 +0100 Subject: [PATCH 33/38] Remove erroneous outputs --- doc/examples/martini/martini-benzene.ipynb | 6165 ++++++++++++-------- 1 file changed, 3811 insertions(+), 2354 deletions(-) diff --git a/doc/examples/martini/martini-benzene.ipynb b/doc/examples/martini/martini-benzene.ipynb index d4c775bc..21638773 100644 --- a/doc/examples/martini/martini-benzene.ipynb +++ b/doc/examples/martini/martini-benzene.ipynb @@ -19,13 +19,14 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 35, "metadata": {}, "outputs": [], "source": [ "from pathlib import Path\n", "from typing import Optional\n", "\n", + "import gromacs\n", "import requests as req\n", "\n", "\n", @@ -88,7 +89,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 36, "metadata": {}, "outputs": [ { @@ -97,7 +98,7 @@ "56" ] }, - "execution_count": 2, + "execution_count": 36, "metadata": {}, "output_type": "execute_result" } @@ -117,22 +118,9 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 37, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "mdpow : INFO MDPOW 0+untagged.603.ge92ffd8.dirty starting.\n", - "mdpow : INFO Copyright (c) 2010-2023 Shujie Fan, Ian Kenney, Alia Lescoulie, Cade Duckworth, Bogdan Iorga, and Oliver Beckstein\n", - "mdpow : INFO Released under the GNU Public Licence, version 3.\n", - "mdpow : INFO For bug reports and help: https://github.com/Becksteinlab/MDPOW/issues\n", - "mdpow.config: INFO Using the bundled force fields from GMXLIB='/home/awsm/MDPOW/mdpow/top'.\n", - "mdpow.config: INFO If required, override this behaviour by setting the environment variable GMXLIB yourself.\n" - ] - } - ], + "outputs": [], "source": [ "from mdpow.forcefields import Forcefield, GromacsSolventModel\n", "\n", @@ -162,39 +150,24 @@ ] }, { - "cell_type": "code", - "execution_count": 4, + "cell_type": "markdown", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "octanol\n", - "{'identifier': 'octanol', 'name': 'OCTANOL', 'itp': PosixPath('/home/awsm/MDPOW/doc/examples/martini/martini.ff/martini_v3.0.0_solvents_v1.itp'), 'coordinates': '/home/awsm/MDPOW/doc/examples/martini/octanol.gro', 'description': None, 'forcefield': 'Martini'}\n" - ] - } - ], "source": [ - "from dataclasses import asdict\n", + "## Aqueous simulation\n", "\n", - "for solvent_name, solvent_model in MARTINI.solvent_models.items():\n", - " print(solvent_name)\n", - " print(asdict(solvent_model))" + "We now solvate a benzene molecule in a water box. The first step of this is to set up a `WaterSimulation`, then perform some energy minimisation and create the files needed for relaxation." ] }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 38, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top' (newly created)...\n", "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation' (newly created)...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/water.gro'...\n", " :-) GROMACS - gmx editconf, 2023.2 (-:\n", "\n", @@ -205,7 +178,9 @@ " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 3.0\n", "\n", "\n", - "GROMACS reminds you: \"According to my computations we're overdue for a transformation.\" (Jackson Browne)\n", + "Back Off! I just backed up boxed.gro to ./#boxed.gro.1#\n", + "\n", + "GROMACS reminds you: \"It is a cute toxin.\" (Rebecca Howard)\n", "\n", " :-) GROMACS - gmx solvate, 2023.2 (-:\n", "\n", @@ -230,6 +205,8 @@ "Generated solvent containing 1633 atoms in 1633 residues\n", "Writing generated configuration to solvated.gro\n", "\n", + "Back Off! I just backed up solvated.gro to ./#solvated.gro.1#\n", + "\n", "Output configuration contains 1636 atoms in 1634 residues\n", "Volume : 174.316 (nm^3)\n", "Density : 2860.16 (g/l)\n", @@ -237,9 +214,9 @@ "\n", "Processing topology\n", "\n", - "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#system.top.1#\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#system.top.2#\n", "\n", - "GROMACS reminds you: \"According to my computations we're overdue for a transformation.\" (Jackson Browne)\n", + "GROMACS reminds you: \"It is a cute toxin.\" (Rebecca Howard)\n", "\n", "gromacs.setup: INFO Solvated system with /home/awsm/MDPOW/doc/examples/martini/water.gro\n" ] @@ -307,7 +284,9 @@ "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "\n", - "GROMACS reminds you: \"Expertise is not inherently good.\" (Joe Jordan)\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.2#\n", + "\n", + "GROMACS reminds you: \"Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia.\" (Roald Hoffmann)\n", "\n", " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", "\n", @@ -322,9 +301,9 @@ "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "\n", - "Back Off! I just backed up main.ndx to ./#main.ndx.1#\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.3#\n", "\n", - "GROMACS reminds you: \"Expertise is not inherently good.\" (Joe Jordan)\n", + "GROMACS reminds you: \"Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia.\" (Roald Hoffmann)\n", "\n", " :-) GROMACS - gmx trjconv, 2023.2 (-:\n", "\n", @@ -352,12 +331,14 @@ "Select a group: Reading frames from gro file 'This is an auto generated system', 1636 atoms.\n", "Reading frame 0 time 0.000 \n", "Precision of ionized.gro is 0.001 (nm)\n", + "\n", + "Back Off! I just backed up compact.pdb to ./#compact.pdb.1#\n", "Last frame 0 time 0.000 \n", " -> frame 0 time 0.000 \n", "Last written: frame 0 time 0.000\n", "\n", "\n", - "GROMACS reminds you: \"Expertise is not inherently good.\" (Joe Jordan)\n", + "GROMACS reminds you: \"Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia.\" (Roald Hoffmann)\n", "\n", " :-) GROMACS - gmx grompp, 2023.2 (-:\n", "\n", @@ -365,13 +346,15 @@ "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -f /tmp/tmpec_ojnsf.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -nov\n", + " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -f /tmp/tmp_bobqsmz.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -nov\n", "\n", "\n", - "NOTE 1 [file /tmp/tmpec_ojnsf.mdp]:\n", + "NOTE 1 [file /tmp/tmp_bobqsmz.mdp]:\n", " For a correct single-point energy evaluation with nsteps = 0, use\n", " continuation = yes to avoid constraining the input coordinates.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#pp_system.top.1#\n" ] }, { @@ -449,7 +432,7 @@ "Number of degrees of freedom in T-Coupling group rest is 4902.00\n", "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", "\n", - "NOTE 3 [file /tmp/tmpec_ojnsf.mdp]:\n", + "NOTE 3 [file /tmp/tmp_bobqsmz.mdp]:\n", " NVE simulation with an initial temperature of zero: will use a Verlet\n", " buffer of 10%. Check your energy drift!\n", "\n", @@ -458,10 +441,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Expertise is not inherently good.\" (Joe Jordan)\n", + "GROMACS reminds you: \"I Caught It In the Face\" (P.J. Harvey)\n", "\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top', mdp='em.mdp' ...\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'em.mdp': ['maxwarn', 'pp']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -478,14 +460,16 @@ " gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -maxwarn 1 -pp processed.top\n", "\n", "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", - "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n" + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1526990921\n", + "Setting the LD random seed to -411043105\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -602,7 +586,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Ludwig Boltzmann, who spent much of his life studying statistical mechanics, died in 1906, by his own hand. Paul Ehrenfest, carrying on the same work, died similarly in 1933. Now it is our turn to study statistical mechanics. Perhaps it will be wise to approach the subject cautiously.\" (David Goodstein)\n", + "Back Off! I just backed up em.tpr to ./#em.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Input, output, electricity\" (Joni Mitchell)\n", "\n", "gromacs.run : WARNING No 'mdrun_d' binary found so trying 'mdrun' instead.\n", "(Note that energy minimization runs better with mdrun_d.)\n", @@ -623,7 +609,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 2013264681\n", + "Setting the LD random seed to -71328783\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -683,6 +669,8 @@ "name": "stderr", "output_type": "stream", "text": [ + "\n", + "Back Off! I just backed up em.log to ./#em.log.1#\n", "Reading file em.tpr, VERSION 2023.2 (single precision)\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -693,6 +681,10 @@ "Using 4 OpenMP threads \n", "\n", "\n", + "Back Off! I just backed up em.trr to ./#em.trr.1#\n", + "\n", + "Back Off! I just backed up em.edr to ./#em.edr.1#\n", + "\n", "Steepest Descents:\n", " Tolerance (Fmax) = 1.00000e+01\n", " Number of steps = 1000\n", @@ -705,806 +697,807 @@ "Step= 6, Dmax= 2.5e-02 nm, Epot= 4.76315e+05 Fmax= 1.79135e+05, atom= 1493\n", "Step= 7, Dmax= 3.0e-02 nm, Epot= 3.20697e+05 Fmax= 2.25612e+05, atom= 544\n", "Step= 8, Dmax= 3.6e-02 nm, Epot= 2.54493e+05 Fmax= 9.11997e+04, atom= 1513\n", - "Step= 9, Dmax= 4.3e-02 nm, Epot= 1.57693e+05 Fmax= 1.98551e+05, atom= 544\n", + "Step= 9, Dmax= 4.3e-02 nm, Epot= 1.57693e+05 Fmax= 1.98552e+05, atom= 544\n", "Step= 10, Dmax= 5.2e-02 nm, Epot= 1.29573e+05 Fmax= 6.97811e+04, atom= 1043\n", - "Step= 11, Dmax= 6.2e-02 nm, Epot= 8.43732e+04 Fmax= 2.96444e+05, atom= 200\n", - "Step= 12, Dmax= 7.4e-02 nm, Epot= 7.16052e+04 Fmax= 2.00454e+04, atom= 200\n", - "Step= 13, Dmax= 8.9e-02 nm, Epot= 1.52005e+04 Fmax= 5.75866e+04, atom= 200\n", - "Step= 14, Dmax= 1.1e-01 nm, Epot= 7.52938e+03 Fmax= 2.23148e+04, atom= 200\n", - "Step= 15, Dmax= 1.3e-01 nm, Epot= -2.26040e+03 Fmax= 3.65168e+04, atom= 1107\n", - "Step= 16, Dmax= 1.5e-01 nm, Epot= -7.31706e+03 Fmax= 3.22986e+04, atom= 1107\n", - "Step= 17, Dmax= 1.8e-01 nm, Epot= -8.75316e+03 Fmax= 1.04774e+05, atom= 898\n", - "Step= 18, Dmax= 2.2e-01 nm, Epot= -1.05843e+04 Fmax= 7.90213e+04, atom= 818\n", - "Step= 20, Dmax= 1.3e-01 nm, Epot= -1.44389e+04 Fmax= 1.77137e+04, atom= 1591\n", - "Step= 22, Dmax= 8.0e-02 nm, Epot= -1.69180e+04 Fmax= 2.36072e+04, atom= 1591\n", - "Step= 23, Dmax= 9.6e-02 nm, Epot= -1.85682e+04 Fmax= 1.69728e+04, atom= 1267\n", - "Step= 24, Dmax= 1.2e-01 nm, Epot= -2.05149e+04 Fmax= 1.35047e+04, atom= 1586\n", - "Step= 26, Dmax= 6.9e-02 nm, Epot= -2.22957e+04 Fmax= 7.78833e+03, atom= 1606\n", - "Step= 27, Dmax= 8.3e-02 nm, Epot= -2.46065e+04 Fmax= 8.23724e+03, atom= 1606\n", - "Step= 28, Dmax= 9.9e-02 nm, Epot= -2.60463e+04 Fmax= 2.03930e+04, atom= 1586\n", - "Step= 29, Dmax= 1.2e-01 nm, Epot= -2.71109e+04 Fmax= 8.51178e+03, atom= 1267\n", - "Step= 30, Dmax= 1.4e-01 nm, Epot= -2.77852e+04 Fmax= 5.10263e+04, atom= 1490\n", - "Step= 31, Dmax= 1.7e-01 nm, Epot= -2.89093e+04 Fmax= 8.58695e+03, atom= 1446\n", - "Step= 32, Dmax= 2.1e-01 nm, Epot= -3.02288e+04 Fmax= 2.27389e+04, atom= 1550\n", - "Step= 34, Dmax= 1.2e-01 nm, Epot= -3.08778e+04 Fmax= 1.66821e+04, atom= 1550\n", - "Step= 35, Dmax= 1.5e-01 nm, Epot= -3.15210e+04 Fmax= 7.84232e+03, atom= 468\n", - "Step= 36, Dmax= 1.8e-01 nm, Epot= -3.26742e+04 Fmax= 4.75748e+03, atom= 1596\n", - "Step= 37, Dmax= 2.1e-01 nm, Epot= -3.33775e+04 Fmax= 3.33249e+04, atom= 1461\n", - "Step= 38, Dmax= 2.6e-01 nm, Epot= -3.44663e+04 Fmax= 4.50564e+03, atom= 1596\n", - "Step= 40, Dmax= 1.5e-01 nm, Epot= -3.54502e+04 Fmax= 1.55013e+03, atom= 430\n", - "Step= 41, Dmax= 1.8e-01 nm, Epot= -3.68978e+04 Fmax= 1.01688e+04, atom= 430\n", - "Step= 43, Dmax= 1.1e-01 nm, Epot= -3.73994e+04 Fmax= 2.71563e+03, atom= 1090\n", - "Step= 44, Dmax= 1.3e-01 nm, Epot= -3.78345e+04 Fmax= 2.32957e+03, atom= 1200\n", - "Step= 45, Dmax= 1.6e-01 nm, Epot= -3.80154e+04 Fmax= 6.23576e+03, atom= 1363\n", - "Step= 47, Dmax= 9.6e-02 nm, Epot= -3.85620e+04 Fmax= 2.23182e+03, atom= 867\n", - "Step= 48, Dmax= 1.1e-01 nm, Epot= -3.89186e+04 Fmax= 1.51575e+03, atom= 666\n", - "Step= 50, Dmax= 6.9e-02 nm, Epot= -3.92438e+04 Fmax= 1.20553e+03, atom= 1190\n", - "Step= 52, Dmax= 4.1e-02 nm, Epot= -3.94255e+04 Fmax= 1.81611e+03, atom= 1190\n", - "Step= 53, Dmax= 5.0e-02 nm, Epot= -3.95620e+04 Fmax= 1.81494e+03, atom= 1190\n", - "Step= 54, Dmax= 6.0e-02 nm, Epot= -3.96129e+04 Fmax= 3.54853e+03, atom= 1190\n", - "Step= 55, Dmax= 7.1e-02 nm, Epot= -3.97853e+04 Fmax= 1.91470e+03, atom= 652\n", - "Step= 57, Dmax= 4.3e-02 nm, Epot= -3.99181e+04 Fmax= 1.12190e+03, atom= 1469\n", - "Step= 58, Dmax= 5.1e-02 nm, Epot= -4.00826e+04 Fmax= 1.67277e+03, atom= 652\n", - "Step= 59, Dmax= 6.2e-02 nm, Epot= -4.01534e+04 Fmax= 2.68809e+03, atom= 652\n", - "Step= 60, Dmax= 7.4e-02 nm, Epot= -4.02825e+04 Fmax= 2.17815e+03, atom= 1190\n", - "Step= 61, Dmax= 8.9e-02 nm, Epot= -4.03034e+04 Fmax= 2.91113e+03, atom= 1190\n", - "Step= 63, Dmax= 5.3e-02 nm, Epot= -4.05242e+04 Fmax= 7.06199e+02, atom= 5920\n", - "Step= 64, Dmax= 6.4e-02 nm, Epot= -4.07516e+04 Fmax= 1.27266e+03, atom= 620\n", - "Step= 66, Dmax= 3.8e-02 nm, Epot= -4.08794e+04 Fmax= 1.06149e+03, atom= 620\n", - "Step= 67, Dmax= 4.6e-02 nm, Epot= -4.09733e+04 Fmax= 1.25278e+03, atom= 1190\n", + "Step= 11, Dmax= 6.2e-02 nm, Epot= 8.43733e+04 Fmax= 2.96448e+05, atom= 200\n", + "Step= 12, Dmax= 7.4e-02 nm, Epot= 7.16053e+04 Fmax= 2.00453e+04, atom= 200\n", + "Step= 13, Dmax= 8.9e-02 nm, Epot= 1.52004e+04 Fmax= 5.75859e+04, atom= 200\n", + "Step= 14, Dmax= 1.1e-01 nm, Epot= 7.52929e+03 Fmax= 2.23154e+04, atom= 200\n", + "Step= 15, Dmax= 1.3e-01 nm, Epot= -2.26025e+03 Fmax= 3.65146e+04, atom= 1107\n", + "Step= 16, Dmax= 1.5e-01 nm, Epot= -7.31692e+03 Fmax= 3.23004e+04, atom= 1107\n", + "Step= 17, Dmax= 1.8e-01 nm, Epot= -8.75253e+03 Fmax= 1.04774e+05, atom= 898\n", + "Step= 18, Dmax= 2.2e-01 nm, Epot= -1.05838e+04 Fmax= 7.90194e+04, atom= 818\n", + "Step= 20, Dmax= 1.3e-01 nm, Epot= -1.44387e+04 Fmax= 1.77139e+04, atom= 1591\n", + "Step= 22, Dmax= 8.0e-02 nm, Epot= -1.69178e+04 Fmax= 2.36072e+04, atom= 1591\n", + "Step= 23, Dmax= 9.6e-02 nm, Epot= -1.85681e+04 Fmax= 1.69728e+04, atom= 1267\n", + "Step= 24, Dmax= 1.2e-01 nm, Epot= -2.05149e+04 Fmax= 1.35050e+04, atom= 1586\n", + "Step= 26, Dmax= 6.9e-02 nm, Epot= -2.22956e+04 Fmax= 7.78836e+03, atom= 1606\n", + "Step= 27, Dmax= 8.3e-02 nm, Epot= -2.46064e+04 Fmax= 8.23711e+03, atom= 1606\n", + "Step= 28, Dmax= 9.9e-02 nm, Epot= -2.60463e+04 Fmax= 2.03933e+04, atom= 1586\n", + "Step= 29, Dmax= 1.2e-01 nm, Epot= -2.71109e+04 Fmax= 8.51193e+03, atom= 1267\n", + "Step= 30, Dmax= 1.4e-01 nm, Epot= -2.77852e+04 Fmax= 5.10258e+04, atom= 1490\n", + "Step= 31, Dmax= 1.7e-01 nm, Epot= -2.89093e+04 Fmax= 8.58690e+03, atom= 1446\n", + "Step= 32, Dmax= 2.1e-01 nm, Epot= -3.02287e+04 Fmax= 2.27404e+04, atom= 1550\n", + "Step= 34, Dmax= 1.2e-01 nm, Epot= -3.08777e+04 Fmax= 1.66820e+04, atom= 1550\n", + "Step= 35, Dmax= 1.5e-01 nm, Epot= -3.15210e+04 Fmax= 7.84227e+03, atom= 468\n", + "Step= 36, Dmax= 1.8e-01 nm, Epot= -3.26742e+04 Fmax= 4.75746e+03, atom= 1596\n", + "Step= 37, Dmax= 2.1e-01 nm, Epot= -3.33775e+04 Fmax= 3.33251e+04, atom= 1461\n", + "Step= 38, Dmax= 2.6e-01 nm, Epot= -3.44663e+04 Fmax= 4.50561e+03, atom= 1596\n", + "Step= 40, Dmax= 1.5e-01 nm, Epot= -3.54502e+04 Fmax= 1.55014e+03, atom= 430\n", + "Step= 41, Dmax= 1.8e-01 nm, Epot= -3.68978e+04 Fmax= 1.01690e+04, atom= 430\n", + "Step= 43, Dmax= 1.1e-01 nm, Epot= -3.73994e+04 Fmax= 2.71559e+03, atom= 1090\n", + "Step= 44, Dmax= 1.3e-01 nm, Epot= -3.78346e+04 Fmax= 2.32965e+03, atom= 1200\n", + "Step= 45, Dmax= 1.6e-01 nm, Epot= -3.80156e+04 Fmax= 6.23591e+03, atom= 1363\n", + "Step= 47, Dmax= 9.6e-02 nm, Epot= -3.85621e+04 Fmax= 2.23179e+03, atom= 867\n", + "Step= 48, Dmax= 1.1e-01 nm, Epot= -3.89186e+04 Fmax= 1.51574e+03, atom= 666\n", + "Step= 50, Dmax= 6.9e-02 nm, Epot= -3.92438e+04 Fmax= 1.20551e+03, atom= 1190\n", + "Step= 52, Dmax= 4.1e-02 nm, Epot= -3.94255e+04 Fmax= 1.81594e+03, atom= 1190\n", + "Step= 53, Dmax= 5.0e-02 nm, Epot= -3.95620e+04 Fmax= 1.81514e+03, atom= 1190\n", + "Step= 54, Dmax= 6.0e-02 nm, Epot= -3.96129e+04 Fmax= 3.54761e+03, atom= 1190\n", + "Step= 55, Dmax= 7.1e-02 nm, Epot= -3.97852e+04 Fmax= 1.91578e+03, atom= 652\n", + "Step= 57, Dmax= 4.3e-02 nm, Epot= -3.99180e+04 Fmax= 1.12184e+03, atom= 1469\n", + "Step= 58, Dmax= 5.1e-02 nm, Epot= -4.00826e+04 Fmax= 1.67238e+03, atom= 652\n", + "Step= 59, Dmax= 6.2e-02 nm, Epot= -4.01535e+04 Fmax= 2.68774e+03, atom= 652\n", + "Step= 60, Dmax= 7.4e-02 nm, Epot= -4.02825e+04 Fmax= 2.17868e+03, atom= 1190\n", + "Step= 61, Dmax= 8.9e-02 nm, Epot= -4.03033e+04 Fmax= 2.91221e+03, atom= 1190\n", + "Step= 63, Dmax= 5.3e-02 nm, Epot= -4.05242e+04 Fmax= 7.05796e+02, atom= 5920\n", + "Step= 64, Dmax= 6.4e-02 nm, Epot= -4.07518e+04 Fmax= 1.27201e+03, atom= 620\n", + "Step= 66, Dmax= 3.8e-02 nm, Epot= -4.08795e+04 Fmax= 1.06263e+03, atom= 620\n", + "Step= 67, Dmax= 4.6e-02 nm, Epot= -4.09734e+04 Fmax= 1.25273e+03, atom= 1190\n", "Step= 68, Dmax= 5.5e-02 nm, Epot= -4.10696e+04 Fmax= 1.23272e+03, atom= 652\n", - "Step= 69, Dmax= 6.6e-02 nm, Epot= -4.10937e+04 Fmax= 2.04367e+03, atom= 652\n", - "Step= 70, Dmax= 8.0e-02 nm, Epot= -4.11796e+04 Fmax= 2.15705e+03, atom= 652\n", - "Step= 72, Dmax= 4.8e-02 nm, Epot= -4.13411e+04 Fmax= 5.25685e+02, atom= 1469\n", - "Step= 73, Dmax= 5.7e-02 nm, Epot= -4.14434e+04 Fmax= 4.45001e+03, atom= 113\n", - "Step= 74, Dmax= 6.9e-02 nm, Epot= -4.15758e+04 Fmax= 1.05509e+03, atom= 170\n", - "Step= 75, Dmax= 8.3e-02 nm, Epot= -4.16118e+04 Fmax= 4.05136e+03, atom= 170\n", - "Step= 76, Dmax= 9.9e-02 nm, Epot= -4.17121e+04 Fmax= 1.42697e+03, atom= 113\n", - "Step= 78, Dmax= 5.9e-02 nm, Epot= -4.18215e+04 Fmax= 6.13638e+02, atom= 1281\n", - "Step= 79, Dmax= 7.1e-02 nm, Epot= -4.19450e+04 Fmax= 1.31910e+03, atom= 1281\n", - "Step= 81, Dmax= 4.3e-02 nm, Epot= -4.20505e+04 Fmax= 6.91802e+02, atom= 170\n", - "Step= 82, Dmax= 5.1e-02 nm, Epot= -4.21356e+04 Fmax= 8.32550e+02, atom= 170\n", - "Step= 83, Dmax= 6.2e-02 nm, Epot= -4.22091e+04 Fmax= 1.12090e+03, atom= 170\n", - "Step= 84, Dmax= 7.4e-02 nm, Epot= -4.22628e+04 Fmax= 1.29047e+03, atom= 170\n", - "Step= 85, Dmax= 8.9e-02 nm, Epot= -4.22998e+04 Fmax= 1.20931e+03, atom= 1281\n", - "Step= 87, Dmax= 5.3e-02 nm, Epot= -4.24262e+04 Fmax= 6.06238e+02, atom= 240\n", - "Step= 88, Dmax= 6.4e-02 nm, Epot= -4.24605e+04 Fmax= 1.74500e+03, atom= 850\n", - "Step= 89, Dmax= 7.7e-02 nm, Epot= -4.25572e+04 Fmax= 1.22862e+03, atom= 850\n", - "Step= 91, Dmax= 4.6e-02 nm, Epot= -4.26389e+04 Fmax= 4.53331e+02, atom= 70\n", - "Step= 92, Dmax= 5.5e-02 nm, Epot= -4.27303e+04 Fmax= 7.46617e+02, atom= 70\n", - "Step= 94, Dmax= 3.3e-02 nm, Epot= -4.27945e+04 Fmax= 3.51139e+02, atom= 1589\n", - "Step= 95, Dmax= 4.0e-02 nm, Epot= -4.28458e+04 Fmax= 1.50975e+03, atom= 1589\n", - "Step= 96, Dmax= 4.8e-02 nm, Epot= -4.29169e+04 Fmax= 4.34395e+02, atom= 434\n", - "Step= 97, Dmax= 5.7e-02 nm, Epot= -4.29790e+04 Fmax= 1.84347e+03, atom= 434\n", - "Step= 98, Dmax= 6.9e-02 nm, Epot= -4.30295e+04 Fmax= 6.99437e+02, atom= 1589\n", - "Step= 100, Dmax= 4.1e-02 nm, Epot= -4.30858e+04 Fmax= 3.84717e+02, atom= 3179\n", - "Step= 101, Dmax= 4.9e-02 nm, Epot= -4.31399e+04 Fmax= 1.11457e+03, atom= 1589\n", - "Step= 102, Dmax= 5.9e-02 nm, Epot= -4.31821e+04 Fmax= 1.23817e+03, atom= 1589\n", - "Step= 103, Dmax= 7.1e-02 nm, Epot= -4.32218e+04 Fmax= 9.44305e+02, atom= 434\n", - "Step= 104, Dmax= 8.5e-02 nm, Epot= -4.32496e+04 Fmax= 1.23802e+03, atom= 317\n", - "Step= 106, Dmax= 5.1e-02 nm, Epot= -4.33232e+04 Fmax= 2.80499e+02, atom= 421\n", - "Step= 107, Dmax= 6.2e-02 nm, Epot= -4.33684e+04 Fmax= 1.22256e+03, atom= 317\n", - "Step= 109, Dmax= 3.7e-02 nm, Epot= -4.34593e+04 Fmax= 3.28381e+02, atom= 434\n", - "Step= 110, Dmax= 4.4e-02 nm, Epot= -4.35167e+04 Fmax= 5.77616e+02, atom= 434\n", - "Step= 111, Dmax= 5.3e-02 nm, Epot= -4.35590e+04 Fmax= 4.92084e+02, atom= 434\n", - "Step= 112, Dmax= 6.4e-02 nm, Epot= -4.35752e+04 Fmax= 1.25946e+03, atom= 434\n", - "Step= 113, Dmax= 7.7e-02 nm, Epot= -4.36228e+04 Fmax= 6.72230e+02, atom= 434\n", - "Step= 115, Dmax= 4.6e-02 nm, Epot= -4.36728e+04 Fmax= 4.09361e+02, atom= 317\n", - "Step= 116, Dmax= 5.5e-02 nm, Epot= -4.37177e+04 Fmax= 4.93751e+02, atom= 317\n", - "Step= 118, Dmax= 3.3e-02 nm, Epot= -4.37555e+04 Fmax= 1.90875e+02, atom= 317\n", - "Step= 119, Dmax= 4.0e-02 nm, Epot= -4.37799e+04 Fmax= 8.72544e+02, atom= 317\n", - "Step= 120, Dmax= 4.8e-02 nm, Epot= -4.38416e+04 Fmax= 3.21396e+02, atom= 317\n", - "Step= 122, Dmax= 2.9e-02 nm, Epot= -4.38683e+04 Fmax= 3.75706e+02, atom= 983\n", - "Step= 123, Dmax= 3.4e-02 nm, Epot= -4.38805e+04 Fmax= 6.54084e+02, atom= 983\n", - "Step= 124, Dmax= 4.1e-02 nm, Epot= -4.39104e+04 Fmax= 6.00286e+02, atom= 983\n", - "Step= 125, Dmax= 4.9e-02 nm, Epot= -4.39152e+04 Fmax= 8.68779e+02, atom= 983\n", - "Step= 126, Dmax= 5.9e-02 nm, Epot= -4.39302e+04 Fmax= 1.08168e+03, atom= 983\n", - "Step= 127, Dmax= 7.1e-02 nm, Epot= -4.39395e+04 Fmax= 9.88661e+02, atom= 983\n", - "Step= 129, Dmax= 4.3e-02 nm, Epot= -4.39979e+04 Fmax= 3.41137e+02, atom= 939\n", - "Step= 130, Dmax= 5.1e-02 nm, Epot= -4.40179e+04 Fmax= 6.91514e+02, atom= 939\n", - "Step= 132, Dmax= 3.1e-02 nm, Epot= -4.40575e+04 Fmax= 3.17552e+02, atom= 983\n", - "Step= 133, Dmax= 3.7e-02 nm, Epot= -4.40739e+04 Fmax= 6.66329e+02, atom= 983\n", - "Step= 134, Dmax= 4.4e-02 nm, Epot= -4.40973e+04 Fmax= 4.71807e+02, atom= 983\n", - "Step= 136, Dmax= 2.7e-02 nm, Epot= -4.41213e+04 Fmax= 2.13679e+02, atom= 983\n", - "Step= 137, Dmax= 3.2e-02 nm, Epot= -4.41340e+04 Fmax= 8.04992e+02, atom= 983\n", - "Step= 138, Dmax= 3.8e-02 nm, Epot= -4.41653e+04 Fmax= 4.08978e+02, atom= 983\n", - "Step= 139, Dmax= 4.6e-02 nm, Epot= -4.41654e+04 Fmax= 9.12027e+02, atom= 983\n", - "Step= 140, Dmax= 5.5e-02 nm, Epot= -4.41841e+04 Fmax= 6.40748e+02, atom= 983\n", - "Step= 142, Dmax= 3.3e-02 nm, Epot= -4.42228e+04 Fmax= 1.94678e+02, atom= 1550\n", - "Step= 143, Dmax= 4.0e-02 nm, Epot= -4.42232e+04 Fmax= 9.91222e+02, atom= 983\n", - "Step= 144, Dmax= 4.8e-02 nm, Epot= -4.42676e+04 Fmax= 5.88017e+02, atom= 983\n", - "Step= 146, Dmax= 2.9e-02 nm, Epot= -4.42914e+04 Fmax= 2.00081e+02, atom= 292\n", - "Step= 147, Dmax= 3.4e-02 nm, Epot= -4.43066e+04 Fmax= 6.57932e+02, atom= 983\n", - "Step= 148, Dmax= 4.1e-02 nm, Epot= -4.43211e+04 Fmax= 6.61051e+02, atom= 983\n", - "Step= 149, Dmax= 4.9e-02 nm, Epot= -4.43348e+04 Fmax= 5.51796e+02, atom= 1550\n", - "Step= 151, Dmax= 3.0e-02 nm, Epot= -4.43616e+04 Fmax= 2.86698e+02, atom= 681\n", - "Step= 152, Dmax= 3.5e-02 nm, Epot= -4.43737e+04 Fmax= 6.52987e+02, atom= 681\n", - "Step= 153, Dmax= 4.3e-02 nm, Epot= -4.43882e+04 Fmax= 4.78678e+02, atom= 681\n", - "Step= 155, Dmax= 2.6e-02 nm, Epot= -4.44101e+04 Fmax= 1.28188e+02, atom= 983\n", - "Step= 156, Dmax= 3.1e-02 nm, Epot= -4.44202e+04 Fmax= 7.33390e+02, atom= 983\n", - "Step= 157, Dmax= 3.7e-02 nm, Epot= -4.44518e+04 Fmax= 3.99576e+02, atom= 681\n", - "Step= 159, Dmax= 2.2e-02 nm, Epot= -4.44669e+04 Fmax= 2.09813e+02, atom= 681\n", - "Step= 160, Dmax= 2.6e-02 nm, Epot= -4.44788e+04 Fmax= 5.11277e+02, atom= 681\n", - "Step= 161, Dmax= 3.2e-02 nm, Epot= -4.44914e+04 Fmax= 3.36731e+02, atom= 681\n", - "Step= 162, Dmax= 3.8e-02 nm, Epot= -4.44938e+04 Fmax= 7.53557e+02, atom= 681\n", - "Step= 163, Dmax= 4.6e-02 nm, Epot= -4.45092e+04 Fmax= 4.64951e+02, atom= 681\n", - "Step= 165, Dmax= 2.7e-02 nm, Epot= -4.45278e+04 Fmax= 1.18372e+02, atom= 983\n", - "Step= 167, Dmax= 1.6e-02 nm, Epot= -4.45403e+04 Fmax= 3.23636e+02, atom= 681\n", - "Step= 168, Dmax= 2.0e-02 nm, Epot= -4.45534e+04 Fmax= 1.92375e+02, atom= 681\n", - "Step= 169, Dmax= 2.4e-02 nm, Epot= -4.45599e+04 Fmax= 4.12217e+02, atom= 681\n", - "Step= 170, Dmax= 2.8e-02 nm, Epot= -4.45729e+04 Fmax= 3.01949e+02, atom= 681\n", - "Step= 172, Dmax= 1.7e-02 nm, Epot= -4.45842e+04 Fmax= 1.46158e+02, atom= 681\n", - "Step= 173, Dmax= 2.1e-02 nm, Epot= -4.45943e+04 Fmax= 3.90585e+02, atom= 681\n", - "Step= 174, Dmax= 2.5e-02 nm, Epot= -4.46044e+04 Fmax= 2.59083e+02, atom= 681\n", - "Step= 175, Dmax= 3.0e-02 nm, Epot= -4.46081e+04 Fmax= 5.38443e+02, atom= 681\n", - "Step= 176, Dmax= 3.5e-02 nm, Epot= -4.46187e+04 Fmax= 3.74000e+02, atom= 681\n", - "Step= 178, Dmax= 2.1e-02 nm, Epot= -4.46318e+04 Fmax= 9.02203e+01, atom= 983\n", - "Step= 179, Dmax= 2.6e-02 nm, Epot= -4.46325e+04 Fmax= 6.66137e+02, atom= 681\n", - "Step= 180, Dmax= 3.1e-02 nm, Epot= -4.46619e+04 Fmax= 1.99727e+02, atom= 681\n", - "Step= 182, Dmax= 1.8e-02 nm, Epot= -4.46696e+04 Fmax= 2.44846e+02, atom= 6810\n", - "Step= 183, Dmax= 2.2e-02 nm, Epot= -4.46765e+04 Fmax= 2.94585e+02, atom= 681\n", - "Step= 184, Dmax= 2.6e-02 nm, Epot= -4.46816e+04 Fmax= 3.47376e+02, atom= 681\n", - "Step= 185, Dmax= 3.2e-02 nm, Epot= -4.46868e+04 Fmax= 4.39946e+02, atom= 681\n", - "Step= 186, Dmax= 3.8e-02 nm, Epot= -4.46898e+04 Fmax= 4.71115e+02, atom= 681\n", - "Step= 187, Dmax= 4.6e-02 nm, Epot= -4.46898e+04 Fmax= 6.77977e+02, atom= 681\n", - "Step= 188, Dmax= 5.5e-02 nm, Epot= -4.46925e+04 Fmax= 6.10074e+02, atom= 681\n", - "Step= 190, Dmax= 3.3e-02 nm, Epot= -4.47210e+04 Fmax= 1.01508e+02, atom= 983\n", - "Step= 192, Dmax= 2.0e-02 nm, Epot= -4.47298e+04 Fmax= 2.69819e+02, atom= 681\n", - "Step= 193, Dmax= 2.4e-02 nm, Epot= -4.47359e+04 Fmax= 3.46552e+02, atom= 681\n", - "Step= 194, Dmax= 2.8e-02 nm, Epot= -4.47430e+04 Fmax= 3.27692e+02, atom= 681\n", - "Step= 196, Dmax= 1.7e-02 nm, Epot= -4.47558e+04 Fmax= 5.07418e+01, atom= 642\n", - "Step= 197, Dmax= 2.0e-02 nm, Epot= -4.47571e+04 Fmax= 6.92420e+02, atom= 642\n", - "Step= 198, Dmax= 2.5e-02 nm, Epot= -4.47880e+04 Fmax= 1.27053e+02, atom= 1455\n", - "Step= 200, Dmax= 1.5e-02 nm, Epot= -4.47949e+04 Fmax= 2.45018e+02, atom= 642\n", - "Step= 201, Dmax= 1.8e-02 nm, Epot= -4.48003e+04 Fmax= 1.99268e+02, atom= 642\n", - "Step= 202, Dmax= 2.1e-02 nm, Epot= -4.48046e+04 Fmax= 3.81867e+02, atom= 642\n", - "Step= 203, Dmax= 2.5e-02 nm, Epot= -4.48107e+04 Fmax= 2.66375e+02, atom= 642\n", - "Step= 204, Dmax= 3.1e-02 nm, Epot= -4.48110e+04 Fmax= 6.07559e+02, atom= 642\n", - "Step= 205, Dmax= 3.7e-02 nm, Epot= -4.48195e+04 Fmax= 3.41567e+02, atom= 642\n", - "Step= 207, Dmax= 2.2e-02 nm, Epot= -4.48299e+04 Fmax= 1.05062e+02, atom= 642\n", - "Step= 209, Dmax= 1.3e-02 nm, Epot= -4.48363e+04 Fmax= 2.31245e+02, atom= 642\n", - "Step= 210, Dmax= 1.6e-02 nm, Epot= -4.48430e+04 Fmax= 1.63280e+02, atom= 642\n", - "Step= 211, Dmax= 1.9e-02 nm, Epot= -4.48474e+04 Fmax= 2.83732e+02, atom= 642\n", - "Step= 212, Dmax= 2.3e-02 nm, Epot= -4.48535e+04 Fmax= 2.78904e+02, atom= 642\n", - "Step= 213, Dmax= 2.7e-02 nm, Epot= -4.48555e+04 Fmax= 3.67479e+02, atom= 642\n", - "Step= 214, Dmax= 3.3e-02 nm, Epot= -4.48593e+04 Fmax= 4.58425e+02, atom= 642\n", - "Step= 215, Dmax= 3.9e-02 nm, Epot= -4.48603e+04 Fmax= 4.68145e+02, atom= 642\n", - "Step= 217, Dmax= 2.4e-02 nm, Epot= -4.48776e+04 Fmax= 8.09518e+01, atom= 566\n", - "Step= 219, Dmax= 1.4e-02 nm, Epot= -4.48858e+04 Fmax= 2.02442e+02, atom= 809\n", - "Step= 220, Dmax= 1.7e-02 nm, Epot= -4.48911e+04 Fmax= 2.16388e+02, atom= 809\n", - "Step= 221, Dmax= 2.0e-02 nm, Epot= -4.48947e+04 Fmax= 2.72316e+02, atom= 809\n", - "Step= 222, Dmax= 2.5e-02 nm, Epot= -4.48976e+04 Fmax= 3.23222e+02, atom= 809\n", - "Step= 223, Dmax= 2.9e-02 nm, Epot= -4.48989e+04 Fmax= 3.85369e+02, atom= 809\n", - "Step= 225, Dmax= 1.8e-02 nm, Epot= -4.49146e+04 Fmax= 7.07322e+01, atom= 1517\n", - "Step= 226, Dmax= 2.1e-02 nm, Epot= -4.49244e+04 Fmax= 4.20600e+02, atom= 1517\n", - "Step= 227, Dmax= 2.5e-02 nm, Epot= -4.49333e+04 Fmax= 2.49944e+02, atom= 809\n", - "Step= 229, Dmax= 1.5e-02 nm, Epot= -4.49396e+04 Fmax= 9.11969e+01, atom= 809\n", - "Step= 230, Dmax= 1.8e-02 nm, Epot= -4.49417e+04 Fmax= 4.04562e+02, atom= 809\n", - "Step= 231, Dmax= 2.2e-02 nm, Epot= -4.49536e+04 Fmax= 1.37484e+02, atom= 809\n", - "Step= 233, Dmax= 1.3e-02 nm, Epot= -4.49582e+04 Fmax= 1.63833e+02, atom= 809\n", - "Step= 234, Dmax= 1.6e-02 nm, Epot= -4.49617e+04 Fmax= 2.04513e+02, atom= 809\n", - "Step= 235, Dmax= 1.9e-02 nm, Epot= -4.49640e+04 Fmax= 2.56307e+02, atom= 401\n", - "Step= 236, Dmax= 2.3e-02 nm, Epot= -4.49657e+04 Fmax= 3.34286e+02, atom= 401\n", - "Step= 237, Dmax= 2.7e-02 nm, Epot= -4.49688e+04 Fmax= 3.87506e+02, atom= 401\n", - "Step= 238, Dmax= 3.3e-02 nm, Epot= -4.49703e+04 Fmax= 4.62960e+02, atom= 401\n", - "Step= 240, Dmax= 2.0e-02 nm, Epot= -4.49872e+04 Fmax= 6.32842e+01, atom= 732\n", - "Step= 241, Dmax= 2.4e-02 nm, Epot= -4.49890e+04 Fmax= 6.36481e+02, atom= 401\n", - "Step= 242, Dmax= 2.8e-02 nm, Epot= -4.50072e+04 Fmax= 2.93148e+02, atom= 401\n", - "Step= 244, Dmax= 1.7e-02 nm, Epot= -4.50125e+04 Fmax= 1.27292e+02, atom= 401\n", - "Step= 245, Dmax= 2.0e-02 nm, Epot= -4.50138e+04 Fmax= 4.35828e+02, atom= 401\n", - "Step= 246, Dmax= 2.4e-02 nm, Epot= -4.50225e+04 Fmax= 2.00383e+02, atom= 401\n", - "Step= 248, Dmax= 1.5e-02 nm, Epot= -4.50270e+04 Fmax= 1.44593e+02, atom= 401\n", - "Step= 249, Dmax= 1.8e-02 nm, Epot= -4.50292e+04 Fmax= 3.14123e+02, atom= 401\n", - "Step= 250, Dmax= 2.1e-02 nm, Epot= -4.50349e+04 Fmax= 2.31536e+02, atom= 401\n", - "Step= 252, Dmax= 1.3e-02 nm, Epot= -4.50402e+04 Fmax= 8.56108e+01, atom= 401\n", - "Step= 253, Dmax= 1.5e-02 nm, Epot= -4.50449e+04 Fmax= 3.04497e+02, atom= 401\n", - "Step= 254, Dmax= 1.8e-02 nm, Epot= -4.50510e+04 Fmax= 1.61504e+02, atom= 401\n", - "Step= 256, Dmax= 1.1e-02 nm, Epot= -4.50551e+04 Fmax= 1.01147e+02, atom= 401\n", - "Step= 257, Dmax= 1.3e-02 nm, Epot= -4.50588e+04 Fmax= 2.37717e+02, atom= 401\n", - "Step= 258, Dmax= 1.6e-02 nm, Epot= -4.50637e+04 Fmax= 1.64128e+02, atom= 401\n", - "Step= 259, Dmax= 1.9e-02 nm, Epot= -4.50650e+04 Fmax= 3.18171e+02, atom= 401\n", - "Step= 260, Dmax= 2.3e-02 nm, Epot= -4.50699e+04 Fmax= 2.68223e+02, atom= 401\n", - "Step= 262, Dmax= 1.4e-02 nm, Epot= -4.50763e+04 Fmax= 7.52588e+01, atom= 401\n", - "Step= 263, Dmax= 1.6e-02 nm, Epot= -4.50810e+04 Fmax= 3.45060e+02, atom= 401\n", - "Step= 264, Dmax= 2.0e-02 nm, Epot= -4.50880e+04 Fmax= 1.59837e+02, atom= 401\n", - "Step= 266, Dmax= 1.2e-02 nm, Epot= -4.50918e+04 Fmax= 1.20073e+02, atom= 401\n", - "Step= 267, Dmax= 1.4e-02 nm, Epot= -4.50946e+04 Fmax= 2.39634e+02, atom= 401\n", - "Step= 268, Dmax= 1.7e-02 nm, Epot= -4.50990e+04 Fmax= 1.90055e+02, atom= 401\n", - "Step= 269, Dmax= 2.0e-02 nm, Epot= -4.50997e+04 Fmax= 3.24806e+02, atom= 401\n", - "Step= 270, Dmax= 2.4e-02 nm, Epot= -4.51036e+04 Fmax= 3.05721e+02, atom= 401\n", - "Step= 272, Dmax= 1.5e-02 nm, Epot= -4.51111e+04 Fmax= 6.60527e+01, atom= 401\n", - "Step= 273, Dmax= 1.8e-02 nm, Epot= -4.51161e+04 Fmax= 3.82814e+02, atom= 401\n", - "Step= 274, Dmax= 2.1e-02 nm, Epot= -4.51237e+04 Fmax= 1.63521e+02, atom= 401\n", - "Step= 276, Dmax= 1.3e-02 nm, Epot= -4.51273e+04 Fmax= 1.36521e+02, atom= 401\n", - "Step= 277, Dmax= 1.5e-02 nm, Epot= -4.51294e+04 Fmax= 2.45335e+02, atom= 401\n", - "Step= 278, Dmax= 1.8e-02 nm, Epot= -4.51333e+04 Fmax= 2.14659e+02, atom= 401\n", - "Step= 279, Dmax= 2.2e-02 nm, Epot= -4.51336e+04 Fmax= 3.34622e+02, atom= 401\n", - "Step= 280, Dmax= 2.6e-02 nm, Epot= -4.51364e+04 Fmax= 3.46212e+02, atom= 401\n", - "Step= 282, Dmax= 1.6e-02 nm, Epot= -4.51453e+04 Fmax= 5.70057e+01, atom= 401\n", - "Step= 283, Dmax= 1.9e-02 nm, Epot= -4.51516e+04 Fmax= 4.16424e+02, atom= 401\n", - "Step= 284, Dmax= 2.3e-02 nm, Epot= -4.51593e+04 Fmax= 1.73258e+02, atom= 401\n", - "Step= 286, Dmax= 1.4e-02 nm, Epot= -4.51626e+04 Fmax= 1.52974e+02, atom= 401\n", - "Step= 287, Dmax= 1.6e-02 nm, Epot= -4.51643e+04 Fmax= 2.52309e+02, atom= 401\n", - "Step= 288, Dmax= 2.0e-02 nm, Epot= -4.51675e+04 Fmax= 2.42247e+02, atom= 401\n", - "Step= 290, Dmax= 1.2e-02 nm, Epot= -4.51730e+04 Fmax= 5.38744e+01, atom= 401\n", - "Step= 291, Dmax= 1.4e-02 nm, Epot= -4.51789e+04 Fmax= 2.88017e+02, atom= 401\n", - "Step= 292, Dmax= 1.7e-02 nm, Epot= -4.51843e+04 Fmax= 1.35095e+02, atom= 401\n", - "Step= 294, Dmax= 1.0e-02 nm, Epot= -4.51874e+04 Fmax= 1.07492e+02, atom= 401\n", - "Step= 295, Dmax= 1.2e-02 nm, Epot= -4.51899e+04 Fmax= 1.94901e+02, atom= 401\n", - "Step= 296, Dmax= 1.5e-02 nm, Epot= -4.51932e+04 Fmax= 1.70760e+02, atom= 401\n", - "Step= 297, Dmax= 1.8e-02 nm, Epot= -4.51944e+04 Fmax= 2.63306e+02, atom= 401\n", - "Step= 298, Dmax= 2.1e-02 nm, Epot= -4.51971e+04 Fmax= 2.73339e+02, atom= 401\n", - "Step= 299, Dmax= 2.5e-02 nm, Epot= -4.51971e+04 Fmax= 3.51506e+02, atom= 401\n", - "Step= 301, Dmax= 1.5e-02 nm, Epot= -4.52067e+04 Fmax= 5.00179e+01, atom= 732\n", - "Step= 302, Dmax= 1.8e-02 nm, Epot= -4.52134e+04 Fmax= 3.31663e+02, atom= 732\n", - "Step= 303, Dmax= 2.2e-02 nm, Epot= -4.52186e+04 Fmax= 2.61202e+02, atom= 1356\n", - "Step= 305, Dmax= 1.3e-02 nm, Epot= -4.52239e+04 Fmax= 7.50971e+01, atom= 401\n", - "Step= 306, Dmax= 1.6e-02 nm, Epot= -4.52271e+04 Fmax= 3.02770e+02, atom= 401\n", - "Step= 307, Dmax= 1.9e-02 nm, Epot= -4.52323e+04 Fmax= 1.51597e+02, atom= 401\n", - "Step= 309, Dmax= 1.1e-02 nm, Epot= -4.52355e+04 Fmax= 1.13761e+02, atom= 401\n", - "Step= 310, Dmax= 1.4e-02 nm, Epot= -4.52372e+04 Fmax= 2.18595e+02, atom= 401\n", - "Step= 311, Dmax= 1.6e-02 nm, Epot= -4.52407e+04 Fmax= 1.88675e+02, atom= 401\n", - "Step= 312, Dmax= 2.0e-02 nm, Epot= -4.52410e+04 Fmax= 2.86985e+02, atom= 401\n", - "Step= 313, Dmax= 2.3e-02 nm, Epot= -4.52431e+04 Fmax= 3.11899e+02, atom= 401\n", - "Step= 315, Dmax= 1.4e-02 nm, Epot= -4.52510e+04 Fmax= 4.49427e+01, atom= 401\n", - "Step= 316, Dmax= 1.7e-02 nm, Epot= -4.52589e+04 Fmax= 3.31565e+02, atom= 401\n", - "Step= 317, Dmax= 2.0e-02 nm, Epot= -4.52642e+04 Fmax= 1.64041e+02, atom= 1356\n", - "Step= 319, Dmax= 1.2e-02 nm, Epot= -4.52673e+04 Fmax= 1.24027e+02, atom= 401\n", - "Step= 320, Dmax= 1.5e-02 nm, Epot= -4.52684e+04 Fmax= 2.30370e+02, atom= 1356\n", - "Step= 321, Dmax= 1.8e-02 nm, Epot= -4.52718e+04 Fmax= 2.02402e+02, atom= 401\n", - "Step= 323, Dmax= 1.1e-02 nm, Epot= -4.52763e+04 Fmax= 5.69089e+01, atom= 4016\n", - "Step= 324, Dmax= 1.3e-02 nm, Epot= -4.52803e+04 Fmax= 2.35743e+02, atom= 401\n", - "Step= 325, Dmax= 1.5e-02 nm, Epot= -4.52845e+04 Fmax= 1.23375e+02, atom= 1356\n", - "Step= 327, Dmax= 9.1e-03 nm, Epot= -4.52873e+04 Fmax= 8.89979e+01, atom= 401\n", - "Step= 328, Dmax= 1.1e-02 nm, Epot= -4.52894e+04 Fmax= 1.75425e+02, atom= 1356\n", - "Step= 329, Dmax= 1.3e-02 nm, Epot= -4.52925e+04 Fmax= 1.40784e+02, atom= 1356\n", - "Step= 330, Dmax= 1.6e-02 nm, Epot= -4.52932e+04 Fmax= 2.40298e+02, atom= 1356\n", - "Step= 331, Dmax= 1.9e-02 nm, Epot= -4.52962e+04 Fmax= 2.16653e+02, atom= 1356\n", - "Step= 333, Dmax= 1.1e-02 nm, Epot= -4.53011e+04 Fmax= 5.95828e+01, atom= 4016\n", - "Step= 334, Dmax= 1.4e-02 nm, Epot= -4.53043e+04 Fmax= 2.50744e+02, atom= 401\n", - "Step= 335, Dmax= 1.6e-02 nm, Epot= -4.53087e+04 Fmax= 1.33888e+02, atom= 1356\n", - "Step= 337, Dmax= 9.8e-03 nm, Epot= -4.53114e+04 Fmax= 9.00042e+01, atom= 1356\n", - "Step= 338, Dmax= 1.2e-02 nm, Epot= -4.53128e+04 Fmax= 1.95609e+02, atom= 1356\n", - "Step= 339, Dmax= 1.4e-02 nm, Epot= -4.53162e+04 Fmax= 1.40319e+02, atom= 1356\n", - "Step= 341, Dmax= 8.4e-03 nm, Epot= -4.53191e+04 Fmax= 5.90424e+01, atom= 4016\n", - "Step= 342, Dmax= 1.0e-02 nm, Epot= -4.53217e+04 Fmax= 1.77152e+02, atom= 401\n", - "Step= 343, Dmax= 1.2e-02 nm, Epot= -4.53249e+04 Fmax= 1.07718e+02, atom= 1356\n", - "Step= 344, Dmax= 1.5e-02 nm, Epot= -4.53251e+04 Fmax= 2.43520e+02, atom= 401\n", - "Step= 345, Dmax= 1.8e-02 nm, Epot= -4.53290e+04 Fmax= 1.67318e+02, atom= 1356\n", - "Step= 347, Dmax= 1.1e-02 nm, Epot= -4.53323e+04 Fmax= 7.74304e+01, atom= 732\n", - "Step= 348, Dmax= 1.3e-02 nm, Epot= -4.53333e+04 Fmax= 2.19156e+02, atom= 1356\n", - "Step= 349, Dmax= 1.5e-02 nm, Epot= -4.53371e+04 Fmax= 1.41075e+02, atom= 1356\n", - "Step= 351, Dmax= 9.1e-03 nm, Epot= -4.53399e+04 Fmax= 6.69161e+01, atom= 4016\n", - "Step= 352, Dmax= 1.1e-02 nm, Epot= -4.53415e+04 Fmax= 1.85721e+02, atom= 401\n", - "Step= 353, Dmax= 1.3e-02 nm, Epot= -4.53448e+04 Fmax= 1.18214e+02, atom= 1356\n", - "Step= 355, Dmax= 7.8e-03 nm, Epot= -4.53472e+04 Fmax= 6.13028e+01, atom= 732\n", - "Step= 356, Dmax= 9.4e-03 nm, Epot= -4.53491e+04 Fmax= 1.58820e+02, atom= 1356\n", - "Step= 357, Dmax= 1.1e-02 nm, Epot= -4.53519e+04 Fmax= 1.03229e+02, atom= 1356\n", - "Step= 358, Dmax= 1.4e-02 nm, Epot= -4.53522e+04 Fmax= 2.17340e+02, atom= 1356\n", - "Step= 359, Dmax= 1.6e-02 nm, Epot= -4.53554e+04 Fmax= 1.58522e+02, atom= 1356\n", - "Step= 361, Dmax= 9.8e-03 nm, Epot= -4.53585e+04 Fmax= 6.23680e+01, atom= 401\n", - "Step= 362, Dmax= 1.2e-02 nm, Epot= -4.53596e+04 Fmax= 2.04066e+02, atom= 401\n", - "Step= 363, Dmax= 1.4e-02 nm, Epot= -4.53633e+04 Fmax= 1.21447e+02, atom= 1356\n", - "Step= 365, Dmax= 8.4e-03 nm, Epot= -4.53657e+04 Fmax= 6.97432e+01, atom= 7326\n", - "Step= 366, Dmax= 1.0e-02 nm, Epot= -4.53672e+04 Fmax= 1.61126e+02, atom= 732\n", - "Step= 367, Dmax= 1.2e-02 nm, Epot= -4.53698e+04 Fmax= 1.12871e+02, atom= 1356\n", - "Step= 369, Dmax= 7.3e-03 nm, Epot= -4.53721e+04 Fmax= 4.85567e+01, atom= 1356\n", - "Step= 370, Dmax= 8.7e-03 nm, Epot= -4.53740e+04 Fmax= 1.49619e+02, atom= 1356\n", - "Step= 371, Dmax= 1.0e-02 nm, Epot= -4.53769e+04 Fmax= 9.05348e+01, atom= 1356\n", - "Step= 372, Dmax= 1.3e-02 nm, Epot= -4.53771e+04 Fmax= 1.91229e+02, atom= 1356\n", - "Step= 373, Dmax= 1.5e-02 nm, Epot= -4.53800e+04 Fmax= 1.54674e+02, atom= 732\n", - "Step= 375, Dmax= 9.1e-03 nm, Epot= -4.53832e+04 Fmax= 5.34967e+01, atom= 7326\n", - "Step= 376, Dmax= 1.1e-02 nm, Epot= -4.53848e+04 Fmax= 1.88271e+02, atom= 732\n", - "Step= 377, Dmax= 1.3e-02 nm, Epot= -4.53881e+04 Fmax= 1.03203e+02, atom= 732\n", - "Step= 379, Dmax= 7.8e-03 nm, Epot= -4.53902e+04 Fmax= 6.70056e+01, atom= 732\n", - "Step= 380, Dmax= 9.4e-03 nm, Epot= -4.53914e+04 Fmax= 1.40503e+02, atom= 732\n", - "Step= 381, Dmax= 1.1e-02 nm, Epot= -4.53938e+04 Fmax= 1.13925e+02, atom= 732\n", - "Step= 382, Dmax= 1.4e-02 nm, Epot= -4.53938e+04 Fmax= 1.82442e+02, atom= 732\n", - "Step= 383, Dmax= 1.6e-02 nm, Epot= -4.53956e+04 Fmax= 1.86432e+02, atom= 732\n", - "Step= 385, Dmax= 9.7e-03 nm, Epot= -4.54002e+04 Fmax= 3.45548e+01, atom= 732\n", - "Step= 386, Dmax= 1.2e-02 nm, Epot= -4.54021e+04 Fmax= 2.22666e+02, atom= 732\n", - "Step= 387, Dmax= 1.4e-02 nm, Epot= -4.54072e+04 Fmax= 9.98106e+01, atom= 1264\n", - "Step= 389, Dmax= 8.4e-03 nm, Epot= -4.54092e+04 Fmax= 8.52490e+01, atom= 1264\n", - "Step= 390, Dmax= 1.0e-02 nm, Epot= -4.54101e+04 Fmax= 1.42023e+02, atom= 1264\n", - "Step= 391, Dmax= 1.2e-02 nm, Epot= -4.54122e+04 Fmax= 1.32120e+02, atom= 1264\n", - "Step= 392, Dmax= 1.5e-02 nm, Epot= -4.54123e+04 Fmax= 1.95726e+02, atom= 1264\n", - "Step= 393, Dmax= 1.7e-02 nm, Epot= -4.54141e+04 Fmax= 2.01007e+02, atom= 1264\n", - "Step= 395, Dmax= 1.0e-02 nm, Epot= -4.54190e+04 Fmax= 4.75607e+01, atom= 5824\n", - "Step= 396, Dmax= 1.3e-02 nm, Epot= -4.54211e+04 Fmax= 2.24722e+02, atom= 582\n", - "Step= 397, Dmax= 1.5e-02 nm, Epot= -4.54246e+04 Fmax= 1.24923e+02, atom= 1264\n", - "Step= 399, Dmax= 9.0e-03 nm, Epot= -4.54267e+04 Fmax= 6.83893e+01, atom= 1264\n", - "Step= 400, Dmax= 1.1e-02 nm, Epot= -4.54277e+04 Fmax= 1.77135e+02, atom= 1264\n", - "Step= 401, Dmax= 1.3e-02 nm, Epot= -4.54306e+04 Fmax= 1.16403e+02, atom= 1264\n", - "Step= 403, Dmax= 7.8e-03 nm, Epot= -4.54327e+04 Fmax= 5.91627e+01, atom= 1264\n", - "Step= 404, Dmax= 9.4e-03 nm, Epot= -4.54344e+04 Fmax= 1.60136e+02, atom= 1264\n", - "Step= 405, Dmax= 1.1e-02 nm, Epot= -4.54369e+04 Fmax= 9.59752e+01, atom= 1264\n", - "Step= 406, Dmax= 1.4e-02 nm, Epot= -4.54372e+04 Fmax= 2.22145e+02, atom= 1264\n", - "Step= 407, Dmax= 1.6e-02 nm, Epot= -4.54403e+04 Fmax= 1.46206e+02, atom= 1264\n", - "Step= 409, Dmax= 9.7e-03 nm, Epot= -4.54429e+04 Fmax= 6.10649e+01, atom= 1264\n", - "Step= 410, Dmax= 1.2e-02 nm, Epot= -4.54435e+04 Fmax= 2.10118e+02, atom= 1264\n", - "Step= 411, Dmax= 1.4e-02 nm, Epot= -4.54476e+04 Fmax= 1.10080e+02, atom= 1264\n", - "Step= 413, Dmax= 8.4e-03 nm, Epot= -4.54496e+04 Fmax= 7.58745e+01, atom= 1264\n", - "Step= 414, Dmax= 1.0e-02 nm, Epot= -4.54509e+04 Fmax= 1.59076e+02, atom= 1264\n", - "Step= 415, Dmax= 1.2e-02 nm, Epot= -4.54533e+04 Fmax= 1.14893e+02, atom= 1264\n", - "Step= 416, Dmax= 1.5e-02 nm, Epot= -4.54533e+04 Fmax= 2.25622e+02, atom= 1264\n", - "Step= 417, Dmax= 1.7e-02 nm, Epot= -4.54562e+04 Fmax= 1.69988e+02, atom= 1264\n", - "Step= 419, Dmax= 1.0e-02 nm, Epot= -4.54596e+04 Fmax= 5.53755e+01, atom= 7184\n", - "Step= 420, Dmax= 1.3e-02 nm, Epot= -4.54597e+04 Fmax= 2.36358e+02, atom= 1264\n", - "Step= 421, Dmax= 1.5e-02 nm, Epot= -4.54650e+04 Fmax= 1.14802e+02, atom= 1264\n", - "Step= 423, Dmax= 9.0e-03 nm, Epot= -4.54671e+04 Fmax= 8.30082e+01, atom= 1264\n", - "Step= 424, Dmax= 1.1e-02 nm, Epot= -4.54682e+04 Fmax= 1.71070e+02, atom= 1264\n", - "Step= 425, Dmax= 1.3e-02 nm, Epot= -4.54709e+04 Fmax= 1.23981e+02, atom= 1264\n", - "Step= 427, Dmax= 7.8e-03 nm, Epot= -4.54735e+04 Fmax= 4.69152e+01, atom= 1264\n", - "Step= 428, Dmax= 9.4e-03 nm, Epot= -4.54754e+04 Fmax= 1.66723e+02, atom= 1264\n", - "Step= 429, Dmax= 1.1e-02 nm, Epot= -4.54789e+04 Fmax= 9.07986e+01, atom= 1264\n", - "Step= 431, Dmax= 6.7e-03 nm, Epot= -4.54810e+04 Fmax= 5.99520e+01, atom= 1264\n", - "Step= 432, Dmax= 8.1e-03 nm, Epot= -4.54829e+04 Fmax= 1.29197e+02, atom= 1264\n", - "Step= 433, Dmax= 9.7e-03 nm, Epot= -4.54854e+04 Fmax= 9.15278e+01, atom= 1264\n", - "Step= 434, Dmax= 1.2e-02 nm, Epot= -4.54863e+04 Fmax= 1.81738e+02, atom= 1264\n", - "Step= 435, Dmax= 1.4e-02 nm, Epot= -4.54892e+04 Fmax= 1.37133e+02, atom= 1264\n", - "Step= 437, Dmax= 8.4e-03 nm, Epot= -4.54922e+04 Fmax= 4.61792e+01, atom= 1264\n", - "Step= 438, Dmax= 1.0e-02 nm, Epot= -4.54938e+04 Fmax= 1.91067e+02, atom= 1264\n", - "Step= 439, Dmax= 1.2e-02 nm, Epot= -4.54983e+04 Fmax= 8.91475e+01, atom= 1264\n", - "Step= 441, Dmax= 7.2e-03 nm, Epot= -4.55005e+04 Fmax= 7.20804e+01, atom= 1264\n", - "Step= 442, Dmax= 8.7e-03 nm, Epot= -4.55023e+04 Fmax= 1.30895e+02, atom= 1264\n", - "Step= 443, Dmax= 1.0e-02 nm, Epot= -4.55048e+04 Fmax= 1.06668e+02, atom= 1264\n", - "Step= 444, Dmax= 1.3e-02 nm, Epot= -4.55056e+04 Fmax= 1.86899e+02, atom= 1264\n", - "Step= 445, Dmax= 1.5e-02 nm, Epot= -4.55084e+04 Fmax= 1.56771e+02, atom= 1264\n", - "Step= 447, Dmax= 9.0e-03 nm, Epot= -4.55121e+04 Fmax= 4.47535e+01, atom= 7184\n", - "Step= 448, Dmax= 1.1e-02 nm, Epot= -4.55141e+04 Fmax= 1.99787e+02, atom= 1264\n", - "Step= 449, Dmax= 1.3e-02 nm, Epot= -4.55189e+04 Fmax= 1.06720e+02, atom= 1264\n", - "Step= 451, Dmax= 7.8e-03 nm, Epot= -4.55214e+04 Fmax= 6.72726e+01, atom= 1264\n", - "Step= 452, Dmax= 9.4e-03 nm, Epot= -4.55231e+04 Fmax= 1.55689e+02, atom= 1264\n", - "Step= 453, Dmax= 1.1e-02 nm, Epot= -4.55262e+04 Fmax= 1.03024e+02, atom= 1264\n", - "Step= 454, Dmax= 1.3e-02 nm, Epot= -4.55267e+04 Fmax= 2.17718e+02, atom= 1264\n", - "Step= 455, Dmax= 1.6e-02 nm, Epot= -4.55304e+04 Fmax= 1.55432e+02, atom= 1264\n", - "Step= 457, Dmax= 9.7e-03 nm, Epot= -4.55338e+04 Fmax= 5.67265e+01, atom= 7184\n", - "Step= 458, Dmax= 1.2e-02 nm, Epot= -4.55349e+04 Fmax= 2.21905e+02, atom= 1264\n", - "Step= 459, Dmax= 1.4e-02 nm, Epot= -4.55402e+04 Fmax= 1.05630e+02, atom= 1264\n", - "Step= 461, Dmax= 8.4e-03 nm, Epot= -4.55426e+04 Fmax= 8.11209e+01, atom= 1264\n", - "Step= 462, Dmax= 1.0e-02 nm, Epot= -4.55444e+04 Fmax= 1.56235e+02, atom= 1264\n", - "Step= 463, Dmax= 1.2e-02 nm, Epot= -4.55473e+04 Fmax= 1.20712e+02, atom= 1264\n", - "Step= 464, Dmax= 1.4e-02 nm, Epot= -4.55478e+04 Fmax= 2.22606e+02, atom= 1264\n", - "Step= 465, Dmax= 1.7e-02 nm, Epot= -4.55511e+04 Fmax= 1.77102e+02, atom= 1264\n", - "Step= 467, Dmax= 1.0e-02 nm, Epot= -4.55550e+04 Fmax= 5.61709e+01, atom= 7184\n", - "Step= 468, Dmax= 1.3e-02 nm, Epot= -4.55566e+04 Fmax= 2.26963e+02, atom= 1264\n", - "Step= 469, Dmax= 1.5e-02 nm, Epot= -4.55615e+04 Fmax= 1.29722e+02, atom= 1264\n", - "Step= 471, Dmax= 9.0e-03 nm, Epot= -4.55642e+04 Fmax= 7.08086e+01, atom= 1264\n", - "Step= 472, Dmax= 1.1e-02 nm, Epot= -4.55658e+04 Fmax= 1.92649e+02, atom= 1264\n", - "Step= 473, Dmax= 1.3e-02 nm, Epot= -4.55694e+04 Fmax= 1.08901e+02, atom= 1264\n", - "Step= 475, Dmax= 7.8e-03 nm, Epot= -4.55718e+04 Fmax= 6.45256e+01, atom= 1264\n", - "Step= 476, Dmax= 9.3e-03 nm, Epot= -4.55739e+04 Fmax= 1.48044e+02, atom= 1264\n", - "Step= 477, Dmax= 1.1e-02 nm, Epot= -4.55767e+04 Fmax= 1.10633e+02, atom= 1264\n", - "Step= 478, Dmax= 1.3e-02 nm, Epot= -4.55776e+04 Fmax= 1.95536e+02, atom= 1264\n", - "Step= 479, Dmax= 1.6e-02 nm, Epot= -4.55803e+04 Fmax= 1.76651e+02, atom= 1264\n", - "Step= 481, Dmax= 9.7e-03 nm, Epot= -4.55839e+04 Fmax= 5.26737e+01, atom= 5824\n", - "Step= 482, Dmax= 1.2e-02 nm, Epot= -4.55866e+04 Fmax= 2.10209e+02, atom= 1264\n", - "Step= 483, Dmax= 1.4e-02 nm, Epot= -4.55900e+04 Fmax= 1.18189e+02, atom= 1264\n", - "Step= 485, Dmax= 8.4e-03 nm, Epot= -4.55924e+04 Fmax= 6.57998e+01, atom= 1264\n", - "Step= 486, Dmax= 1.0e-02 nm, Epot= -4.55942e+04 Fmax= 1.63159e+02, atom= 1264\n", - "Step= 487, Dmax= 1.2e-02 nm, Epot= -4.55971e+04 Fmax= 1.14192e+02, atom= 1264\n", - "Step= 488, Dmax= 1.4e-02 nm, Epot= -4.55974e+04 Fmax= 2.13428e+02, atom= 1264\n", - "Step= 489, Dmax= 1.7e-02 nm, Epot= -4.56001e+04 Fmax= 1.85925e+02, atom= 1264\n", - "Step= 491, Dmax= 1.0e-02 nm, Epot= -4.56038e+04 Fmax= 5.90512e+01, atom= 5824\n", - "Step= 492, Dmax= 1.2e-02 nm, Epot= -4.56054e+04 Fmax= 2.24859e+02, atom= 1264\n", - "Step= 493, Dmax= 1.5e-02 nm, Epot= -4.56090e+04 Fmax= 1.26452e+02, atom= 1264\n", - "Step= 495, Dmax= 9.0e-03 nm, Epot= -4.56113e+04 Fmax= 6.98403e+01, atom= 1264\n", - "Step= 496, Dmax= 1.1e-02 nm, Epot= -4.56125e+04 Fmax= 1.74811e+02, atom= 1264\n", - "Step= 497, Dmax= 1.3e-02 nm, Epot= -4.56154e+04 Fmax= 1.22608e+02, atom= 1264\n", - "Step= 499, Dmax= 7.8e-03 nm, Epot= -4.56176e+04 Fmax= 5.37046e+01, atom= 5824\n", - "Step= 500, Dmax= 9.3e-03 nm, Epot= -4.56195e+04 Fmax= 1.67245e+02, atom= 1264\n", - "Step= 501, Dmax= 1.1e-02 nm, Epot= -4.56222e+04 Fmax= 8.98307e+01, atom= 1264\n", - "Step= 502, Dmax= 1.3e-02 nm, Epot= -4.56222e+04 Fmax= 2.34486e+02, atom= 1264\n", - "Step= 503, Dmax= 1.6e-02 nm, Epot= -4.56258e+04 Fmax= 1.36234e+02, atom= 1264\n", - "Step= 505, Dmax= 9.7e-03 nm, Epot= -4.56282e+04 Fmax= 7.40982e+01, atom= 1264\n", - "Step= 506, Dmax= 1.2e-02 nm, Epot= -4.56287e+04 Fmax= 1.89739e+02, atom= 1264\n", - "Step= 507, Dmax= 1.4e-02 nm, Epot= -4.56318e+04 Fmax= 1.30278e+02, atom= 1264\n", - "Step= 509, Dmax= 8.3e-03 nm, Epot= -4.56342e+04 Fmax= 5.96627e+01, atom= 5824\n", - "Step= 510, Dmax= 1.0e-02 nm, Epot= -4.56353e+04 Fmax= 1.74925e+02, atom= 1264\n", - "Step= 511, Dmax= 1.2e-02 nm, Epot= -4.56382e+04 Fmax= 1.00090e+02, atom= 1264\n", - "Step= 513, Dmax= 7.2e-03 nm, Epot= -4.56402e+04 Fmax= 5.99708e+01, atom= 1264\n", - "Step= 514, Dmax= 8.7e-03 nm, Epot= -4.56414e+04 Fmax= 1.32142e+02, atom= 1264\n", - "Step= 515, Dmax= 1.0e-02 nm, Epot= -4.56435e+04 Fmax= 1.06018e+02, atom= 1264\n", - "Step= 517, Dmax= 6.2e-03 nm, Epot= -4.56457e+04 Fmax= 3.76699e+01, atom= 5824\n", - "Step= 518, Dmax= 7.5e-03 nm, Epot= -4.56476e+04 Fmax= 1.31954e+02, atom= 1264\n", - "Step= 519, Dmax= 9.0e-03 nm, Epot= -4.56502e+04 Fmax= 7.45799e+01, atom= 626\n", - "Step= 521, Dmax= 5.4e-03 nm, Epot= -4.56519e+04 Fmax= 5.08350e+01, atom= 626\n", - "Step= 522, Dmax= 6.5e-03 nm, Epot= -4.56533e+04 Fmax= 1.04445e+02, atom= 626\n", - "Step= 523, Dmax= 7.8e-03 nm, Epot= -4.56552e+04 Fmax= 7.94883e+01, atom= 626\n", - "Step= 524, Dmax= 9.3e-03 nm, Epot= -4.56561e+04 Fmax= 1.42802e+02, atom= 626\n", - "Step= 525, Dmax= 1.1e-02 nm, Epot= -4.56581e+04 Fmax= 1.23094e+02, atom= 626\n", - "Step= 526, Dmax= 1.3e-02 nm, Epot= -4.56583e+04 Fmax= 1.96708e+02, atom= 626\n", - "Step= 527, Dmax= 1.6e-02 nm, Epot= -4.56600e+04 Fmax= 1.88176e+02, atom= 626\n", - "Step= 529, Dmax= 9.6e-03 nm, Epot= -4.56635e+04 Fmax= 4.08446e+01, atom= 339\n", - "Step= 530, Dmax= 1.2e-02 nm, Epot= -4.56653e+04 Fmax= 2.31817e+02, atom= 626\n", - "Step= 531, Dmax= 1.4e-02 nm, Epot= -4.56688e+04 Fmax= 1.05576e+02, atom= 626\n", - "Step= 533, Dmax= 8.3e-03 nm, Epot= -4.56704e+04 Fmax= 8.48921e+01, atom= 626\n", - "Step= 534, Dmax= 1.0e-02 nm, Epot= -4.56713e+04 Fmax= 1.55737e+02, atom= 626\n", - "Step= 535, Dmax= 1.2e-02 nm, Epot= -4.56730e+04 Fmax= 1.29263e+02, atom= 626\n", - "Step= 536, Dmax= 1.4e-02 nm, Epot= -4.56731e+04 Fmax= 2.15519e+02, atom= 626\n", - "Step= 537, Dmax= 1.7e-02 nm, Epot= -4.56747e+04 Fmax= 1.98912e+02, atom= 626\n", - "Step= 539, Dmax= 1.0e-02 nm, Epot= -4.56779e+04 Fmax= 4.67466e+01, atom= 339\n", - "Step= 540, Dmax= 1.2e-02 nm, Epot= -4.56791e+04 Fmax= 2.47455e+02, atom= 626\n", - "Step= 541, Dmax= 1.5e-02 nm, Epot= -4.56825e+04 Fmax= 1.15021e+02, atom= 626\n", - "Step= 543, Dmax= 9.0e-03 nm, Epot= -4.56840e+04 Fmax= 8.88231e+01, atom= 626\n", - "Step= 544, Dmax= 1.1e-02 nm, Epot= -4.56847e+04 Fmax= 1.70270e+02, atom= 626\n", - "Step= 545, Dmax= 1.3e-02 nm, Epot= -4.56864e+04 Fmax= 1.37225e+02, atom= 626\n", - "Step= 547, Dmax= 7.7e-03 nm, Epot= -4.56883e+04 Fmax= 4.60359e+01, atom= 626\n", - "Step= 548, Dmax= 9.3e-03 nm, Epot= -4.56899e+04 Fmax= 1.71175e+02, atom= 626\n", - "Step= 549, Dmax= 1.1e-02 nm, Epot= -4.56920e+04 Fmax= 9.40015e+01, atom= 626\n", - "Step= 551, Dmax= 6.7e-03 nm, Epot= -4.56934e+04 Fmax= 5.98856e+01, atom= 626\n", - "Step= 552, Dmax= 8.0e-03 nm, Epot= -4.56945e+04 Fmax= 1.34785e+02, atom= 626\n", - "Step= 553, Dmax= 9.6e-03 nm, Epot= -4.56961e+04 Fmax= 9.46899e+01, atom= 626\n", - "Step= 554, Dmax= 1.2e-02 nm, Epot= -4.56965e+04 Fmax= 1.82785e+02, atom= 626\n", - "Step= 555, Dmax= 1.4e-02 nm, Epot= -4.56982e+04 Fmax= 1.49079e+02, atom= 626\n", - "Step= 557, Dmax= 8.3e-03 nm, Epot= -4.57002e+04 Fmax= 4.78267e+01, atom= 626\n", - "Step= 558, Dmax= 1.0e-02 nm, Epot= -4.57014e+04 Fmax= 1.88086e+02, atom= 626\n", - "Step= 559, Dmax= 1.2e-02 nm, Epot= -4.57037e+04 Fmax= 9.81260e+01, atom= 626\n", - "Step= 561, Dmax= 7.2e-03 nm, Epot= -4.57050e+04 Fmax= 6.65660e+01, atom= 626\n", - "Step= 562, Dmax= 8.6e-03 nm, Epot= -4.57059e+04 Fmax= 1.42578e+02, atom= 626\n", - "Step= 563, Dmax= 1.0e-02 nm, Epot= -4.57075e+04 Fmax= 1.04330e+02, atom= 626\n", - "Step= 564, Dmax= 1.2e-02 nm, Epot= -4.57075e+04 Fmax= 1.93645e+02, atom= 626\n", - "Step= 565, Dmax= 1.5e-02 nm, Epot= -4.57092e+04 Fmax= 1.64932e+02, atom= 626\n", - "Step= 567, Dmax= 8.9e-03 nm, Epot= -4.57115e+04 Fmax= 4.80302e+01, atom= 626\n", - "Step= 568, Dmax= 1.1e-02 nm, Epot= -4.57123e+04 Fmax= 2.05861e+02, atom= 626\n", - "Step= 569, Dmax= 1.3e-02 nm, Epot= -4.57149e+04 Fmax= 1.02901e+02, atom= 626\n", - "Step= 571, Dmax= 7.7e-03 nm, Epot= -4.57162e+04 Fmax= 7.43972e+01, atom= 626\n", - "Step= 572, Dmax= 9.3e-03 nm, Epot= -4.57168e+04 Fmax= 1.49815e+02, atom= 626\n", - "Step= 573, Dmax= 1.1e-02 nm, Epot= -4.57183e+04 Fmax= 1.16146e+02, atom= 626\n", - "Step= 575, Dmax= 6.7e-03 nm, Epot= -4.57198e+04 Fmax= 4.34834e+01, atom= 626\n", - "Step= 576, Dmax= 8.0e-03 nm, Epot= -4.57211e+04 Fmax= 1.43232e+02, atom= 626\n", - "Step= 577, Dmax= 9.6e-03 nm, Epot= -4.57228e+04 Fmax= 8.55387e+01, atom= 626\n", - "Step= 578, Dmax= 1.2e-02 nm, Epot= -4.57228e+04 Fmax= 1.92399e+02, atom= 626\n", - "Step= 579, Dmax= 1.4e-02 nm, Epot= -4.57247e+04 Fmax= 1.36339e+02, atom= 626\n", - "Step= 581, Dmax= 8.3e-03 nm, Epot= -4.57264e+04 Fmax= 5.45353e+01, atom= 626\n", - "Step= 582, Dmax= 1.0e-02 nm, Epot= -4.57265e+04 Fmax= 1.96394e+02, atom= 626\n", - "Step= 583, Dmax= 1.2e-02 nm, Epot= -4.57291e+04 Fmax= 9.64268e+01, atom= 626\n", - "Step= 585, Dmax= 7.2e-03 nm, Epot= -4.57303e+04 Fmax= 7.41450e+01, atom= 626\n", - "Step= 586, Dmax= 8.6e-03 nm, Epot= -4.57311e+04 Fmax= 1.29012e+02, atom= 626\n", - "Step= 587, Dmax= 1.0e-02 nm, Epot= -4.57323e+04 Fmax= 1.15697e+02, atom= 626\n", - "Step= 588, Dmax= 1.2e-02 nm, Epot= -4.57324e+04 Fmax= 1.82031e+02, atom= 626\n", - "Step= 589, Dmax= 1.5e-02 nm, Epot= -4.57336e+04 Fmax= 1.69834e+02, atom= 626\n", - "Step= 591, Dmax= 8.9e-03 nm, Epot= -4.57359e+04 Fmax= 3.83471e+01, atom= 111\n", - "Step= 593, Dmax= 5.4e-03 nm, Epot= -4.57372e+04 Fmax= 9.56553e+01, atom= 626\n", - "Step= 594, Dmax= 6.4e-03 nm, Epot= -4.57383e+04 Fmax= 5.84311e+01, atom= 626\n", - "Step= 595, Dmax= 7.7e-03 nm, Epot= -4.57391e+04 Fmax= 1.26123e+02, atom= 626\n", - "Step= 596, Dmax= 9.3e-03 nm, Epot= -4.57405e+04 Fmax= 9.46619e+01, atom= 626\n", - "Step= 597, Dmax= 1.1e-02 nm, Epot= -4.57406e+04 Fmax= 1.70938e+02, atom= 626\n", - "Step= 598, Dmax= 1.3e-02 nm, Epot= -4.57419e+04 Fmax= 1.50439e+02, atom= 626\n", - "Step= 600, Dmax= 8.0e-03 nm, Epot= -4.57439e+04 Fmax= 4.12865e+01, atom= 626\n", - "Step= 601, Dmax= 9.6e-03 nm, Epot= -4.57448e+04 Fmax= 1.85942e+02, atom= 339\n", - "Step= 602, Dmax= 1.2e-02 nm, Epot= -4.57469e+04 Fmax= 8.88933e+01, atom= 626\n", - "Step= 604, Dmax= 6.9e-03 nm, Epot= -4.57480e+04 Fmax= 7.14680e+01, atom= 339\n", - "Step= 605, Dmax= 8.3e-03 nm, Epot= -4.57486e+04 Fmax= 1.26724e+02, atom= 626\n", - "Step= 606, Dmax= 1.0e-02 nm, Epot= -4.57497e+04 Fmax= 1.11488e+02, atom= 626\n", - "Step= 607, Dmax= 1.2e-02 nm, Epot= -4.57498e+04 Fmax= 1.73017e+02, atom= 626\n", - "Step= 608, Dmax= 1.4e-02 nm, Epot= -4.57507e+04 Fmax= 1.73464e+02, atom= 626\n", - "Step= 610, Dmax= 8.6e-03 nm, Epot= -4.57532e+04 Fmax= 3.38567e+01, atom= 626\n", - "Step= 611, Dmax= 1.0e-02 nm, Epot= -4.57544e+04 Fmax= 2.09504e+02, atom= 339\n", - "Step= 612, Dmax= 1.2e-02 nm, Epot= -4.57568e+04 Fmax= 8.74946e+01, atom= 626\n", - "Step= 614, Dmax= 7.4e-03 nm, Epot= -4.57577e+04 Fmax= 8.69064e+01, atom= 339\n", - "Step= 615, Dmax= 8.9e-03 nm, Epot= -4.57583e+04 Fmax= 1.23988e+02, atom= 626\n", - "Step= 616, Dmax= 1.1e-02 nm, Epot= -4.57591e+04 Fmax= 1.31773e+02, atom= 626\n", - "Step= 617, Dmax= 1.3e-02 nm, Epot= -4.57594e+04 Fmax= 1.72500e+02, atom= 626\n", - "Step= 618, Dmax= 1.5e-02 nm, Epot= -4.57597e+04 Fmax= 2.00409e+02, atom= 626\n", - "Step= 620, Dmax= 9.2e-03 nm, Epot= -4.57627e+04 Fmax= 2.39675e+01, atom= 339\n", - "Step= 621, Dmax= 1.1e-02 nm, Epot= -4.57653e+04 Fmax= 2.31660e+02, atom= 339\n", - "Step= 622, Dmax= 1.3e-02 nm, Epot= -4.57678e+04 Fmax= 8.94231e+01, atom= 626\n", - "Step= 624, Dmax= 8.0e-03 nm, Epot= -4.57686e+04 Fmax= 1.03530e+02, atom= 339\n", - "Step= 625, Dmax= 9.6e-03 nm, Epot= -4.57693e+04 Fmax= 1.21607e+02, atom= 626\n", - "Step= 626, Dmax= 1.2e-02 nm, Epot= -4.57698e+04 Fmax= 1.55201e+02, atom= 339\n", - "Step= 627, Dmax= 1.4e-02 nm, Epot= -4.57704e+04 Fmax= 1.70058e+02, atom= 626\n", - "Step= 629, Dmax= 8.3e-03 nm, Epot= -4.57727e+04 Fmax= 2.72581e+01, atom= 111\n", - "Step= 630, Dmax= 9.9e-03 nm, Epot= -4.57733e+04 Fmax= 2.16085e+02, atom= 339\n", - "Step= 631, Dmax= 1.2e-02 nm, Epot= -4.57766e+04 Fmax= 9.24663e+01, atom= 626\n", - "Step= 633, Dmax= 7.2e-03 nm, Epot= -4.57776e+04 Fmax= 7.42935e+01, atom= 626\n", - "Step= 634, Dmax= 8.6e-03 nm, Epot= -4.57781e+04 Fmax= 1.31618e+02, atom= 339\n", - "Step= 635, Dmax= 1.0e-02 nm, Epot= -4.57792e+04 Fmax= 1.10678e+02, atom= 339\n", - "Step= 637, Dmax= 6.2e-03 nm, Epot= -4.57805e+04 Fmax= 3.43018e+01, atom= 339\n", - "Step= 638, Dmax= 7.4e-03 nm, Epot= -4.57814e+04 Fmax= 1.47363e+02, atom= 339\n", - "Step= 639, Dmax= 8.9e-03 nm, Epot= -4.57831e+04 Fmax= 6.95464e+01, atom= 339\n", - "Step= 641, Dmax= 5.3e-03 nm, Epot= -4.57840e+04 Fmax= 5.67596e+01, atom= 339\n", - "Step= 642, Dmax= 6.4e-03 nm, Epot= -4.57848e+04 Fmax= 9.61592e+01, atom= 339\n", - "Step= 643, Dmax= 7.7e-03 nm, Epot= -4.57857e+04 Fmax= 8.50610e+01, atom= 339\n", - "Step= 644, Dmax= 9.2e-03 nm, Epot= -4.57862e+04 Fmax= 1.37083e+02, atom= 339\n", - "Step= 645, Dmax= 1.1e-02 nm, Epot= -4.57872e+04 Fmax= 1.23699e+02, atom= 339\n", - "Step= 647, Dmax= 6.6e-03 nm, Epot= -4.57886e+04 Fmax= 3.11872e+01, atom= 339\n", - "Step= 648, Dmax= 8.0e-03 nm, Epot= -4.57894e+04 Fmax= 1.69219e+02, atom= 339\n", - "Step= 649, Dmax= 9.6e-03 nm, Epot= -4.57916e+04 Fmax= 6.72612e+01, atom= 339\n", - "Step= 651, Dmax= 5.7e-03 nm, Epot= -4.57924e+04 Fmax= 6.75795e+01, atom= 339\n", - "Step= 652, Dmax= 6.9e-03 nm, Epot= -4.57932e+04 Fmax= 9.69829e+01, atom= 339\n", - "Step= 653, Dmax= 8.3e-03 nm, Epot= -4.57940e+04 Fmax= 9.75978e+01, atom= 339\n", - "Step= 654, Dmax= 9.9e-03 nm, Epot= -4.57944e+04 Fmax= 1.40862e+02, atom= 339\n", - "Step= 655, Dmax= 1.2e-02 nm, Epot= -4.57953e+04 Fmax= 1.39190e+02, atom= 339\n", - "Step= 657, Dmax= 7.1e-03 nm, Epot= -4.57969e+04 Fmax= 2.73913e+01, atom= 339\n", - "Step= 658, Dmax= 8.6e-03 nm, Epot= -4.57976e+04 Fmax= 1.95066e+02, atom= 339\n", - "Step= 659, Dmax= 1.0e-02 nm, Epot= -4.58004e+04 Fmax= 6.36849e+01, atom= 339\n", - "Step= 661, Dmax= 6.2e-03 nm, Epot= -4.58013e+04 Fmax= 8.04211e+01, atom= 339\n", - "Step= 662, Dmax= 7.4e-03 nm, Epot= -4.58020e+04 Fmax= 9.60683e+01, atom= 339\n", - "Step= 663, Dmax= 8.9e-03 nm, Epot= -4.58027e+04 Fmax= 1.13041e+02, atom= 339\n", - "Step= 664, Dmax= 1.1e-02 nm, Epot= -4.58032e+04 Fmax= 1.42921e+02, atom= 339\n", - "Step= 665, Dmax= 1.3e-02 nm, Epot= -4.58038e+04 Fmax= 1.57267e+02, atom= 339\n", - "Step= 667, Dmax= 7.7e-03 nm, Epot= -4.58057e+04 Fmax= 2.35192e+01, atom= 373\n", - "Step= 668, Dmax= 9.2e-03 nm, Epot= -4.58066e+04 Fmax= 2.15002e+02, atom= 339\n", - "Step= 669, Dmax= 1.1e-02 nm, Epot= -4.58099e+04 Fmax= 6.96320e+01, atom= 339\n", - "Step= 671, Dmax= 6.6e-03 nm, Epot= -4.58107e+04 Fmax= 8.30808e+01, atom= 339\n", - "Step= 672, Dmax= 8.0e-03 nm, Epot= -4.58113e+04 Fmax= 1.06300e+02, atom= 339\n", - "Step= 673, Dmax= 9.6e-03 nm, Epot= -4.58120e+04 Fmax= 1.17744e+02, atom= 339\n", - "Step= 674, Dmax= 1.1e-02 nm, Epot= -4.58123e+04 Fmax= 1.57048e+02, atom= 339\n", - "Step= 675, Dmax= 1.4e-02 nm, Epot= -4.58130e+04 Fmax= 1.65546e+02, atom= 339\n", - "Step= 677, Dmax= 8.3e-03 nm, Epot= -4.58151e+04 Fmax= 2.78218e+01, atom= 373\n", - "Step= 678, Dmax= 9.9e-03 nm, Epot= -4.58151e+04 Fmax= 2.34164e+02, atom= 339\n", - "Step= 679, Dmax= 1.2e-02 nm, Epot= -4.58188e+04 Fmax= 7.10347e+01, atom= 339\n", - "Step= 681, Dmax= 7.1e-03 nm, Epot= -4.58195e+04 Fmax= 9.26905e+01, atom= 339\n", - "Step= 682, Dmax= 8.6e-03 nm, Epot= -4.58202e+04 Fmax= 1.09829e+02, atom= 339\n", - "Step= 683, Dmax= 1.0e-02 nm, Epot= -4.58208e+04 Fmax= 1.30072e+02, atom= 339\n", - "Step= 684, Dmax= 1.2e-02 nm, Epot= -4.58211e+04 Fmax= 1.64335e+02, atom= 339\n", - "Step= 685, Dmax= 1.5e-02 nm, Epot= -4.58216e+04 Fmax= 1.80792e+02, atom= 339\n", - "Step= 687, Dmax= 8.9e-03 nm, Epot= -4.58240e+04 Fmax= 2.92893e+01, atom= 373\n", - "Step= 689, Dmax= 5.3e-03 nm, Epot= -4.58251e+04 Fmax= 9.78425e+01, atom= 339\n", - "Step= 690, Dmax= 6.4e-03 nm, Epot= -4.58262e+04 Fmax= 5.70152e+01, atom= 339\n", - "Step= 691, Dmax= 7.7e-03 nm, Epot= -4.58267e+04 Fmax= 1.22595e+02, atom= 339\n", - "Step= 692, Dmax= 9.2e-03 nm, Epot= -4.58278e+04 Fmax= 9.57025e+01, atom= 339\n", - "Step= 693, Dmax= 1.1e-02 nm, Epot= -4.58278e+04 Fmax= 1.63069e+02, atom= 339\n", - "Step= 694, Dmax= 1.3e-02 nm, Epot= -4.58288e+04 Fmax= 1.53822e+02, atom= 339\n", - "Step= 696, Dmax= 7.9e-03 nm, Epot= -4.58307e+04 Fmax= 3.37759e+01, atom= 626\n", - "Step= 697, Dmax= 9.5e-03 nm, Epot= -4.58315e+04 Fmax= 1.89961e+02, atom= 339\n", - "Step= 698, Dmax= 1.1e-02 nm, Epot= -4.58336e+04 Fmax= 8.22114e+01, atom= 339\n", - "Step= 700, Dmax= 6.9e-03 nm, Epot= -4.58345e+04 Fmax= 7.66694e+01, atom= 339\n", - "Step= 701, Dmax= 8.2e-03 nm, Epot= -4.58350e+04 Fmax= 1.16153e+02, atom= 339\n", - "Step= 702, Dmax= 9.9e-03 nm, Epot= -4.58358e+04 Fmax= 1.17988e+02, atom= 339\n", - "Step= 703, Dmax= 1.2e-02 nm, Epot= -4.58361e+04 Fmax= 1.59671e+02, atom= 339\n", - "Step= 704, Dmax= 1.4e-02 nm, Epot= -4.58365e+04 Fmax= 1.80375e+02, atom= 339\n", - "Step= 706, Dmax= 8.5e-03 nm, Epot= -4.58389e+04 Fmax= 2.33530e+01, atom= 626\n", - "Step= 707, Dmax= 1.0e-02 nm, Epot= -4.58411e+04 Fmax= 2.03565e+02, atom= 626\n", - "Step= 708, Dmax= 1.2e-02 nm, Epot= -4.58433e+04 Fmax= 9.12305e+01, atom= 339\n", - "Step= 710, Dmax= 7.4e-03 nm, Epot= -4.58441e+04 Fmax= 8.27932e+01, atom= 339\n", - "Step= 711, Dmax= 8.9e-03 nm, Epot= -4.58447e+04 Fmax= 1.23413e+02, atom= 339\n", - "Step= 712, Dmax= 1.1e-02 nm, Epot= -4.58454e+04 Fmax= 1.28785e+02, atom= 339\n", - "Step= 713, Dmax= 1.3e-02 nm, Epot= -4.58456e+04 Fmax= 1.69024e+02, atom= 339\n", - "Step= 714, Dmax= 1.5e-02 nm, Epot= -4.58459e+04 Fmax= 1.96916e+02, atom= 339\n", - "Step= 716, Dmax= 9.2e-03 nm, Epot= -4.58487e+04 Fmax= 2.28121e+01, atom= 626\n", - "Step= 717, Dmax= 1.1e-02 nm, Epot= -4.58512e+04 Fmax= 2.16066e+02, atom= 626\n", - "Step= 718, Dmax= 1.3e-02 nm, Epot= -4.58535e+04 Fmax= 1.00925e+02, atom= 339\n", - "Step= 720, Dmax= 7.9e-03 nm, Epot= -4.58544e+04 Fmax= 8.63834e+01, atom= 339\n", - "Step= 721, Dmax= 9.5e-03 nm, Epot= -4.58548e+04 Fmax= 1.35204e+02, atom= 339\n", - "Step= 722, Dmax= 1.1e-02 nm, Epot= -4.58557e+04 Fmax= 1.35654e+02, atom= 339\n", - "Step= 723, Dmax= 1.4e-02 nm, Epot= -4.58557e+04 Fmax= 1.84251e+02, atom= 339\n", - "Step= 724, Dmax= 1.6e-02 nm, Epot= -4.58561e+04 Fmax= 2.08713e+02, atom= 339\n", - "Step= 726, Dmax= 9.9e-03 nm, Epot= -4.58591e+04 Fmax= 2.69558e+01, atom= 626\n", - "Step= 727, Dmax= 1.2e-02 nm, Epot= -4.58610e+04 Fmax= 2.30049e+02, atom= 626\n", - "Step= 728, Dmax= 1.4e-02 nm, Epot= -4.58635e+04 Fmax= 1.11443e+02, atom= 339\n", - "Step= 730, Dmax= 8.5e-03 nm, Epot= -4.58645e+04 Fmax= 8.79935e+01, atom= 339\n", - "Step= 731, Dmax= 1.0e-02 nm, Epot= -4.58648e+04 Fmax= 1.50752e+02, atom= 339\n", - "Step= 732, Dmax= 1.2e-02 nm, Epot= -4.58658e+04 Fmax= 1.39305e+02, atom= 339\n", - "Step= 734, Dmax= 7.4e-03 nm, Epot= -4.58675e+04 Fmax= 3.31729e+01, atom= 626\n", - "Step= 735, Dmax= 8.8e-03 nm, Epot= -4.58687e+04 Fmax= 1.72629e+02, atom= 339\n", - "Step= 736, Dmax= 1.1e-02 nm, Epot= -4.58706e+04 Fmax= 7.76954e+01, atom= 339\n", - "Step= 738, Dmax= 6.4e-03 nm, Epot= -4.58715e+04 Fmax= 6.80183e+01, atom= 339\n", - "Step= 739, Dmax= 7.6e-03 nm, Epot= -4.58723e+04 Fmax= 1.10730e+02, atom= 339\n", - "Step= 740, Dmax= 9.2e-03 nm, Epot= -4.58732e+04 Fmax= 1.04167e+02, atom= 339\n", - "Step= 741, Dmax= 1.1e-02 nm, Epot= -4.58737e+04 Fmax= 1.52042e+02, atom= 339\n", - "Step= 742, Dmax= 1.3e-02 nm, Epot= -4.58744e+04 Fmax= 1.59245e+02, atom= 339\n", - "Step= 744, Dmax= 7.9e-03 nm, Epot= -4.58764e+04 Fmax= 2.68021e+01, atom= 626\n", - "Step= 745, Dmax= 9.5e-03 nm, Epot= -4.58785e+04 Fmax= 1.86342e+02, atom= 339\n", - "Step= 746, Dmax= 1.1e-02 nm, Epot= -4.58805e+04 Fmax= 8.42300e+01, atom= 339\n", - "Step= 748, Dmax= 6.8e-03 nm, Epot= -4.58815e+04 Fmax= 7.29713e+01, atom= 339\n", - "Step= 749, Dmax= 8.2e-03 nm, Epot= -4.58822e+04 Fmax= 1.18122e+02, atom= 339\n", - "Step= 750, Dmax= 9.9e-03 nm, Epot= -4.58832e+04 Fmax= 1.12316e+02, atom= 339\n", - "Step= 751, Dmax= 1.2e-02 nm, Epot= -4.58836e+04 Fmax= 1.61764e+02, atom= 339\n", - "Step= 752, Dmax= 1.4e-02 nm, Epot= -4.58844e+04 Fmax= 1.71788e+02, atom= 339\n", - "Step= 754, Dmax= 8.5e-03 nm, Epot= -4.58866e+04 Fmax= 2.84467e+01, atom= 626\n", - "Step= 755, Dmax= 1.0e-02 nm, Epot= -4.58887e+04 Fmax= 1.95087e+02, atom= 626\n", - "Step= 756, Dmax= 1.2e-02 nm, Epot= -4.58909e+04 Fmax= 9.54889e+01, atom= 339\n", - "Step= 758, Dmax= 7.4e-03 nm, Epot= -4.58919e+04 Fmax= 7.29046e+01, atom= 339\n", - "Step= 759, Dmax= 8.8e-03 nm, Epot= -4.58927e+04 Fmax= 1.31941e+02, atom= 339\n", - "Step= 760, Dmax= 1.1e-02 nm, Epot= -4.58938e+04 Fmax= 1.15030e+02, atom= 339\n", - "Step= 761, Dmax= 1.3e-02 nm, Epot= -4.58940e+04 Fmax= 1.79516e+02, atom= 339\n", - "Step= 762, Dmax= 1.5e-02 nm, Epot= -4.58950e+04 Fmax= 1.78274e+02, atom= 339\n", - "Step= 764, Dmax= 9.2e-03 nm, Epot= -4.58975e+04 Fmax= 3.50347e+01, atom= 626\n", - "Step= 765, Dmax= 1.1e-02 nm, Epot= -4.58989e+04 Fmax= 2.10127e+02, atom= 339\n", - "Step= 766, Dmax= 1.3e-02 nm, Epot= -4.59014e+04 Fmax= 1.00796e+02, atom= 339\n", - "Step= 768, Dmax= 7.9e-03 nm, Epot= -4.59025e+04 Fmax= 7.79165e+01, atom= 339\n", - "Step= 769, Dmax= 9.5e-03 nm, Epot= -4.59031e+04 Fmax= 1.42516e+02, atom= 339\n", - "Step= 770, Dmax= 1.1e-02 nm, Epot= -4.59044e+04 Fmax= 1.22166e+02, atom= 339\n", - "Step= 771, Dmax= 1.4e-02 nm, Epot= -4.59044e+04 Fmax= 1.93761e+02, atom= 339\n", - "Step= 772, Dmax= 1.6e-02 nm, Epot= -4.59055e+04 Fmax= 1.90051e+02, atom= 339\n", - "Step= 774, Dmax= 9.8e-03 nm, Epot= -4.59082e+04 Fmax= 3.91080e+01, atom= 626\n", - "Step= 775, Dmax= 1.2e-02 nm, Epot= -4.59094e+04 Fmax= 2.19922e+02, atom= 626\n", - "Step= 776, Dmax= 1.4e-02 nm, Epot= -4.59120e+04 Fmax= 1.13231e+02, atom= 339\n", - "Step= 778, Dmax= 8.5e-03 nm, Epot= -4.59133e+04 Fmax= 7.78003e+01, atom= 339\n", - "Step= 779, Dmax= 1.0e-02 nm, Epot= -4.59137e+04 Fmax= 1.60113e+02, atom= 339\n", - "Step= 780, Dmax= 1.2e-02 nm, Epot= -4.59153e+04 Fmax= 1.23893e+02, atom= 339\n", - "Step= 782, Dmax= 7.3e-03 nm, Epot= -4.59169e+04 Fmax= 4.34073e+01, atom= 339\n", - "Step= 783, Dmax= 8.8e-03 nm, Epot= -4.59180e+04 Fmax= 1.60361e+02, atom= 339\n", - "Step= 784, Dmax= 1.1e-02 nm, Epot= -4.59199e+04 Fmax= 8.34727e+01, atom= 339\n", - "Step= 786, Dmax= 6.3e-03 nm, Epot= -4.59210e+04 Fmax= 5.90294e+01, atom= 339\n", - "Step= 787, Dmax= 7.6e-03 nm, Epot= -4.59220e+04 Fmax= 1.17917e+02, atom= 339\n", - "Step= 788, Dmax= 9.1e-03 nm, Epot= -4.59233e+04 Fmax= 9.33944e+01, atom= 339\n", - "Step= 789, Dmax= 1.1e-02 nm, Epot= -4.59238e+04 Fmax= 1.59164e+02, atom= 339\n", - "Step= 790, Dmax= 1.3e-02 nm, Epot= -4.59251e+04 Fmax= 1.45658e+02, atom= 339\n", - "Step= 792, Dmax= 7.9e-03 nm, Epot= -4.59270e+04 Fmax= 3.54126e+01, atom= 626\n", - "Step= 793, Dmax= 9.5e-03 nm, Epot= -4.59287e+04 Fmax= 1.77841e+02, atom= 339\n", - "Step= 794, Dmax= 1.1e-02 nm, Epot= -4.59309e+04 Fmax= 8.54512e+01, atom= 339\n", - "Step= 796, Dmax= 6.8e-03 nm, Epot= -4.59321e+04 Fmax= 6.73159e+01, atom= 339\n", - "Step= 797, Dmax= 8.2e-03 nm, Epot= -4.59331e+04 Fmax= 1.21367e+02, atom= 339\n", - "Step= 798, Dmax= 9.8e-03 nm, Epot= -4.59343e+04 Fmax= 1.04717e+02, atom= 339\n", - "Step= 799, Dmax= 1.2e-02 nm, Epot= -4.59348e+04 Fmax= 1.65276e+02, atom= 339\n", - "Step= 800, Dmax= 1.4e-02 nm, Epot= -4.59360e+04 Fmax= 1.61438e+02, atom= 339\n", - "Step= 802, Dmax= 8.5e-03 nm, Epot= -4.59382e+04 Fmax= 3.35367e+01, atom= 626\n", - "Step= 803, Dmax= 1.0e-02 nm, Epot= -4.59403e+04 Fmax= 1.88881e+02, atom= 626\n", - "Step= 804, Dmax= 1.2e-02 nm, Epot= -4.59427e+04 Fmax= 9.43843e+01, atom= 339\n", - "Step= 806, Dmax= 7.3e-03 nm, Epot= -4.59439e+04 Fmax= 6.94536e+01, atom= 339\n", - "Step= 807, Dmax= 8.8e-03 nm, Epot= -4.59449e+04 Fmax= 1.32682e+02, atom= 339\n", - "Step= 808, Dmax= 1.1e-02 nm, Epot= -4.59463e+04 Fmax= 1.09795e+02, atom= 339\n", - "Step= 809, Dmax= 1.3e-02 nm, Epot= -4.59467e+04 Fmax= 1.79183e+02, atom= 339\n", - "Step= 810, Dmax= 1.5e-02 nm, Epot= -4.59480e+04 Fmax= 1.70905e+02, atom= 339\n", - "Step= 812, Dmax= 9.1e-03 nm, Epot= -4.59505e+04 Fmax= 3.74880e+01, atom= 626\n", - "Step= 813, Dmax= 1.1e-02 nm, Epot= -4.59524e+04 Fmax= 2.00786e+02, atom= 626\n", - "Step= 814, Dmax= 1.3e-02 nm, Epot= -4.59550e+04 Fmax= 1.02289e+02, atom= 339\n", - "Step= 816, Dmax= 7.9e-03 nm, Epot= -4.59563e+04 Fmax= 7.28154e+01, atom= 339\n", - "Step= 817, Dmax= 9.5e-03 nm, Epot= -4.59573e+04 Fmax= 1.43715e+02, atom= 339\n", - "Step= 818, Dmax= 1.1e-02 nm, Epot= -4.59588e+04 Fmax= 1.15034e+02, atom= 339\n", - "Step= 819, Dmax= 1.4e-02 nm, Epot= -4.59590e+04 Fmax= 1.94107e+02, atom= 339\n", - "Step= 820, Dmax= 1.6e-02 nm, Epot= -4.59605e+04 Fmax= 1.80866e+02, atom= 339\n", - "Step= 822, Dmax= 9.8e-03 nm, Epot= -4.59633e+04 Fmax= 4.16821e+01, atom= 626\n", - "Step= 823, Dmax= 1.2e-02 nm, Epot= -4.59649e+04 Fmax= 2.13495e+02, atom= 626\n", - "Step= 824, Dmax= 1.4e-02 nm, Epot= -4.59677e+04 Fmax= 1.10673e+02, atom= 339\n", - "Step= 826, Dmax= 8.5e-03 nm, Epot= -4.59692e+04 Fmax= 7.58230e+01, atom= 339\n", - "Step= 827, Dmax= 1.0e-02 nm, Epot= -4.59700e+04 Fmax= 1.56275e+02, atom= 339\n", - "Step= 828, Dmax= 1.2e-02 nm, Epot= -4.59718e+04 Fmax= 1.20715e+02, atom= 339\n", - "Step= 830, Dmax= 7.3e-03 nm, Epot= -4.59735e+04 Fmax= 4.24621e+01, atom= 339\n", - "Step= 831, Dmax= 8.8e-03 nm, Epot= -4.59752e+04 Fmax= 1.55357e+02, atom= 339\n", - "Step= 832, Dmax= 1.1e-02 nm, Epot= -4.59773e+04 Fmax= 8.19048e+01, atom= 339\n", - "Step= 833, Dmax= 1.3e-02 nm, Epot= -4.59774e+04 Fmax= 2.07308e+02, atom= 339\n", - "Step= 834, Dmax= 1.5e-02 nm, Epot= -4.59799e+04 Fmax= 1.31297e+02, atom= 339\n", - "Step= 836, Dmax= 9.1e-03 nm, Epot= -4.59817e+04 Fmax= 6.74730e+01, atom= 339\n", - "Step= 837, Dmax= 1.1e-02 nm, Epot= -4.59823e+04 Fmax= 1.86538e+02, atom= 339\n", - "Step= 838, Dmax= 1.3e-02 nm, Epot= -4.59847e+04 Fmax= 1.14235e+02, atom= 339\n", - "Step= 840, Dmax= 7.9e-03 nm, Epot= -4.59863e+04 Fmax= 5.96225e+01, atom= 339\n", - "Step= 841, Dmax= 9.4e-03 nm, Epot= -4.59874e+04 Fmax= 1.50472e+02, atom= 339\n", - "Step= 842, Dmax= 1.1e-02 nm, Epot= -4.59892e+04 Fmax= 1.00988e+02, atom= 339\n", - "Step= 844, Dmax= 6.8e-03 nm, Epot= -4.59907e+04 Fmax= 4.82523e+01, atom= 339\n", - "Step= 845, Dmax= 8.2e-03 nm, Epot= -4.59921e+04 Fmax= 1.38474e+02, atom= 339\n", - "Step= 846, Dmax= 9.8e-03 nm, Epot= -4.59939e+04 Fmax= 8.34365e+01, atom= 339\n", - "Step= 847, Dmax= 1.2e-02 nm, Epot= -4.59942e+04 Fmax= 1.80634e+02, atom= 339\n", - "Step= 848, Dmax= 1.4e-02 nm, Epot= -4.59962e+04 Fmax= 1.37406e+02, atom= 339\n", - "Step= 850, Dmax= 8.5e-03 nm, Epot= -4.59981e+04 Fmax= 4.80834e+01, atom= 626\n", - "Step= 851, Dmax= 1.0e-02 nm, Epot= -4.59992e+04 Fmax= 1.79239e+02, atom= 339\n", - "Step= 852, Dmax= 1.2e-02 nm, Epot= -4.60015e+04 Fmax= 9.23964e+01, atom= 339\n", - "Step= 854, Dmax= 7.3e-03 nm, Epot= -4.60028e+04 Fmax= 6.56046e+01, atom= 339\n", - "Step= 855, Dmax= 8.8e-03 nm, Epot= -4.60038e+04 Fmax= 1.30952e+02, atom= 339\n", - "Step= 856, Dmax= 1.1e-02 nm, Epot= -4.60053e+04 Fmax= 1.03950e+02, atom= 339\n", - "Step= 857, Dmax= 1.3e-02 nm, Epot= -4.60056e+04 Fmax= 1.76467e+02, atom= 339\n", - "Step= 858, Dmax= 1.5e-02 nm, Epot= -4.60069e+04 Fmax= 1.63622e+02, atom= 339\n", - "Step= 860, Dmax= 9.1e-03 nm, Epot= -4.60093e+04 Fmax= 3.73812e+01, atom= 626\n", - "Step= 861, Dmax= 1.1e-02 nm, Epot= -4.60108e+04 Fmax= 1.95469e+02, atom= 339\n", - "Step= 862, Dmax= 1.3e-02 nm, Epot= -4.60133e+04 Fmax= 9.79406e+01, atom= 339\n", - "Step= 864, Dmax= 7.9e-03 nm, Epot= -4.60145e+04 Fmax= 7.10330e+01, atom= 339\n", - "Step= 865, Dmax= 9.4e-03 nm, Epot= -4.60152e+04 Fmax= 1.38319e+02, atom= 339\n", - "Step= 866, Dmax= 1.1e-02 nm, Epot= -4.60166e+04 Fmax= 1.12971e+02, atom= 339\n", - "Step= 867, Dmax= 1.4e-02 nm, Epot= -4.60166e+04 Fmax= 1.86197e+02, atom= 339\n", - "Step= 868, Dmax= 1.6e-02 nm, Epot= -4.60178e+04 Fmax= 1.77816e+02, atom= 339\n", - "Step= 870, Dmax= 9.8e-03 nm, Epot= -4.60204e+04 Fmax= 3.77205e+01, atom= 626\n", - "Step= 871, Dmax= 1.2e-02 nm, Epot= -4.60216e+04 Fmax= 2.07593e+02, atom= 626\n", - "Step= 872, Dmax= 1.4e-02 nm, Epot= -4.60241e+04 Fmax= 1.06280e+02, atom= 339\n", - "Step= 874, Dmax= 8.4e-03 nm, Epot= -4.60253e+04 Fmax= 7.44738e+01, atom= 339\n", - "Step= 875, Dmax= 1.0e-02 nm, Epot= -4.60257e+04 Fmax= 1.50066e+02, atom= 339\n", - "Step= 876, Dmax= 1.2e-02 nm, Epot= -4.60271e+04 Fmax= 1.18824e+02, atom= 339\n", - "Step= 878, Dmax= 7.3e-03 nm, Epot= -4.60286e+04 Fmax= 3.98415e+01, atom= 339\n", - "Step= 879, Dmax= 8.8e-03 nm, Epot= -4.60296e+04 Fmax= 1.51006e+02, atom= 339\n", - "Step= 880, Dmax= 1.1e-02 nm, Epot= -4.60314e+04 Fmax= 7.89362e+01, atom= 339\n", - "Step= 882, Dmax= 6.3e-03 nm, Epot= -4.60324e+04 Fmax= 5.61341e+01, atom= 339\n", - "Step= 883, Dmax= 7.6e-03 nm, Epot= -4.60332e+04 Fmax= 1.10035e+02, atom= 339\n", - "Step= 884, Dmax= 9.1e-03 nm, Epot= -4.60343e+04 Fmax= 8.91024e+01, atom= 339\n", - "Step= 885, Dmax= 1.1e-02 nm, Epot= -4.60346e+04 Fmax= 1.48725e+02, atom= 339\n", - "Step= 886, Dmax= 1.3e-02 nm, Epot= -4.60357e+04 Fmax= 1.39380e+02, atom= 339\n", - "Step= 888, Dmax= 7.8e-03 nm, Epot= -4.60375e+04 Fmax= 3.12563e+01, atom= 626\n", - "Step= 889, Dmax= 9.4e-03 nm, Epot= -4.60387e+04 Fmax= 1.71736e+02, atom= 339\n", - "Step= 890, Dmax= 1.1e-02 nm, Epot= -4.60408e+04 Fmax= 7.72520e+01, atom= 339\n", - "Step= 892, Dmax= 6.8e-03 nm, Epot= -4.60417e+04 Fmax= 6.74849e+01, atom= 339\n", - "Step= 893, Dmax= 8.1e-03 nm, Epot= -4.60423e+04 Fmax= 1.09795e+02, atom= 339\n", - "Step= 894, Dmax= 9.8e-03 nm, Epot= -4.60432e+04 Fmax= 1.03174e+02, atom= 339\n", - "Step= 895, Dmax= 1.2e-02 nm, Epot= -4.60435e+04 Fmax= 1.50259e+02, atom= 339\n", - "Step= 896, Dmax= 1.4e-02 nm, Epot= -4.60442e+04 Fmax= 1.58043e+02, atom= 339\n", - "Step= 898, Dmax= 8.4e-03 nm, Epot= -4.60463e+04 Fmax= 2.61751e+01, atom= 626\n", - "Step= 899, Dmax= 1.0e-02 nm, Epot= -4.60478e+04 Fmax= 1.81278e+02, atom= 626\n", - "Step= 900, Dmax= 1.2e-02 nm, Epot= -4.60499e+04 Fmax= 8.68027e+01, atom= 339\n", - "Step= 902, Dmax= 7.3e-03 nm, Epot= -4.60508e+04 Fmax= 6.90929e+01, atom= 339\n", - "Step= 903, Dmax= 8.7e-03 nm, Epot= -4.60512e+04 Fmax= 1.20307e+02, atom= 339\n", - "Step= 904, Dmax= 1.0e-02 nm, Epot= -4.60522e+04 Fmax= 1.07849e+02, atom= 339\n", - "Step= 906, Dmax= 6.3e-03 nm, Epot= -4.60535e+04 Fmax= 2.74008e+01, atom= 339\n", - "Step= 907, Dmax= 7.6e-03 nm, Epot= -4.60546e+04 Fmax= 1.35223e+02, atom= 339\n", - "Step= 908, Dmax= 9.1e-03 nm, Epot= -4.60562e+04 Fmax= 6.11478e+01, atom= 339\n", - "Step= 910, Dmax= 5.4e-03 nm, Epot= -4.60570e+04 Fmax= 5.44143e+01, atom= 339\n", - "Step= 911, Dmax= 6.5e-03 nm, Epot= -4.60576e+04 Fmax= 8.66402e+01, atom= 339\n", - "Step= 912, Dmax= 7.8e-03 nm, Epot= -4.60583e+04 Fmax= 8.25002e+01, atom= 339\n", - "Step= 913, Dmax= 9.4e-03 nm, Epot= -4.60586e+04 Fmax= 1.19756e+02, atom= 339\n", - "Step= 914, Dmax= 1.1e-02 nm, Epot= -4.60592e+04 Fmax= 1.24849e+02, atom= 339\n", - "Step= 916, Dmax= 6.8e-03 nm, Epot= -4.60610e+04 Fmax= 2.10007e+01, atom= 626\n", - "Step= 917, Dmax= 8.1e-03 nm, Epot= -4.60619e+04 Fmax= 1.48160e+02, atom= 339\n", - "Step= 918, Dmax= 9.7e-03 nm, Epot= -4.60642e+04 Fmax= 6.43929e+01, atom= 339\n", - "Step= 920, Dmax= 5.8e-03 nm, Epot= -4.60650e+04 Fmax= 5.98242e+01, atom= 339\n", - "Step= 921, Dmax= 7.0e-03 nm, Epot= -4.60652e+04 Fmax= 9.92604e+01, atom= 1368\n", - "Step= 922, Dmax= 8.4e-03 nm, Epot= -4.60661e+04 Fmax= 8.97723e+01, atom= 1368\n", - "Step= 924, Dmax= 5.1e-03 nm, Epot= -4.60675e+04 Fmax= 2.15263e+01, atom= 1368\n", - "Step= 925, Dmax= 6.1e-03 nm, Epot= -4.60684e+04 Fmax= 1.15788e+02, atom= 1368\n", - "Step= 926, Dmax= 7.3e-03 nm, Epot= -4.60700e+04 Fmax= 4.81783e+01, atom= 1368\n", - "Step= 928, Dmax= 4.4e-03 nm, Epot= -4.60707e+04 Fmax= 4.94505e+01, atom= 1368\n", - "Step= 929, Dmax= 5.2e-03 nm, Epot= -4.60713e+04 Fmax= 6.82019e+01, atom= 1368\n", - "Step= 930, Dmax= 6.3e-03 nm, Epot= -4.60720e+04 Fmax= 7.24909e+01, atom= 1368\n", - "Step= 931, Dmax= 7.5e-03 nm, Epot= -4.60724e+04 Fmax= 9.72356e+01, atom= 1368\n", - "Step= 932, Dmax= 9.1e-03 nm, Epot= -4.60730e+04 Fmax= 1.04855e+02, atom= 1368\n", - "Step= 933, Dmax= 1.1e-02 nm, Epot= -4.60731e+04 Fmax= 1.41015e+02, atom= 1368\n", - "Step= 934, Dmax= 1.3e-02 nm, Epot= -4.60735e+04 Fmax= 1.49464e+02, atom= 1368\n", - "Step= 936, Dmax= 7.8e-03 nm, Epot= -4.60758e+04 Fmax= 1.99619e+01, atom= 1368\n", - "Step= 938, Dmax= 4.7e-03 nm, Epot= -4.60768e+04 Fmax= 8.99570e+01, atom= 1368\n", - "Step= 939, Dmax= 5.6e-03 nm, Epot= -4.60779e+04 Fmax= 3.81441e+01, atom= 1368\n", - "Step= 940, Dmax= 6.8e-03 nm, Epot= -4.60781e+04 Fmax= 1.09635e+02, atom= 1368\n", - "Step= 941, Dmax= 8.1e-03 nm, Epot= -4.60794e+04 Fmax= 6.98445e+01, atom= 1368\n", - "Step= 943, Dmax= 4.9e-03 nm, Epot= -4.60803e+04 Fmax= 3.94161e+01, atom= 1368\n", - "Step= 944, Dmax= 5.8e-03 nm, Epot= -4.60807e+04 Fmax= 9.22727e+01, atom= 1368\n", - "Step= 945, Dmax= 7.0e-03 nm, Epot= -4.60817e+04 Fmax= 6.52531e+01, atom= 1368\n", - "Step= 947, Dmax= 4.2e-03 nm, Epot= -4.60826e+04 Fmax= 2.73306e+01, atom= 1368\n", - "Step= 948, Dmax= 5.0e-03 nm, Epot= -4.60831e+04 Fmax= 8.60369e+01, atom= 1026\n", - "Step= 949, Dmax= 6.1e-03 nm, Epot= -4.60843e+04 Fmax= 5.11679e+01, atom= 1026\n", - "Step= 951, Dmax= 3.6e-03 nm, Epot= -4.60850e+04 Fmax= 3.00145e+01, atom= 1026\n", - "Step= 952, Dmax= 4.4e-03 nm, Epot= -4.60856e+04 Fmax= 6.71428e+01, atom= 1026\n", - "Step= 953, Dmax= 5.2e-03 nm, Epot= -4.60865e+04 Fmax= 5.07159e+01, atom= 1026\n", - "Step= 954, Dmax= 6.3e-03 nm, Epot= -4.60867e+04 Fmax= 8.89054e+01, atom= 1026\n", - "Step= 955, Dmax= 7.5e-03 nm, Epot= -4.60875e+04 Fmax= 8.11168e+01, atom= 1026\n", - "Step= 957, Dmax= 4.5e-03 nm, Epot= -4.60886e+04 Fmax= 2.18573e+01, atom= 1026\n", - "Step= 958, Dmax= 5.4e-03 nm, Epot= -4.60895e+04 Fmax= 1.04464e+02, atom= 1026\n", - "Step= 959, Dmax= 6.5e-03 nm, Epot= -4.60908e+04 Fmax= 4.48000e+01, atom= 1026\n", - "Step= 961, Dmax= 3.9e-03 nm, Epot= -4.60914e+04 Fmax= 4.28859e+01, atom= 1026\n", - "Step= 962, Dmax= 4.7e-03 nm, Epot= -4.60920e+04 Fmax= 6.15801e+01, atom= 1026\n", - "Step= 963, Dmax= 5.6e-03 nm, Epot= -4.60926e+04 Fmax= 6.56971e+01, atom= 1026\n", - "Step= 964, Dmax= 6.7e-03 nm, Epot= -4.60931e+04 Fmax= 8.46946e+01, atom= 1026\n", - "Step= 965, Dmax= 8.1e-03 nm, Epot= -4.60936e+04 Fmax= 9.90914e+01, atom= 1026\n", - "Step= 966, Dmax= 9.7e-03 nm, Epot= -4.60939e+04 Fmax= 1.17320e+02, atom= 1026\n", - "Step= 967, Dmax= 1.2e-02 nm, Epot= -4.60941e+04 Fmax= 1.46918e+02, atom= 1026\n", - "Step= 968, Dmax= 1.4e-02 nm, Epot= -4.60942e+04 Fmax= 1.63409e+02, atom= 1026\n", - "Step= 970, Dmax= 8.4e-03 nm, Epot= -4.60967e+04 Fmax= 1.96308e+01, atom= 4826\n", - "Step= 972, Dmax= 5.0e-03 nm, Epot= -4.60977e+04 Fmax= 8.77423e+01, atom= 1026\n", - "Step= 973, Dmax= 6.0e-03 nm, Epot= -4.60987e+04 Fmax= 5.22804e+01, atom= 1026\n", - "Step= 974, Dmax= 7.3e-03 nm, Epot= -4.60988e+04 Fmax= 1.06596e+02, atom= 1026\n", - "Step= 975, Dmax= 8.7e-03 nm, Epot= -4.60997e+04 Fmax= 8.86450e+01, atom= 1026\n", - "Step= 977, Dmax= 5.2e-03 nm, Epot= -4.61008e+04 Fmax= 2.98101e+01, atom= 1026\n", - "Step= 978, Dmax= 6.3e-03 nm, Epot= -4.61012e+04 Fmax= 1.15733e+02, atom= 1026\n", - "Step= 979, Dmax= 7.5e-03 nm, Epot= -4.61025e+04 Fmax= 5.60872e+01, atom= 1026\n", - "Step= 981, Dmax= 4.5e-03 nm, Epot= -4.61031e+04 Fmax= 4.45764e+01, atom= 1026\n", - "Step= 982, Dmax= 5.4e-03 nm, Epot= -4.61036e+04 Fmax= 7.54621e+01, atom= 1026\n", - "Step= 983, Dmax= 6.5e-03 nm, Epot= -4.61042e+04 Fmax= 7.08865e+01, atom= 1026\n", - "Step= 984, Dmax= 7.8e-03 nm, Epot= -4.61046e+04 Fmax= 1.01943e+02, atom= 1026\n", - "Step= 985, Dmax= 9.4e-03 nm, Epot= -4.61051e+04 Fmax= 1.09669e+02, atom= 1026\n", - "Step= 986, Dmax= 1.1e-02 nm, Epot= -4.61051e+04 Fmax= 1.39034e+02, atom= 1026\n", - "Step= 987, Dmax= 1.3e-02 nm, Epot= -4.61053e+04 Fmax= 1.66041e+02, atom= 1026\n", - "Step= 989, Dmax= 8.1e-03 nm, Epot= -4.61075e+04 Fmax= 2.46161e+01, atom= 4336\n", - "Step= 990, Dmax= 9.7e-03 nm, Epot= -4.61084e+04 Fmax= 1.87621e+02, atom= 1026\n", - "Step= 991, Dmax= 1.2e-02 nm, Epot= -4.61101e+04 Fmax= 8.92817e+01, atom= 1026\n", - "Step= 993, Dmax= 7.0e-03 nm, Epot= -4.61108e+04 Fmax= 6.53803e+01, atom= 1026\n", - "Step= 994, Dmax= 8.4e-03 nm, Epot= -4.61110e+04 Fmax= 1.19211e+02, atom= 1026\n", - "Step= 995, Dmax= 1.0e-02 nm, Epot= -4.61118e+04 Fmax= 1.05027e+02, atom= 1026\n", - "Step= 997, Dmax= 6.0e-03 nm, Epot= -4.61127e+04 Fmax= 3.14732e+01, atom= 1026\n", - "Step= 998, Dmax= 7.2e-03 nm, Epot= -4.61132e+04 Fmax= 1.38389e+02, atom= 1026\n", - "Step= 999, Dmax= 8.7e-03 nm, Epot= -4.61144e+04 Fmax= 6.15178e+01, atom= 1026\n", - "Step= 1000, Dmax= 1.0e-02 nm, Epot= -4.61141e+04 Fmax= 1.83454e+02, atom= 1026\n", + "Step= 69, Dmax= 6.6e-02 nm, Epot= -4.10939e+04 Fmax= 2.04464e+03, atom= 652\n", + "Step= 70, Dmax= 8.0e-02 nm, Epot= -4.11802e+04 Fmax= 2.15417e+03, atom= 652\n", + "Step= 72, Dmax= 4.8e-02 nm, Epot= -4.13412e+04 Fmax= 5.26577e+02, atom= 1469\n", + "Step= 73, Dmax= 5.7e-02 nm, Epot= -4.14448e+04 Fmax= 4.39032e+03, atom= 113\n", + "Step= 74, Dmax= 6.9e-02 nm, Epot= -4.15754e+04 Fmax= 1.06623e+03, atom= 170\n", + "Step= 75, Dmax= 8.3e-02 nm, Epot= -4.16106e+04 Fmax= 4.02645e+03, atom= 170\n", + "Step= 76, Dmax= 9.9e-02 nm, Epot= -4.17108e+04 Fmax= 1.42297e+03, atom= 113\n", + "Step= 78, Dmax= 5.9e-02 nm, Epot= -4.18203e+04 Fmax= 6.25564e+02, atom= 1281\n", + "Step= 79, Dmax= 7.1e-02 nm, Epot= -4.19431e+04 Fmax= 1.31156e+03, atom= 1281\n", + "Step= 81, Dmax= 4.3e-02 nm, Epot= -4.20475e+04 Fmax= 6.75956e+02, atom= 170\n", + "Step= 82, Dmax= 5.1e-02 nm, Epot= -4.21342e+04 Fmax= 8.44703e+02, atom= 170\n", + "Step= 83, Dmax= 6.2e-02 nm, Epot= -4.22080e+04 Fmax= 1.08376e+03, atom= 170\n", + "Step= 84, Dmax= 7.4e-02 nm, Epot= -4.22579e+04 Fmax= 1.35636e+03, atom= 170\n", + "Step= 85, Dmax= 8.9e-02 nm, Epot= -4.23002e+04 Fmax= 1.18031e+03, atom= 1281\n", + "Step= 87, Dmax= 5.3e-02 nm, Epot= -4.24241e+04 Fmax= 5.93261e+02, atom= 240\n", + "Step= 88, Dmax= 6.4e-02 nm, Epot= -4.24516e+04 Fmax= 1.85303e+03, atom= 850\n", + "Step= 89, Dmax= 7.7e-02 nm, Epot= -4.25603e+04 Fmax= 1.13979e+03, atom= 850\n", + "Step= 91, Dmax= 4.6e-02 nm, Epot= -4.26388e+04 Fmax= 4.70422e+02, atom= 70\n", + "Step= 92, Dmax= 5.5e-02 nm, Epot= -4.27223e+04 Fmax= 7.49647e+02, atom= 70\n", + "Step= 94, Dmax= 3.3e-02 nm, Epot= -4.27898e+04 Fmax= 3.79446e+02, atom= 1589\n", + "Step= 95, Dmax= 4.0e-02 nm, Epot= -4.28411e+04 Fmax= 1.38630e+03, atom= 1589\n", + "Step= 96, Dmax= 4.8e-02 nm, Epot= -4.29084e+04 Fmax= 4.60233e+02, atom= 434\n", + "Step= 97, Dmax= 5.7e-02 nm, Epot= -4.29653e+04 Fmax= 1.77860e+03, atom= 434\n", + "Step= 98, Dmax= 6.9e-02 nm, Epot= -4.30177e+04 Fmax= 6.70254e+02, atom= 1589\n", + "Step= 100, Dmax= 4.1e-02 nm, Epot= -4.30756e+04 Fmax= 4.30153e+02, atom= 3179\n", + "Step= 101, Dmax= 4.9e-02 nm, Epot= -4.31321e+04 Fmax= 8.24552e+02, atom= 1589\n", + "Step= 102, Dmax= 5.9e-02 nm, Epot= -4.31471e+04 Fmax= 1.75411e+03, atom= 1589\n", + "Step= 103, Dmax= 7.1e-02 nm, Epot= -4.32164e+04 Fmax= 6.37465e+02, atom= 434\n", + "Step= 104, Dmax= 8.5e-02 nm, Epot= -4.32407e+04 Fmax= 2.03419e+03, atom= 434\n", + "Step= 105, Dmax= 1.0e-01 nm, Epot= -4.32805e+04 Fmax= 1.15510e+03, atom= 1589\n", + "Step= 107, Dmax= 6.2e-02 nm, Epot= -4.33413e+04 Fmax= 7.60702e+02, atom= 317\n", + "Step= 108, Dmax= 7.4e-02 nm, Epot= -4.33930e+04 Fmax= 5.24166e+02, atom= 421\n", + "Step= 110, Dmax= 4.4e-02 nm, Epot= -4.34409e+04 Fmax= 4.94250e+02, atom= 1310\n", + "Step= 111, Dmax= 5.3e-02 nm, Epot= -4.34520e+04 Fmax= 7.46669e+02, atom= 809\n", + "Step= 112, Dmax= 6.4e-02 nm, Epot= -4.34530e+04 Fmax= 1.01330e+03, atom= 1338\n", + "Step= 113, Dmax= 7.7e-02 nm, Epot= -4.34772e+04 Fmax= 9.73190e+02, atom= 1338\n", + "Step= 115, Dmax= 4.6e-02 nm, Epot= -4.36055e+04 Fmax= 2.26279e+02, atom= 8764\n", + "Step= 117, Dmax= 2.8e-02 nm, Epot= -4.36482e+04 Fmax= 3.53046e+02, atom= 9764\n", + "Step= 118, Dmax= 3.3e-02 nm, Epot= -4.36615e+04 Fmax= 5.72281e+02, atom= 97\n", + "Step= 119, Dmax= 4.0e-02 nm, Epot= -4.37004e+04 Fmax= 5.89451e+02, atom= 97\n", + "Step= 120, Dmax= 4.8e-02 nm, Epot= -4.37113e+04 Fmax= 7.40817e+02, atom= 97\n", + "Step= 121, Dmax= 5.7e-02 nm, Epot= -4.37209e+04 Fmax= 8.89442e+02, atom= 97\n", + "Step= 123, Dmax= 3.4e-02 nm, Epot= -4.37990e+04 Fmax= 2.50053e+02, atom= 292\n", + "Step= 124, Dmax= 4.1e-02 nm, Epot= -4.38149e+04 Fmax= 1.67266e+03, atom= 983\n", + "Step= 125, Dmax= 4.9e-02 nm, Epot= -4.38634e+04 Fmax= 4.25221e+02, atom= 983\n", + "Step= 127, Dmax= 3.0e-02 nm, Epot= -4.38911e+04 Fmax= 2.60399e+02, atom= 983\n", + "Step= 128, Dmax= 3.6e-02 nm, Epot= -4.39122e+04 Fmax= 8.88130e+02, atom= 983\n", + "Step= 129, Dmax= 4.3e-02 nm, Epot= -4.39451e+04 Fmax= 4.05544e+02, atom= 983\n", + "Step= 131, Dmax= 2.6e-02 nm, Epot= -4.39673e+04 Fmax= 2.67327e+02, atom= 983\n", + "Step= 132, Dmax= 3.1e-02 nm, Epot= -4.39873e+04 Fmax= 7.50607e+02, atom= 983\n", + "Step= 133, Dmax= 3.7e-02 nm, Epot= -4.40119e+04 Fmax= 3.91773e+02, atom= 983\n", + "Step= 134, Dmax= 4.4e-02 nm, Epot= -4.40212e+04 Fmax= 1.06100e+03, atom= 983\n", + "Step= 135, Dmax= 5.3e-02 nm, Epot= -4.40482e+04 Fmax= 5.30381e+02, atom= 983\n", + "Step= 137, Dmax= 3.2e-02 nm, Epot= -4.40755e+04 Fmax= 2.33595e+02, atom= 1550\n", + "Step= 138, Dmax= 3.8e-02 nm, Epot= -4.40792e+04 Fmax= 1.02432e+03, atom= 983\n", + "Step= 139, Dmax= 4.6e-02 nm, Epot= -4.41246e+04 Fmax= 5.36538e+02, atom= 983\n", + "Step= 140, Dmax= 5.5e-02 nm, Epot= -4.41284e+04 Fmax= 8.92441e+02, atom= 983\n", + "Step= 141, Dmax= 6.6e-02 nm, Epot= -4.41372e+04 Fmax= 9.81172e+02, atom= 983\n", + "Step= 143, Dmax= 4.0e-02 nm, Epot= -4.41830e+04 Fmax= 2.21421e+02, atom= 292\n", + "Step= 144, Dmax= 4.8e-02 nm, Epot= -4.41959e+04 Fmax= 9.82634e+02, atom= 681\n", + "Step= 145, Dmax= 5.7e-02 nm, Epot= -4.42008e+04 Fmax= 1.27957e+03, atom= 983\n", + "Step= 146, Dmax= 6.8e-02 nm, Epot= -4.42377e+04 Fmax= 5.80174e+02, atom= 983\n", + "Step= 148, Dmax= 4.1e-02 nm, Epot= -4.42668e+04 Fmax= 3.80146e+02, atom= 681\n", + "Step= 150, Dmax= 2.5e-02 nm, Epot= -4.42906e+04 Fmax= 1.43903e+02, atom= 681\n", + "Step= 151, Dmax= 3.0e-02 nm, Epot= -4.42986e+04 Fmax= 8.00341e+02, atom= 681\n", + "Step= 152, Dmax= 3.5e-02 nm, Epot= -4.43427e+04 Fmax= 2.10513e+02, atom= 681\n", + "Step= 154, Dmax= 2.1e-02 nm, Epot= -4.43587e+04 Fmax= 3.21124e+02, atom= 681\n", + "Step= 155, Dmax= 2.6e-02 nm, Epot= -4.43728e+04 Fmax= 3.68379e+02, atom= 681\n", + "Step= 156, Dmax= 3.1e-02 nm, Epot= -4.43838e+04 Fmax= 4.31187e+02, atom= 681\n", + "Step= 157, Dmax= 3.7e-02 nm, Epot= -4.43941e+04 Fmax= 5.81376e+02, atom= 681\n", + "Step= 158, Dmax= 4.4e-02 nm, Epot= -4.44034e+04 Fmax= 5.63750e+02, atom= 681\n", + "Step= 160, Dmax= 2.6e-02 nm, Epot= -4.44308e+04 Fmax= 9.28600e+01, atom= 983\n", + "Step= 161, Dmax= 3.2e-02 nm, Epot= -4.44547e+04 Fmax= 8.00824e+02, atom= 983\n", + "Step= 162, Dmax= 3.8e-02 nm, Epot= -4.44837e+04 Fmax= 4.80872e+02, atom= 681\n", + "Step= 164, Dmax= 2.3e-02 nm, Epot= -4.44992e+04 Fmax= 2.08877e+02, atom= 681\n", + "Step= 165, Dmax= 2.7e-02 nm, Epot= -4.45087e+04 Fmax= 5.78343e+02, atom= 681\n", + "Step= 166, Dmax= 3.3e-02 nm, Epot= -4.45223e+04 Fmax= 3.13594e+02, atom= 681\n", + "Step= 168, Dmax= 2.0e-02 nm, Epot= -4.45345e+04 Fmax= 1.32850e+02, atom= 681\n", + "Step= 169, Dmax= 2.4e-02 nm, Epot= -4.45434e+04 Fmax= 5.16686e+02, atom= 681\n", + "Step= 170, Dmax= 2.8e-02 nm, Epot= -4.45622e+04 Fmax= 2.22004e+02, atom= 681\n", + "Step= 172, Dmax= 1.7e-02 nm, Epot= -4.45718e+04 Fmax= 2.13735e+02, atom= 681\n", + "Step= 173, Dmax= 2.1e-02 nm, Epot= -4.45806e+04 Fmax= 3.12405e+02, atom= 681\n", + "Step= 174, Dmax= 2.5e-02 nm, Epot= -4.45886e+04 Fmax= 3.18511e+02, atom= 681\n", + "Step= 175, Dmax= 3.0e-02 nm, Epot= -4.45949e+04 Fmax= 4.49565e+02, atom= 681\n", + "Step= 176, Dmax= 3.5e-02 nm, Epot= -4.46012e+04 Fmax= 4.41628e+02, atom= 681\n", + "Step= 177, Dmax= 4.3e-02 nm, Epot= -4.46024e+04 Fmax= 6.80731e+02, atom= 681\n", + "Step= 178, Dmax= 5.1e-02 nm, Epot= -4.46087e+04 Fmax= 5.79259e+02, atom= 681\n", + "Step= 180, Dmax= 3.1e-02 nm, Epot= -4.46340e+04 Fmax= 1.09441e+02, atom= 983\n", + "Step= 182, Dmax= 1.8e-02 nm, Epot= -4.46458e+04 Fmax= 2.53528e+02, atom= 983\n", + "Step= 183, Dmax= 2.2e-02 nm, Epot= -4.46526e+04 Fmax= 3.37533e+02, atom= 681\n", + "Step= 184, Dmax= 2.6e-02 nm, Epot= -4.46607e+04 Fmax= 3.22827e+02, atom= 681\n", + "Step= 185, Dmax= 3.2e-02 nm, Epot= -4.46640e+04 Fmax= 4.85920e+02, atom= 681\n", + "Step= 186, Dmax= 3.8e-02 nm, Epot= -4.46706e+04 Fmax= 4.41631e+02, atom= 681\n", + "Step= 188, Dmax= 2.3e-02 nm, Epot= -4.46878e+04 Fmax= 6.99539e+01, atom= 983\n", + "Step= 189, Dmax= 2.7e-02 nm, Epot= -4.46916e+04 Fmax= 6.72942e+02, atom= 983\n", + "Step= 190, Dmax= 3.3e-02 nm, Epot= -4.47196e+04 Fmax= 3.42267e+02, atom= 681\n", + "Step= 192, Dmax= 2.0e-02 nm, Epot= -4.47291e+04 Fmax= 1.69135e+02, atom= 681\n", + "Step= 193, Dmax= 2.4e-02 nm, Epot= -4.47341e+04 Fmax= 4.38089e+02, atom= 681\n", + "Step= 194, Dmax= 2.8e-02 nm, Epot= -4.47428e+04 Fmax= 2.60042e+02, atom= 681\n", + "Step= 196, Dmax= 1.7e-02 nm, Epot= -4.47509e+04 Fmax= 1.00247e+02, atom= 681\n", + "Step= 197, Dmax= 2.0e-02 nm, Epot= -4.47564e+04 Fmax= 4.08079e+02, atom= 681\n", + "Step= 198, Dmax= 2.5e-02 nm, Epot= -4.47696e+04 Fmax= 1.69258e+02, atom= 681\n", + "Step= 200, Dmax= 1.5e-02 nm, Epot= -4.47760e+04 Fmax= 1.79183e+02, atom= 681\n", + "Step= 201, Dmax= 1.8e-02 nm, Epot= -4.47820e+04 Fmax= 2.30397e+02, atom= 681\n", + "Step= 202, Dmax= 2.1e-02 nm, Epot= -4.47871e+04 Fmax= 2.66957e+02, atom= 681\n", + "Step= 203, Dmax= 2.5e-02 nm, Epot= -4.47922e+04 Fmax= 3.29333e+02, atom= 681\n", + "Step= 204, Dmax= 3.1e-02 nm, Epot= -4.47953e+04 Fmax= 3.71861e+02, atom= 681\n", + "Step= 205, Dmax= 3.7e-02 nm, Epot= -4.47976e+04 Fmax= 4.93454e+02, atom= 681\n", + "Step= 206, Dmax= 4.4e-02 nm, Epot= -4.47986e+04 Fmax= 4.95148e+02, atom= 681\n", + "Step= 208, Dmax= 2.6e-02 nm, Epot= -4.48210e+04 Fmax= 6.43185e+01, atom= 983\n", + "Step= 210, Dmax= 1.6e-02 nm, Epot= -4.48271e+04 Fmax= 2.21498e+02, atom= 681\n", + "Step= 211, Dmax= 1.9e-02 nm, Epot= -4.48332e+04 Fmax= 2.63512e+02, atom= 642\n", + "Step= 212, Dmax= 2.3e-02 nm, Epot= -4.48369e+04 Fmax= 2.88733e+02, atom= 642\n", + "Step= 213, Dmax= 2.7e-02 nm, Epot= -4.48374e+04 Fmax= 4.27319e+02, atom= 642\n", + "Step= 214, Dmax= 3.3e-02 nm, Epot= -4.48457e+04 Fmax= 3.65651e+02, atom= 642\n", + "Step= 216, Dmax= 2.0e-02 nm, Epot= -4.48645e+04 Fmax= 6.75728e+01, atom= 566\n", + "Step= 218, Dmax= 1.2e-02 nm, Epot= -4.48702e+04 Fmax= 2.10278e+02, atom= 642\n", + "Step= 219, Dmax= 1.4e-02 nm, Epot= -4.48787e+04 Fmax= 1.59517e+02, atom= 642\n", + "Step= 220, Dmax= 1.7e-02 nm, Epot= -4.48816e+04 Fmax= 2.37098e+02, atom= 642\n", + "Step= 221, Dmax= 2.0e-02 nm, Epot= -4.48863e+04 Fmax= 2.64822e+02, atom= 642\n", + "Step= 222, Dmax= 2.5e-02 nm, Epot= -4.48878e+04 Fmax= 3.15225e+02, atom= 642\n", + "Step= 223, Dmax= 2.9e-02 nm, Epot= -4.48880e+04 Fmax= 4.17213e+02, atom= 642\n", + "Step= 224, Dmax= 3.5e-02 nm, Epot= -4.48898e+04 Fmax= 4.16968e+02, atom= 642\n", + "Step= 226, Dmax= 2.1e-02 nm, Epot= -4.49124e+04 Fmax= 8.02827e+01, atom= 1517\n", + "Step= 228, Dmax= 1.3e-02 nm, Epot= -4.49177e+04 Fmax= 2.24192e+02, atom= 809\n", + "Step= 229, Dmax= 1.5e-02 nm, Epot= -4.49250e+04 Fmax= 1.52218e+02, atom= 809\n", + "Step= 230, Dmax= 1.8e-02 nm, Epot= -4.49260e+04 Fmax= 2.90450e+02, atom= 809\n", + "Step= 231, Dmax= 2.2e-02 nm, Epot= -4.49326e+04 Fmax= 2.40121e+02, atom= 809\n", + "Step= 233, Dmax= 1.3e-02 nm, Epot= -4.49417e+04 Fmax= 6.49885e+01, atom= 401\n", + "Step= 235, Dmax= 7.9e-03 nm, Epot= -4.49471e+04 Fmax= 1.35759e+02, atom= 401\n", + "Step= 236, Dmax= 9.5e-03 nm, Epot= -4.49523e+04 Fmax= 1.08182e+02, atom= 401\n", + "Step= 237, Dmax= 1.1e-02 nm, Epot= -4.49565e+04 Fmax= 1.81130e+02, atom= 401\n", + "Step= 238, Dmax= 1.4e-02 nm, Epot= -4.49614e+04 Fmax= 1.69196e+02, atom= 401\n", + "Step= 239, Dmax= 1.6e-02 nm, Epot= -4.49645e+04 Fmax= 2.52875e+02, atom= 401\n", + "Step= 240, Dmax= 2.0e-02 nm, Epot= -4.49692e+04 Fmax= 2.50626e+02, atom= 401\n", + "Step= 241, Dmax= 2.4e-02 nm, Epot= -4.49705e+04 Fmax= 3.65892e+02, atom= 401\n", + "Step= 242, Dmax= 2.8e-02 nm, Epot= -4.49751e+04 Fmax= 3.59765e+02, atom= 401\n", + "Step= 244, Dmax= 1.7e-02 nm, Epot= -4.49854e+04 Fmax= 6.73207e+01, atom= 401\n", + "Step= 246, Dmax= 1.0e-02 nm, Epot= -4.49913e+04 Fmax= 2.18625e+02, atom= 401\n", + "Step= 247, Dmax= 1.2e-02 nm, Epot= -4.49966e+04 Fmax= 1.06170e+02, atom= 401\n", + "Step= 248, Dmax= 1.5e-02 nm, Epot= -4.50010e+04 Fmax= 2.67906e+02, atom= 401\n", + "Step= 249, Dmax= 1.8e-02 nm, Epot= -4.50063e+04 Fmax= 1.80823e+02, atom= 401\n", + "Step= 250, Dmax= 2.1e-02 nm, Epot= -4.50073e+04 Fmax= 3.71151e+02, atom= 401\n", + "Step= 251, Dmax= 2.5e-02 nm, Epot= -4.50133e+04 Fmax= 2.91756e+02, atom= 401\n", + "Step= 253, Dmax= 1.5e-02 nm, Epot= -4.50202e+04 Fmax= 9.03754e+01, atom= 401\n", + "Step= 254, Dmax= 1.8e-02 nm, Epot= -4.50237e+04 Fmax= 4.05349e+02, atom= 401\n", + "Step= 255, Dmax= 2.2e-02 nm, Epot= -4.50323e+04 Fmax= 1.73953e+02, atom= 401\n", + "Step= 257, Dmax= 1.3e-02 nm, Epot= -4.50365e+04 Fmax= 1.37803e+02, atom= 401\n", + "Step= 258, Dmax= 1.6e-02 nm, Epot= -4.50395e+04 Fmax= 2.67295e+02, atom= 401\n", + "Step= 259, Dmax= 1.9e-02 nm, Epot= -4.50443e+04 Fmax= 2.16125e+02, atom= 401\n", + "Step= 260, Dmax= 2.3e-02 nm, Epot= -4.50449e+04 Fmax= 3.64110e+02, atom= 401\n", + "Step= 261, Dmax= 2.7e-02 nm, Epot= -4.50491e+04 Fmax= 3.46302e+02, atom= 401\n", + "Step= 263, Dmax= 1.6e-02 nm, Epot= -4.50579e+04 Fmax= 6.90870e+01, atom= 401\n", + "Step= 264, Dmax= 2.0e-02 nm, Epot= -4.50631e+04 Fmax= 4.63914e+02, atom= 401\n", + "Step= 265, Dmax= 2.4e-02 nm, Epot= -4.50730e+04 Fmax= 1.72436e+02, atom= 401\n", + "Step= 267, Dmax= 1.4e-02 nm, Epot= -4.50768e+04 Fmax= 1.59719e+02, atom= 401\n", + "Step= 268, Dmax= 1.7e-02 nm, Epot= -4.50793e+04 Fmax= 2.67016e+02, atom= 401\n", + "Step= 269, Dmax= 2.0e-02 nm, Epot= -4.50833e+04 Fmax= 2.47747e+02, atom= 401\n", + "Step= 270, Dmax= 2.4e-02 nm, Epot= -4.50836e+04 Fmax= 3.68733e+02, atom= 401\n", + "Step= 271, Dmax= 2.9e-02 nm, Epot= -4.50861e+04 Fmax= 3.95854e+02, atom= 401\n", + "Step= 273, Dmax= 1.8e-02 nm, Epot= -4.50968e+04 Fmax= 5.60686e+01, atom= 401\n", + "Step= 274, Dmax= 2.1e-02 nm, Epot= -4.51039e+04 Fmax= 5.17311e+02, atom= 401\n", + "Step= 275, Dmax= 2.5e-02 nm, Epot= -4.51143e+04 Fmax= 1.85720e+02, atom= 401\n", + "Step= 277, Dmax= 1.5e-02 nm, Epot= -4.51178e+04 Fmax= 1.75657e+02, atom= 401\n", + "Step= 278, Dmax= 1.8e-02 nm, Epot= -4.51196e+04 Fmax= 2.78257e+02, atom= 401\n", + "Step= 279, Dmax= 2.2e-02 nm, Epot= -4.51230e+04 Fmax= 2.73040e+02, atom= 401\n", + "Step= 281, Dmax= 1.3e-02 nm, Epot= -4.51292e+04 Fmax= 5.69754e+01, atom= 401\n", + "Step= 282, Dmax= 1.6e-02 nm, Epot= -4.51354e+04 Fmax= 3.42278e+02, atom= 401\n", + "Step= 283, Dmax= 1.9e-02 nm, Epot= -4.51422e+04 Fmax= 1.44151e+02, atom= 401\n", + "Step= 285, Dmax= 1.1e-02 nm, Epot= -4.51455e+04 Fmax= 1.24741e+02, atom= 401\n", + "Step= 286, Dmax= 1.4e-02 nm, Epot= -4.51481e+04 Fmax= 2.14771e+02, atom= 401\n", + "Step= 287, Dmax= 1.6e-02 nm, Epot= -4.51516e+04 Fmax= 1.94119e+02, atom= 401\n", + "Step= 288, Dmax= 2.0e-02 nm, Epot= -4.51526e+04 Fmax= 2.94393e+02, atom= 401\n", + "Step= 289, Dmax= 2.4e-02 nm, Epot= -4.51553e+04 Fmax= 3.07843e+02, atom= 401\n", + "Step= 291, Dmax= 1.4e-02 nm, Epot= -4.51628e+04 Fmax= 5.11250e+01, atom= 401\n", + "Step= 292, Dmax= 1.7e-02 nm, Epot= -4.51698e+04 Fmax= 3.67684e+02, atom= 401\n", + "Step= 293, Dmax= 2.0e-02 nm, Epot= -4.51767e+04 Fmax= 1.53383e+02, atom= 401\n", + "Step= 295, Dmax= 1.2e-02 nm, Epot= -4.51798e+04 Fmax= 1.39341e+02, atom= 401\n", + "Step= 296, Dmax= 1.5e-02 nm, Epot= -4.51818e+04 Fmax= 2.21630e+02, atom= 401\n", + "Step= 297, Dmax= 1.8e-02 nm, Epot= -4.51849e+04 Fmax= 2.19558e+02, atom= 401\n", + "Step= 298, Dmax= 2.1e-02 nm, Epot= -4.51857e+04 Fmax= 3.01374e+02, atom= 401\n", + "Step= 299, Dmax= 2.5e-02 nm, Epot= -4.51871e+04 Fmax= 3.50012e+02, atom= 401\n", + "Step= 300, Dmax= 3.0e-02 nm, Epot= -4.51874e+04 Fmax= 4.01144e+02, atom= 401\n", + "Step= 302, Dmax= 1.8e-02 nm, Epot= -4.51991e+04 Fmax= 7.91110e+01, atom= 732\n", + "Step= 303, Dmax= 2.2e-02 nm, Epot= -4.51996e+04 Fmax= 4.03636e+02, atom= 732\n", + "Step= 304, Dmax= 2.6e-02 nm, Epot= -4.52062e+04 Fmax= 3.25164e+02, atom= 401\n", + "Step= 306, Dmax= 1.6e-02 nm, Epot= -4.52135e+04 Fmax= 8.16744e+01, atom= 401\n", + "Step= 307, Dmax= 1.9e-02 nm, Epot= -4.52162e+04 Fmax= 3.57140e+02, atom= 401\n", + "Step= 308, Dmax= 2.3e-02 nm, Epot= -4.52222e+04 Fmax= 1.83389e+02, atom= 401\n", + "Step= 310, Dmax= 1.4e-02 nm, Epot= -4.52256e+04 Fmax= 1.33658e+02, atom= 401\n", + "Step= 311, Dmax= 1.6e-02 nm, Epot= -4.52262e+04 Fmax= 2.66531e+02, atom= 401\n", + "Step= 312, Dmax= 2.0e-02 nm, Epot= -4.52303e+04 Fmax= 2.27669e+02, atom= 401\n", + "Step= 314, Dmax= 1.2e-02 nm, Epot= -4.52355e+04 Fmax= 6.32919e+01, atom= 401\n", + "Step= 315, Dmax= 1.4e-02 nm, Epot= -4.52396e+04 Fmax= 2.64077e+02, atom= 401\n", + "Step= 316, Dmax= 1.7e-02 nm, Epot= -4.52444e+04 Fmax= 1.42809e+02, atom= 401\n", + "Step= 318, Dmax= 1.0e-02 nm, Epot= -4.52476e+04 Fmax= 9.54287e+01, atom= 401\n", + "Step= 319, Dmax= 1.2e-02 nm, Epot= -4.52497e+04 Fmax= 2.01162e+02, atom= 401\n", + "Step= 320, Dmax= 1.5e-02 nm, Epot= -4.52533e+04 Fmax= 1.60504e+02, atom= 401\n", + "Step= 321, Dmax= 1.8e-02 nm, Epot= -4.52539e+04 Fmax= 2.62924e+02, atom= 401\n", + "Step= 322, Dmax= 2.1e-02 nm, Epot= -4.52566e+04 Fmax= 2.67672e+02, atom= 401\n", + "Step= 324, Dmax= 1.3e-02 nm, Epot= -4.52632e+04 Fmax= 4.78890e+01, atom= 401\n", + "Step= 325, Dmax= 1.5e-02 nm, Epot= -4.52696e+04 Fmax= 2.89863e+02, atom= 401\n", + "Step= 326, Dmax= 1.8e-02 nm, Epot= -4.52745e+04 Fmax= 1.46259e+02, atom= 1356\n", + "Step= 328, Dmax= 1.1e-02 nm, Epot= -4.52774e+04 Fmax= 1.08762e+02, atom= 401\n", + "Step= 329, Dmax= 1.3e-02 nm, Epot= -4.52790e+04 Fmax= 2.08804e+02, atom= 1356\n", + "Step= 330, Dmax= 1.6e-02 nm, Epot= -4.52823e+04 Fmax= 1.72575e+02, atom= 401\n", + "Step= 332, Dmax= 9.4e-03 nm, Epot= -4.52861e+04 Fmax= 5.70415e+01, atom= 4016\n", + "Step= 333, Dmax= 1.1e-02 nm, Epot= -4.52898e+04 Fmax= 2.05683e+02, atom= 401\n", + "Step= 334, Dmax= 1.4e-02 nm, Epot= -4.52935e+04 Fmax= 1.13823e+02, atom= 401\n", + "Step= 336, Dmax= 8.1e-03 nm, Epot= -4.52962e+04 Fmax= 7.54581e+01, atom= 401\n", + "Step= 337, Dmax= 9.8e-03 nm, Epot= -4.52985e+04 Fmax= 1.61216e+02, atom= 1356\n", + "Step= 338, Dmax= 1.2e-02 nm, Epot= -4.53015e+04 Fmax= 1.20143e+02, atom= 1356\n", + "Step= 339, Dmax= 1.4e-02 nm, Epot= -4.53025e+04 Fmax= 2.19162e+02, atom= 1356\n", + "Step= 340, Dmax= 1.7e-02 nm, Epot= -4.53055e+04 Fmax= 1.87068e+02, atom= 1356\n", + "Step= 342, Dmax= 1.0e-02 nm, Epot= -4.53095e+04 Fmax= 5.70910e+01, atom= 4016\n", + "Step= 343, Dmax= 1.2e-02 nm, Epot= -4.53125e+04 Fmax= 2.22705e+02, atom= 401\n", + "Step= 344, Dmax= 1.5e-02 nm, Epot= -4.53164e+04 Fmax= 1.20191e+02, atom= 1356\n", + "Step= 346, Dmax= 8.8e-03 nm, Epot= -4.53189e+04 Fmax= 8.00550e+01, atom= 1356\n", + "Step= 347, Dmax= 1.1e-02 nm, Epot= -4.53206e+04 Fmax= 1.73454e+02, atom= 1356\n", + "Step= 348, Dmax= 1.3e-02 nm, Epot= -4.53235e+04 Fmax= 1.24943e+02, atom= 1356\n", + "Step= 349, Dmax= 1.5e-02 nm, Epot= -4.53237e+04 Fmax= 2.38134e+02, atom= 1356\n", + "Step= 350, Dmax= 1.8e-02 nm, Epot= -4.53269e+04 Fmax= 1.92623e+02, atom= 1356\n", + "Step= 352, Dmax= 1.1e-02 nm, Epot= -4.53309e+04 Fmax= 6.47061e+01, atom= 4016\n", + "Step= 353, Dmax= 1.3e-02 nm, Epot= -4.53325e+04 Fmax= 2.33340e+02, atom= 401\n", + "Step= 354, Dmax= 1.6e-02 nm, Epot= -4.53366e+04 Fmax= 1.32755e+02, atom= 1356\n", + "Step= 356, Dmax= 9.4e-03 nm, Epot= -4.53391e+04 Fmax= 7.97862e+01, atom= 732\n", + "Step= 357, Dmax= 1.1e-02 nm, Epot= -4.53402e+04 Fmax= 1.90449e+02, atom= 1356\n", + "Step= 358, Dmax= 1.4e-02 nm, Epot= -4.53434e+04 Fmax= 1.26101e+02, atom= 1356\n", + "Step= 360, Dmax= 8.1e-03 nm, Epot= -4.53459e+04 Fmax= 5.88508e+01, atom= 4016\n", + "Step= 361, Dmax= 9.8e-03 nm, Epot= -4.53478e+04 Fmax= 1.65977e+02, atom= 401\n", + "Step= 362, Dmax= 1.2e-02 nm, Epot= -4.53508e+04 Fmax= 1.05645e+02, atom= 1356\n", + "Step= 363, Dmax= 1.4e-02 nm, Epot= -4.53508e+04 Fmax= 2.19347e+02, atom= 1356\n", + "Step= 364, Dmax= 1.7e-02 nm, Epot= -4.53540e+04 Fmax= 1.71196e+02, atom= 1356\n", + "Step= 366, Dmax= 1.0e-02 nm, Epot= -4.53574e+04 Fmax= 6.38905e+01, atom= 7326\n", + "Step= 367, Dmax= 1.2e-02 nm, Epot= -4.53585e+04 Fmax= 2.11677e+02, atom= 732\n", + "Step= 368, Dmax= 1.5e-02 nm, Epot= -4.53621e+04 Fmax= 1.23472e+02, atom= 1356\n", + "Step= 370, Dmax= 8.7e-03 nm, Epot= -4.53644e+04 Fmax= 6.90884e+01, atom= 1356\n", + "Step= 371, Dmax= 1.0e-02 nm, Epot= -4.53655e+04 Fmax= 1.70116e+02, atom= 1356\n", + "Step= 372, Dmax= 1.3e-02 nm, Epot= -4.53684e+04 Fmax= 1.17780e+02, atom= 1356\n", + "Step= 374, Dmax= 7.6e-03 nm, Epot= -4.53708e+04 Fmax= 5.43108e+01, atom= 7326\n", + "Step= 375, Dmax= 9.1e-03 nm, Epot= -4.53727e+04 Fmax= 1.49716e+02, atom= 732\n", + "Step= 376, Dmax= 1.1e-02 nm, Epot= -4.53752e+04 Fmax= 9.37573e+01, atom= 732\n", + "Step= 377, Dmax= 1.3e-02 nm, Epot= -4.53753e+04 Fmax= 2.13574e+02, atom= 732\n", + "Step= 378, Dmax= 1.6e-02 nm, Epot= -4.53787e+04 Fmax= 1.38101e+02, atom= 732\n", + "Step= 380, Dmax= 9.4e-03 nm, Epot= -4.53813e+04 Fmax= 6.41603e+01, atom= 1356\n", + "Step= 381, Dmax= 1.1e-02 nm, Epot= -4.53816e+04 Fmax= 1.92141e+02, atom= 1356\n", + "Step= 382, Dmax= 1.4e-02 nm, Epot= -4.53854e+04 Fmax= 1.15458e+02, atom= 732\n", + "Step= 384, Dmax= 8.1e-03 nm, Epot= -4.53877e+04 Fmax= 6.75705e+01, atom= 7326\n", + "Step= 385, Dmax= 9.7e-03 nm, Epot= -4.53890e+04 Fmax= 1.47951e+02, atom= 732\n", + "Step= 386, Dmax= 1.2e-02 nm, Epot= -4.53914e+04 Fmax= 1.09483e+02, atom= 732\n", + "Step= 388, Dmax= 7.0e-03 nm, Epot= -4.53936e+04 Fmax= 4.14989e+01, atom= 732\n", + "Step= 389, Dmax= 8.4e-03 nm, Epot= -4.53953e+04 Fmax= 1.47392e+02, atom= 732\n", + "Step= 390, Dmax= 1.0e-02 nm, Epot= -4.53985e+04 Fmax= 7.96769e+01, atom= 732\n", + "Step= 392, Dmax= 6.1e-03 nm, Epot= -4.54004e+04 Fmax= 5.41914e+01, atom= 732\n", + "Step= 393, Dmax= 7.3e-03 nm, Epot= -4.54020e+04 Fmax= 1.05904e+02, atom= 732\n", + "Step= 394, Dmax= 8.7e-03 nm, Epot= -4.54040e+04 Fmax= 8.51007e+01, atom= 732\n", + "Step= 395, Dmax= 1.0e-02 nm, Epot= -4.54046e+04 Fmax= 1.49032e+02, atom= 732\n", + "Step= 396, Dmax= 1.3e-02 nm, Epot= -4.54068e+04 Fmax= 1.31882e+02, atom= 1264\n", + "Step= 398, Dmax= 7.5e-03 nm, Epot= -4.54100e+04 Fmax= 3.98925e+01, atom= 7184\n", + "Step= 399, Dmax= 9.0e-03 nm, Epot= -4.54121e+04 Fmax= 1.50702e+02, atom= 718\n", + "Step= 400, Dmax= 1.1e-02 nm, Epot= -4.54150e+04 Fmax= 9.65127e+01, atom= 1264\n", + "Step= 402, Dmax= 6.5e-03 nm, Epot= -4.54170e+04 Fmax= 4.84820e+01, atom= 1264\n", + "Step= 403, Dmax= 7.8e-03 nm, Epot= -4.54188e+04 Fmax= 1.34380e+02, atom= 1264\n", + "Step= 404, Dmax= 9.4e-03 nm, Epot= -4.54212e+04 Fmax= 7.88978e+01, atom= 1264\n", + "Step= 405, Dmax= 1.1e-02 nm, Epot= -4.54219e+04 Fmax= 1.84098e+02, atom= 1264\n", + "Step= 406, Dmax= 1.4e-02 nm, Epot= -4.54247e+04 Fmax= 1.21435e+02, atom= 1264\n", + "Step= 408, Dmax= 8.1e-03 nm, Epot= -4.54270e+04 Fmax= 5.42474e+01, atom= 1264\n", + "Step= 409, Dmax= 9.7e-03 nm, Epot= -4.54283e+04 Fmax= 1.67290e+02, atom= 1264\n", + "Step= 410, Dmax= 1.2e-02 nm, Epot= -4.54313e+04 Fmax= 9.76441e+01, atom= 1264\n", + "Step= 412, Dmax= 7.0e-03 nm, Epot= -4.54332e+04 Fmax= 5.88133e+01, atom= 1264\n", + "Step= 413, Dmax= 8.4e-03 nm, Epot= -4.54349e+04 Fmax= 1.36199e+02, atom= 1264\n", + "Step= 414, Dmax= 1.0e-02 nm, Epot= -4.54371e+04 Fmax= 9.17353e+01, atom= 1264\n", + "Step= 415, Dmax= 1.2e-02 nm, Epot= -4.54378e+04 Fmax= 1.90666e+02, atom= 1264\n", + "Step= 416, Dmax= 1.5e-02 nm, Epot= -4.54403e+04 Fmax= 1.37506e+02, atom= 1264\n", + "Step= 418, Dmax= 8.7e-03 nm, Epot= -4.54429e+04 Fmax= 5.01721e+01, atom= 1264\n", + "Step= 419, Dmax= 1.0e-02 nm, Epot= -4.54440e+04 Fmax= 1.92386e+02, atom= 1264\n", + "Step= 420, Dmax= 1.3e-02 nm, Epot= -4.54478e+04 Fmax= 9.50806e+01, atom= 1264\n", + "Step= 422, Dmax= 7.5e-03 nm, Epot= -4.54497e+04 Fmax= 7.13852e+01, atom= 1264\n", + "Step= 423, Dmax= 9.0e-03 nm, Epot= -4.54511e+04 Fmax= 1.38056e+02, atom= 1264\n", + "Step= 424, Dmax= 1.1e-02 nm, Epot= -4.54533e+04 Fmax= 1.06649e+02, atom= 1264\n", + "Step= 425, Dmax= 1.3e-02 nm, Epot= -4.54538e+04 Fmax= 1.96301e+02, atom= 1264\n", + "Step= 426, Dmax= 1.6e-02 nm, Epot= -4.54563e+04 Fmax= 1.57068e+02, atom= 1264\n", + "Step= 428, Dmax= 9.4e-03 nm, Epot= -4.54594e+04 Fmax= 4.62974e+01, atom= 7184\n", + "Step= 429, Dmax= 1.1e-02 nm, Epot= -4.54602e+04 Fmax= 2.15458e+02, atom= 1264\n", + "Step= 430, Dmax= 1.3e-02 nm, Epot= -4.54652e+04 Fmax= 9.90192e+01, atom= 1264\n", + "Step= 432, Dmax= 8.1e-03 nm, Epot= -4.54671e+04 Fmax= 7.86969e+01, atom= 1264\n", + "Step= 433, Dmax= 9.7e-03 nm, Epot= -4.54684e+04 Fmax= 1.47572e+02, atom= 1264\n", + "Step= 434, Dmax= 1.2e-02 nm, Epot= -4.54709e+04 Fmax= 1.16005e+02, atom= 1264\n", + "Step= 435, Dmax= 1.4e-02 nm, Epot= -4.54709e+04 Fmax= 2.11263e+02, atom= 1264\n", + "Step= 436, Dmax= 1.7e-02 nm, Epot= -4.54738e+04 Fmax= 1.70085e+02, atom= 1264\n", + "Step= 438, Dmax= 1.0e-02 nm, Epot= -4.54776e+04 Fmax= 5.06155e+01, atom= 7184\n", + "Step= 439, Dmax= 1.2e-02 nm, Epot= -4.54778e+04 Fmax= 2.24940e+02, atom= 1264\n", + "Step= 440, Dmax= 1.4e-02 nm, Epot= -4.54834e+04 Fmax= 1.15936e+02, atom= 1264\n", + "Step= 442, Dmax= 8.7e-03 nm, Epot= -4.54858e+04 Fmax= 7.58463e+01, atom= 1264\n", + "Step= 443, Dmax= 1.0e-02 nm, Epot= -4.54868e+04 Fmax= 1.71706e+02, atom= 1264\n", + "Step= 444, Dmax= 1.3e-02 nm, Epot= -4.54899e+04 Fmax= 1.14794e+02, atom= 1264\n", + "Step= 446, Dmax= 7.5e-03 nm, Epot= -4.54925e+04 Fmax= 5.08589e+01, atom= 1264\n", + "Step= 447, Dmax= 9.0e-03 nm, Epot= -4.54943e+04 Fmax= 1.55627e+02, atom= 1264\n", + "Step= 448, Dmax= 1.1e-02 nm, Epot= -4.54977e+04 Fmax= 9.23687e+01, atom= 1264\n", + "Step= 449, Dmax= 1.3e-02 nm, Epot= -4.54977e+04 Fmax= 2.01794e+02, atom= 1264\n", + "Step= 450, Dmax= 1.6e-02 nm, Epot= -4.55013e+04 Fmax= 1.54131e+02, atom= 1264\n", + "Step= 452, Dmax= 9.4e-03 nm, Epot= -4.55048e+04 Fmax= 6.08370e+01, atom= 5824\n", + "Step= 453, Dmax= 1.1e-02 nm, Epot= -4.55061e+04 Fmax= 2.05291e+02, atom= 1264\n", + "Step= 454, Dmax= 1.3e-02 nm, Epot= -4.55102e+04 Fmax= 1.10097e+02, atom= 1264\n", + "Step= 456, Dmax= 8.1e-03 nm, Epot= -4.55126e+04 Fmax= 6.75424e+01, atom= 1264\n", + "Step= 457, Dmax= 9.7e-03 nm, Epot= -4.55144e+04 Fmax= 1.53591e+02, atom= 1264\n", + "Step= 458, Dmax= 1.2e-02 nm, Epot= -4.55173e+04 Fmax= 1.13209e+02, atom= 1264\n", + "Step= 459, Dmax= 1.4e-02 nm, Epot= -4.55178e+04 Fmax= 2.05422e+02, atom= 1264\n", + "Step= 460, Dmax= 1.7e-02 nm, Epot= -4.55208e+04 Fmax= 1.79725e+02, atom= 1264\n", + "Step= 462, Dmax= 1.0e-02 nm, Epot= -4.55248e+04 Fmax= 5.70532e+01, atom= 5824\n", + "Step= 463, Dmax= 1.2e-02 nm, Epot= -4.55270e+04 Fmax= 2.20245e+02, atom= 1264\n", + "Step= 464, Dmax= 1.4e-02 nm, Epot= -4.55310e+04 Fmax= 1.21818e+02, atom= 1264\n", + "Step= 466, Dmax= 8.7e-03 nm, Epot= -4.55335e+04 Fmax= 6.85399e+01, atom= 1264\n", + "Step= 467, Dmax= 1.0e-02 nm, Epot= -4.55354e+04 Fmax= 1.71478e+02, atom= 1264\n", + "Step= 468, Dmax= 1.3e-02 nm, Epot= -4.55386e+04 Fmax= 1.16256e+02, atom= 1264\n", + "Step= 469, Dmax= 1.5e-02 nm, Epot= -4.55389e+04 Fmax= 2.28416e+02, atom= 1264\n", + "Step= 470, Dmax= 1.8e-02 nm, Epot= -4.55423e+04 Fmax= 1.86440e+02, atom= 1264\n", + "Step= 472, Dmax= 1.1e-02 nm, Epot= -4.55462e+04 Fmax= 6.65599e+01, atom= 5824\n", + "Step= 473, Dmax= 1.3e-02 nm, Epot= -4.55479e+04 Fmax= 2.35647e+02, atom= 1264\n", + "Step= 474, Dmax= 1.6e-02 nm, Epot= -4.55520e+04 Fmax= 1.32947e+02, atom= 1264\n", + "Step= 476, Dmax= 9.3e-03 nm, Epot= -4.55546e+04 Fmax= 7.12243e+01, atom= 1264\n", + "Step= 477, Dmax= 1.1e-02 nm, Epot= -4.55563e+04 Fmax= 1.88520e+02, atom= 1264\n", + "Step= 478, Dmax= 1.3e-02 nm, Epot= -4.55597e+04 Fmax= 1.21857e+02, atom= 1264\n", + "Step= 480, Dmax= 8.1e-03 nm, Epot= -4.55622e+04 Fmax= 6.11391e+01, atom= 1264\n", + "Step= 481, Dmax= 9.7e-03 nm, Epot= -4.55645e+04 Fmax= 1.72616e+02, atom= 1264\n", + "Step= 482, Dmax= 1.2e-02 nm, Epot= -4.55675e+04 Fmax= 9.73076e+01, atom= 1264\n", + "Step= 483, Dmax= 1.4e-02 nm, Epot= -4.55682e+04 Fmax= 2.39947e+02, atom= 1264\n", + "Step= 484, Dmax= 1.7e-02 nm, Epot= -4.55718e+04 Fmax= 1.48898e+02, atom= 1264\n", + "Step= 486, Dmax= 1.0e-02 nm, Epot= -4.55746e+04 Fmax= 7.07733e+01, atom= 1264\n", + "Step= 487, Dmax= 1.2e-02 nm, Epot= -4.55758e+04 Fmax= 2.11975e+02, atom= 1264\n", + "Step= 488, Dmax= 1.4e-02 nm, Epot= -4.55797e+04 Fmax= 1.24149e+02, atom= 1264\n", + "Step= 490, Dmax= 8.7e-03 nm, Epot= -4.55820e+04 Fmax= 7.05765e+01, atom= 1264\n", + "Step= 491, Dmax= 1.0e-02 nm, Epot= -4.55838e+04 Fmax= 1.80952e+02, atom= 1264\n", + "Step= 492, Dmax= 1.2e-02 nm, Epot= -4.55867e+04 Fmax= 1.08217e+02, atom= 1264\n", + "Step= 493, Dmax= 1.5e-02 nm, Epot= -4.55869e+04 Fmax= 2.55069e+02, atom= 1264\n", + "Step= 494, Dmax= 1.8e-02 nm, Epot= -4.55905e+04 Fmax= 1.62458e+02, atom= 1264\n", + "Step= 496, Dmax= 1.1e-02 nm, Epot= -4.55934e+04 Fmax= 7.19876e+01, atom= 1264\n", + "Step= 497, Dmax= 1.3e-02 nm, Epot= -4.55939e+04 Fmax= 2.33657e+02, atom= 1264\n", + "Step= 498, Dmax= 1.6e-02 nm, Epot= -4.55982e+04 Fmax= 1.29079e+02, atom= 1264\n", + "Step= 500, Dmax= 9.3e-03 nm, Epot= -4.56005e+04 Fmax= 7.82755e+01, atom= 1264\n", + "Step= 501, Dmax= 1.1e-02 nm, Epot= -4.56017e+04 Fmax= 1.91028e+02, atom= 1264\n", + "Step= 502, Dmax= 1.3e-02 nm, Epot= -4.56045e+04 Fmax= 1.17858e+02, atom= 1264\n", + "Step= 504, Dmax= 8.1e-03 nm, Epot= -4.56067e+04 Fmax= 6.12183e+01, atom= 1264\n", + "Step= 505, Dmax= 9.7e-03 nm, Epot= -4.56084e+04 Fmax= 1.57054e+02, atom= 1264\n", + "Step= 506, Dmax= 1.2e-02 nm, Epot= -4.56109e+04 Fmax= 1.11038e+02, atom= 1264\n", + "Step= 507, Dmax= 1.4e-02 nm, Epot= -4.56113e+04 Fmax= 2.02945e+02, atom= 1264\n", + "Step= 508, Dmax= 1.7e-02 nm, Epot= -4.56137e+04 Fmax= 1.82632e+02, atom= 1264\n", + "Step= 510, Dmax= 1.0e-02 nm, Epot= -4.56170e+04 Fmax= 5.44213e+01, atom= 5824\n", + "Step= 511, Dmax= 1.2e-02 nm, Epot= -4.56188e+04 Fmax= 2.14129e+02, atom= 1264\n", + "Step= 512, Dmax= 1.4e-02 nm, Epot= -4.56219e+04 Fmax= 1.22899e+02, atom= 1264\n", + "Step= 514, Dmax= 8.7e-03 nm, Epot= -4.56240e+04 Fmax= 6.72173e+01, atom= 1264\n", + "Step= 515, Dmax= 1.0e-02 nm, Epot= -4.56252e+04 Fmax= 1.68104e+02, atom= 1264\n", + "Step= 516, Dmax= 1.2e-02 nm, Epot= -4.56278e+04 Fmax= 1.19144e+02, atom= 1264\n", + "Step= 518, Dmax= 7.5e-03 nm, Epot= -4.56298e+04 Fmax= 5.14206e+01, atom= 5824\n", + "Step= 519, Dmax= 9.0e-03 nm, Epot= -4.56316e+04 Fmax= 1.59831e+02, atom= 1264\n", + "Step= 520, Dmax= 1.1e-02 nm, Epot= -4.56341e+04 Fmax= 8.75089e+01, atom= 1264\n", + "Step= 521, Dmax= 1.3e-02 nm, Epot= -4.56341e+04 Fmax= 2.25079e+02, atom= 1264\n", + "Step= 522, Dmax= 1.6e-02 nm, Epot= -4.56374e+04 Fmax= 1.31770e+02, atom= 1264\n", + "Step= 524, Dmax= 9.3e-03 nm, Epot= -4.56396e+04 Fmax= 7.20213e+01, atom= 1264\n", + "Step= 525, Dmax= 1.1e-02 nm, Epot= -4.56401e+04 Fmax= 1.81395e+02, atom= 1264\n", + "Step= 526, Dmax= 1.3e-02 nm, Epot= -4.56429e+04 Fmax= 1.27643e+02, atom= 1264\n", + "Step= 528, Dmax= 8.0e-03 nm, Epot= -4.56452e+04 Fmax= 5.65556e+01, atom= 5824\n", + "Step= 529, Dmax= 9.6e-03 nm, Epot= -4.56462e+04 Fmax= 1.68386e+02, atom= 1264\n", + "Step= 530, Dmax= 1.2e-02 nm, Epot= -4.56490e+04 Fmax= 9.67118e+01, atom= 1264\n", + "Step= 532, Dmax= 6.9e-03 nm, Epot= -4.56508e+04 Fmax= 5.82563e+01, atom= 1264\n", + "Step= 533, Dmax= 8.3e-03 nm, Epot= -4.56519e+04 Fmax= 1.26980e+02, atom= 1264\n", + "Step= 534, Dmax= 1.0e-02 nm, Epot= -4.56539e+04 Fmax= 1.03427e+02, atom= 1264\n", + "Step= 536, Dmax= 6.0e-03 nm, Epot= -4.56560e+04 Fmax= 3.59879e+01, atom= 582\n", + "Step= 537, Dmax= 7.2e-03 nm, Epot= -4.56578e+04 Fmax= 1.31417e+02, atom= 626\n", + "Step= 538, Dmax= 8.6e-03 nm, Epot= -4.56602e+04 Fmax= 7.34455e+01, atom= 626\n", + "Step= 539, Dmax= 1.0e-02 nm, Epot= -4.56603e+04 Fmax= 1.73195e+02, atom= 626\n", + "Step= 540, Dmax= 1.2e-02 nm, Epot= -4.56631e+04 Fmax= 1.21107e+02, atom= 626\n", + "Step= 542, Dmax= 7.5e-03 nm, Epot= -4.56653e+04 Fmax= 5.14276e+01, atom= 626\n", + "Step= 543, Dmax= 9.0e-03 nm, Epot= -4.56662e+04 Fmax= 1.71196e+02, atom= 626\n", + "Step= 544, Dmax= 1.1e-02 nm, Epot= -4.56691e+04 Fmax= 8.82880e+01, atom= 626\n", + "Step= 546, Dmax= 6.5e-03 nm, Epot= -4.56706e+04 Fmax= 6.41895e+01, atom= 626\n", + "Step= 547, Dmax= 7.7e-03 nm, Epot= -4.56720e+04 Fmax= 1.17044e+02, atom= 626\n", + "Step= 548, Dmax= 9.3e-03 nm, Epot= -4.56736e+04 Fmax= 1.02734e+02, atom= 626\n", + "Step= 549, Dmax= 1.1e-02 nm, Epot= -4.56743e+04 Fmax= 1.61741e+02, atom= 626\n", + "Step= 550, Dmax= 1.3e-02 nm, Epot= -4.56759e+04 Fmax= 1.54384e+02, atom= 626\n", + "Step= 552, Dmax= 8.0e-03 nm, Epot= -4.56782e+04 Fmax= 3.38864e+01, atom= 111\n", + "Step= 553, Dmax= 9.6e-03 nm, Epot= -4.56801e+04 Fmax= 2.14097e+02, atom= 626\n", + "Step= 554, Dmax= 1.2e-02 nm, Epot= -4.56835e+04 Fmax= 7.52265e+01, atom= 626\n", + "Step= 556, Dmax= 6.9e-03 nm, Epot= -4.56849e+04 Fmax= 8.64305e+01, atom= 626\n", + "Step= 557, Dmax= 8.3e-03 nm, Epot= -4.56861e+04 Fmax= 1.08619e+02, atom= 626\n", + "Step= 558, Dmax= 1.0e-02 nm, Epot= -4.56873e+04 Fmax= 1.27482e+02, atom= 626\n", + "Step= 559, Dmax= 1.2e-02 nm, Epot= -4.56883e+04 Fmax= 1.56156e+02, atom= 626\n", + "Step= 560, Dmax= 1.4e-02 nm, Epot= -4.56892e+04 Fmax= 1.83907e+02, atom= 626\n", + "Step= 561, Dmax= 1.7e-02 nm, Epot= -4.56895e+04 Fmax= 2.29917e+02, atom= 626\n", + "Step= 562, Dmax= 2.1e-02 nm, Epot= -4.56900e+04 Fmax= 2.59564e+02, atom= 626\n", + "Step= 564, Dmax= 1.2e-02 nm, Epot= -4.56946e+04 Fmax= 4.79706e+01, atom= 111\n", + "Step= 565, Dmax= 1.5e-02 nm, Epot= -4.56952e+04 Fmax= 2.71962e+02, atom= 626\n", + "Step= 566, Dmax= 1.8e-02 nm, Epot= -4.56986e+04 Fmax= 1.97401e+02, atom= 626\n", + "Step= 568, Dmax= 1.1e-02 nm, Epot= -4.57012e+04 Fmax= 5.53465e+01, atom= 339\n", + "Step= 569, Dmax= 1.3e-02 nm, Epot= -4.57014e+04 Fmax= 2.54759e+02, atom= 339\n", + "Step= 570, Dmax= 1.5e-02 nm, Epot= -4.57050e+04 Fmax= 1.19686e+02, atom= 626\n", + "Step= 572, Dmax= 9.3e-03 nm, Epot= -4.57064e+04 Fmax= 8.76655e+01, atom= 626\n", + "Step= 573, Dmax= 1.1e-02 nm, Epot= -4.57068e+04 Fmax= 1.81661e+02, atom= 626\n", + "Step= 574, Dmax= 1.3e-02 nm, Epot= -4.57087e+04 Fmax= 1.36746e+02, atom= 626\n", + "Step= 576, Dmax= 8.0e-03 nm, Epot= -4.57106e+04 Fmax= 5.28007e+01, atom= 626\n", + "Step= 577, Dmax= 9.6e-03 nm, Epot= -4.57117e+04 Fmax= 1.71984e+02, atom= 626\n", + "Step= 578, Dmax= 1.2e-02 nm, Epot= -4.57137e+04 Fmax= 1.01928e+02, atom= 626\n", + "Step= 580, Dmax= 6.9e-03 nm, Epot= -4.57151e+04 Fmax= 5.67850e+01, atom= 626\n", + "Step= 581, Dmax= 8.3e-03 nm, Epot= -4.57161e+04 Fmax= 1.45923e+02, atom= 626\n", + "Step= 582, Dmax= 1.0e-02 nm, Epot= -4.57178e+04 Fmax= 9.20070e+01, atom= 626\n", + "Step= 583, Dmax= 1.2e-02 nm, Epot= -4.57179e+04 Fmax= 1.95271e+02, atom= 626\n", + "Step= 584, Dmax= 1.4e-02 nm, Epot= -4.57198e+04 Fmax= 1.49080e+02, atom= 626\n", + "Step= 586, Dmax= 8.6e-03 nm, Epot= -4.57218e+04 Fmax= 5.45235e+01, atom= 626\n", + "Step= 587, Dmax= 1.0e-02 nm, Epot= -4.57226e+04 Fmax= 1.90014e+02, atom= 626\n", + "Step= 588, Dmax= 1.2e-02 nm, Epot= -4.57249e+04 Fmax= 1.05233e+02, atom= 626\n", + "Step= 590, Dmax= 7.4e-03 nm, Epot= -4.57262e+04 Fmax= 6.50171e+01, atom= 626\n", + "Step= 591, Dmax= 8.9e-03 nm, Epot= -4.57269e+04 Fmax= 1.51520e+02, atom= 626\n", + "Step= 592, Dmax= 1.1e-02 nm, Epot= -4.57286e+04 Fmax= 1.04259e+02, atom= 626\n", + "Step= 594, Dmax= 6.4e-03 nm, Epot= -4.57300e+04 Fmax= 4.86618e+01, atom= 626\n", + "Step= 595, Dmax= 7.7e-03 nm, Epot= -4.57312e+04 Fmax= 1.31234e+02, atom= 626\n", + "Step= 596, Dmax= 9.3e-03 nm, Epot= -4.57327e+04 Fmax= 8.79141e+01, atom= 626\n", + "Step= 597, Dmax= 1.1e-02 nm, Epot= -4.57330e+04 Fmax= 1.77630e+02, atom= 626\n", + "Step= 598, Dmax= 1.3e-02 nm, Epot= -4.57346e+04 Fmax= 1.37288e+02, atom= 626\n", + "Step= 600, Dmax= 8.0e-03 nm, Epot= -4.57364e+04 Fmax= 4.65334e+01, atom= 626\n", + "Step= 601, Dmax= 9.6e-03 nm, Epot= -4.57367e+04 Fmax= 1.97158e+02, atom= 626\n", + "Step= 602, Dmax= 1.2e-02 nm, Epot= -4.57395e+04 Fmax= 8.53432e+01, atom= 626\n", + "Step= 604, Dmax= 6.9e-03 nm, Epot= -4.57406e+04 Fmax= 7.80857e+01, atom= 626\n", + "Step= 605, Dmax= 8.3e-03 nm, Epot= -4.57414e+04 Fmax= 1.17089e+02, atom= 626\n", + "Step= 606, Dmax= 1.0e-02 nm, Epot= -4.57425e+04 Fmax= 1.18012e+02, atom= 626\n", + "Step= 607, Dmax= 1.2e-02 nm, Epot= -4.57429e+04 Fmax= 1.66990e+02, atom= 626\n", + "Step= 608, Dmax= 1.4e-02 nm, Epot= -4.57438e+04 Fmax= 1.71056e+02, atom= 626\n", + "Step= 610, Dmax= 8.6e-03 nm, Epot= -4.57461e+04 Fmax= 3.25288e+01, atom= 111\n", + "Step= 611, Dmax= 1.0e-02 nm, Epot= -4.57468e+04 Fmax= 2.21624e+02, atom= 626\n", + "Step= 612, Dmax= 1.2e-02 nm, Epot= -4.57502e+04 Fmax= 9.43645e+01, atom= 626\n", + "Step= 614, Dmax= 7.4e-03 nm, Epot= -4.57512e+04 Fmax= 7.85514e+01, atom= 626\n", + "Step= 615, Dmax= 8.9e-03 nm, Epot= -4.57519e+04 Fmax= 1.32988e+02, atom= 626\n", + "Step= 616, Dmax= 1.1e-02 nm, Epot= -4.57530e+04 Fmax= 1.19382e+02, atom= 626\n", + "Step= 618, Dmax= 6.4e-03 nm, Epot= -4.57544e+04 Fmax= 2.94811e+01, atom= 626\n", + "Step= 619, Dmax= 7.7e-03 nm, Epot= -4.57556e+04 Fmax= 1.67790e+02, atom= 626\n", + "Step= 620, Dmax= 9.2e-03 nm, Epot= -4.57579e+04 Fmax= 5.88097e+01, atom= 626\n", + "Step= 622, Dmax= 5.5e-03 nm, Epot= -4.57589e+04 Fmax= 7.25233e+01, atom= 626\n", + "Step= 623, Dmax= 6.7e-03 nm, Epot= -4.57598e+04 Fmax= 8.45653e+01, atom= 626\n", + "Step= 624, Dmax= 8.0e-03 nm, Epot= -4.57606e+04 Fmax= 1.04557e+02, atom= 626\n", + "Step= 625, Dmax= 9.6e-03 nm, Epot= -4.57614e+04 Fmax= 1.23277e+02, atom= 626\n", + "Step= 626, Dmax= 1.2e-02 nm, Epot= -4.57620e+04 Fmax= 1.48313e+02, atom= 626\n", + "Step= 627, Dmax= 1.4e-02 nm, Epot= -4.57623e+04 Fmax= 1.83356e+02, atom= 626\n", + "Step= 628, Dmax= 1.7e-02 nm, Epot= -4.57627e+04 Fmax= 2.06961e+02, atom= 626\n", + "Step= 630, Dmax= 9.9e-03 nm, Epot= -4.57658e+04 Fmax= 3.36618e+01, atom= 111\n", + "Step= 631, Dmax= 1.2e-02 nm, Epot= -4.57661e+04 Fmax= 2.32675e+02, atom= 626\n", + "Step= 632, Dmax= 1.4e-02 nm, Epot= -4.57693e+04 Fmax= 1.43688e+02, atom= 626\n", + "Step= 634, Dmax= 8.6e-03 nm, Epot= -4.57709e+04 Fmax= 5.70110e+01, atom= 626\n", + "Step= 636, Dmax= 5.2e-03 nm, Epot= -4.57718e+04 Fmax= 6.27797e+01, atom= 626\n", + "Step= 637, Dmax= 6.2e-03 nm, Epot= -4.57727e+04 Fmax= 8.34530e+01, atom= 626\n", + "Step= 638, Dmax= 7.4e-03 nm, Epot= -4.57735e+04 Fmax= 9.19966e+01, atom= 626\n", + "Step= 639, Dmax= 8.9e-03 nm, Epot= -4.57742e+04 Fmax= 1.18256e+02, atom= 626\n", + "Step= 640, Dmax= 1.1e-02 nm, Epot= -4.57749e+04 Fmax= 1.36731e+02, atom= 626\n", + "Step= 641, Dmax= 1.3e-02 nm, Epot= -4.57753e+04 Fmax= 1.65361e+02, atom= 626\n", + "Step= 642, Dmax= 1.5e-02 nm, Epot= -4.57754e+04 Fmax= 2.05899e+02, atom= 626\n", + "Step= 643, Dmax= 1.8e-02 nm, Epot= -4.57756e+04 Fmax= 2.28102e+02, atom= 626\n", + "Step= 645, Dmax= 1.1e-02 nm, Epot= -4.57794e+04 Fmax= 4.02938e+01, atom= 111\n", + "Step= 647, Dmax= 6.6e-03 nm, Epot= -4.57805e+04 Fmax= 1.02959e+02, atom= 626\n", + "Step= 648, Dmax= 8.0e-03 nm, Epot= -4.57815e+04 Fmax= 9.19483e+01, atom= 626\n", + "Step= 649, Dmax= 9.6e-03 nm, Epot= -4.57820e+04 Fmax= 1.32794e+02, atom= 626\n", + "Step= 650, Dmax= 1.1e-02 nm, Epot= -4.57827e+04 Fmax= 1.41105e+02, atom= 626\n", + "Step= 651, Dmax= 1.4e-02 nm, Epot= -4.57829e+04 Fmax= 1.82665e+02, atom= 626\n", + "Step= 652, Dmax= 1.7e-02 nm, Epot= -4.57830e+04 Fmax= 2.16710e+02, atom= 626\n", + "Step= 654, Dmax= 9.9e-03 nm, Epot= -4.57864e+04 Fmax= 2.30861e+01, atom= 339\n", + "Step= 655, Dmax= 1.2e-02 nm, Epot= -4.57890e+04 Fmax= 2.47514e+02, atom= 339\n", + "Step= 656, Dmax= 1.4e-02 nm, Epot= -4.57916e+04 Fmax= 9.66893e+01, atom= 339\n", + "Step= 658, Dmax= 8.6e-03 nm, Epot= -4.57924e+04 Fmax= 1.12369e+02, atom= 339\n", + "Step= 659, Dmax= 1.0e-02 nm, Epot= -4.57930e+04 Fmax= 1.27581e+02, atom= 626\n", + "Step= 660, Dmax= 1.2e-02 nm, Epot= -4.57933e+04 Fmax= 1.70183e+02, atom= 339\n", + "Step= 661, Dmax= 1.5e-02 nm, Epot= -4.57939e+04 Fmax= 1.76601e+02, atom= 339\n", + "Step= 663, Dmax= 8.9e-03 nm, Epot= -4.57963e+04 Fmax= 3.23171e+01, atom= 111\n", + "Step= 665, Dmax= 5.3e-03 nm, Epot= -4.57974e+04 Fmax= 9.66383e+01, atom= 339\n", + "Step= 666, Dmax= 6.4e-03 nm, Epot= -4.57985e+04 Fmax= 5.82051e+01, atom= 626\n", + "Step= 667, Dmax= 7.7e-03 nm, Epot= -4.57991e+04 Fmax= 1.21677e+02, atom= 339\n", + "Step= 668, Dmax= 9.2e-03 nm, Epot= -4.58002e+04 Fmax= 9.81286e+01, atom= 339\n", + "Step= 669, Dmax= 1.1e-02 nm, Epot= -4.58003e+04 Fmax= 1.62097e+02, atom= 339\n", + "Step= 670, Dmax= 1.3e-02 nm, Epot= -4.58012e+04 Fmax= 1.57590e+02, atom= 339\n", + "Step= 672, Dmax= 8.0e-03 nm, Epot= -4.58033e+04 Fmax= 3.24485e+01, atom= 339\n", + "Step= 673, Dmax= 9.6e-03 nm, Epot= -4.58044e+04 Fmax= 1.91130e+02, atom= 339\n", + "Step= 674, Dmax= 1.1e-02 nm, Epot= -4.58066e+04 Fmax= 8.07609e+01, atom= 339\n", + "Step= 676, Dmax= 6.9e-03 nm, Epot= -4.58074e+04 Fmax= 7.90443e+01, atom= 339\n", + "Step= 677, Dmax= 8.3e-03 nm, Epot= -4.58080e+04 Fmax= 1.14352e+02, atom= 339\n", + "Step= 678, Dmax= 9.9e-03 nm, Epot= -4.58088e+04 Fmax= 1.21477e+02, atom= 339\n", + "Step= 679, Dmax= 1.2e-02 nm, Epot= -4.58091e+04 Fmax= 1.56905e+02, atom= 339\n", + "Step= 680, Dmax= 1.4e-02 nm, Epot= -4.58095e+04 Fmax= 1.86347e+02, atom= 339\n", + "Step= 681, Dmax= 1.7e-02 nm, Epot= -4.58096e+04 Fmax= 2.13906e+02, atom= 339\n", + "Step= 683, Dmax= 1.0e-02 nm, Epot= -4.58130e+04 Fmax= 3.28962e+01, atom= 111\n", + "Step= 685, Dmax= 6.2e-03 nm, Epot= -4.58142e+04 Fmax= 1.00185e+02, atom= 339\n", + "Step= 686, Dmax= 7.4e-03 nm, Epot= -4.58153e+04 Fmax= 8.16074e+01, atom= 339\n", + "Step= 687, Dmax= 8.9e-03 nm, Epot= -4.58158e+04 Fmax= 1.25340e+02, atom= 339\n", + "Step= 688, Dmax= 1.1e-02 nm, Epot= -4.58166e+04 Fmax= 1.28269e+02, atom= 339\n", + "Step= 689, Dmax= 1.3e-02 nm, Epot= -4.58168e+04 Fmax= 1.70713e+02, atom= 339\n", + "Step= 690, Dmax= 1.5e-02 nm, Epot= -4.58171e+04 Fmax= 1.98108e+02, atom= 339\n", + "Step= 692, Dmax= 9.2e-03 nm, Epot= -4.58200e+04 Fmax= 2.29123e+01, atom= 339\n", + "Step= 693, Dmax= 1.1e-02 nm, Epot= -4.58226e+04 Fmax= 2.23666e+02, atom= 339\n", + "Step= 694, Dmax= 1.3e-02 nm, Epot= -4.58249e+04 Fmax= 9.22479e+01, atom= 339\n", + "Step= 696, Dmax= 7.9e-03 nm, Epot= -4.58257e+04 Fmax= 9.87011e+01, atom= 339\n", + "Step= 697, Dmax= 9.5e-03 nm, Epot= -4.58264e+04 Fmax= 1.22014e+02, atom= 339\n", + "Step= 698, Dmax= 1.1e-02 nm, Epot= -4.58268e+04 Fmax= 1.51478e+02, atom= 339\n", + "Step= 699, Dmax= 1.4e-02 nm, Epot= -4.58274e+04 Fmax= 1.68389e+02, atom= 339\n", + "Step= 701, Dmax= 8.2e-03 nm, Epot= -4.58296e+04 Fmax= 2.49104e+01, atom= 111\n", + "Step= 702, Dmax= 9.9e-03 nm, Epot= -4.58302e+04 Fmax= 2.22306e+02, atom= 339\n", + "Step= 703, Dmax= 1.2e-02 nm, Epot= -4.58338e+04 Fmax= 8.38243e+01, atom= 339\n", + "Step= 705, Dmax= 7.1e-03 nm, Epot= -4.58347e+04 Fmax= 7.97399e+01, atom= 339\n", + "Step= 706, Dmax= 8.5e-03 nm, Epot= -4.58353e+04 Fmax= 1.22699e+02, atom= 339\n", + "Step= 707, Dmax= 1.0e-02 nm, Epot= -4.58362e+04 Fmax= 1.16140e+02, atom= 339\n", + "Step= 708, Dmax= 1.2e-02 nm, Epot= -4.58362e+04 Fmax= 1.77221e+02, atom= 339\n", + "Step= 709, Dmax= 1.5e-02 nm, Epot= -4.58372e+04 Fmax= 1.65875e+02, atom= 339\n", + "Step= 711, Dmax= 8.9e-03 nm, Epot= -4.58394e+04 Fmax= 3.68963e+01, atom= 339\n", + "Step= 713, Dmax= 5.3e-03 nm, Epot= -4.58404e+04 Fmax= 9.72060e+01, atom= 339\n", + "Step= 714, Dmax= 6.4e-03 nm, Epot= -4.58415e+04 Fmax= 5.42322e+01, atom= 339\n", + "Step= 715, Dmax= 7.7e-03 nm, Epot= -4.58422e+04 Fmax= 1.25504e+02, atom= 339\n", + "Step= 716, Dmax= 9.2e-03 nm, Epot= -4.58434e+04 Fmax= 9.14520e+01, atom= 339\n", + "Step= 717, Dmax= 1.1e-02 nm, Epot= -4.58435e+04 Fmax= 1.66624e+02, atom= 339\n", + "Step= 718, Dmax= 1.3e-02 nm, Epot= -4.58447e+04 Fmax= 1.48350e+02, atom= 339\n", + "Step= 720, Dmax= 7.9e-03 nm, Epot= -4.58466e+04 Fmax= 3.86064e+01, atom= 339\n", + "Step= 721, Dmax= 9.5e-03 nm, Epot= -4.58475e+04 Fmax= 1.82197e+02, atom= 339\n", + "Step= 722, Dmax= 1.1e-02 nm, Epot= -4.58495e+04 Fmax= 8.70904e+01, atom= 339\n", + "Step= 724, Dmax= 6.9e-03 nm, Epot= -4.58505e+04 Fmax= 7.01013e+01, atom= 339\n", + "Step= 725, Dmax= 8.2e-03 nm, Epot= -4.58512e+04 Fmax= 1.22960e+02, atom= 339\n", + "Step= 726, Dmax= 9.9e-03 nm, Epot= -4.58523e+04 Fmax= 1.09954e+02, atom= 339\n", + "Step= 727, Dmax= 1.2e-02 nm, Epot= -4.58525e+04 Fmax= 1.65851e+02, atom= 339\n", + "Step= 728, Dmax= 1.4e-02 nm, Epot= -4.58533e+04 Fmax= 1.72371e+02, atom= 339\n", + "Step= 730, Dmax= 8.5e-03 nm, Epot= -4.58557e+04 Fmax= 2.92063e+01, atom= 626\n", + "Step= 731, Dmax= 1.0e-02 nm, Epot= -4.58575e+04 Fmax= 2.06424e+02, atom= 339\n", + "Step= 732, Dmax= 1.2e-02 nm, Epot= -4.58599e+04 Fmax= 8.49054e+01, atom= 339\n", + "Step= 734, Dmax= 7.4e-03 nm, Epot= -4.58609e+04 Fmax= 8.57352e+01, atom= 339\n", + "Step= 735, Dmax= 8.8e-03 nm, Epot= -4.58617e+04 Fmax= 1.18904e+02, atom= 339\n", + "Step= 736, Dmax= 1.1e-02 nm, Epot= -4.58626e+04 Fmax= 1.30971e+02, atom= 339\n", + "Step= 737, Dmax= 1.3e-02 nm, Epot= -4.58631e+04 Fmax= 1.64207e+02, atom= 339\n", + "Step= 738, Dmax= 1.5e-02 nm, Epot= -4.58634e+04 Fmax= 1.99393e+02, atom= 339\n", + "Step= 739, Dmax= 1.8e-02 nm, Epot= -4.58637e+04 Fmax= 2.24656e+02, atom= 339\n", + "Step= 741, Dmax= 1.1e-02 nm, Epot= -4.58674e+04 Fmax= 3.67078e+01, atom= 373\n", + "Step= 743, Dmax= 6.6e-03 nm, Epot= -4.58688e+04 Fmax= 1.08037e+02, atom= 339\n", + "Step= 744, Dmax= 7.9e-03 nm, Epot= -4.58701e+04 Fmax= 8.31847e+01, atom= 339\n", + "Step= 745, Dmax= 9.5e-03 nm, Epot= -4.58708e+04 Fmax= 1.36275e+02, atom= 339\n", + "Step= 746, Dmax= 1.1e-02 nm, Epot= -4.58718e+04 Fmax= 1.31440e+02, atom= 339\n", + "Step= 747, Dmax= 1.4e-02 nm, Epot= -4.58720e+04 Fmax= 1.86017e+02, atom= 339\n", + "Step= 748, Dmax= 1.6e-02 nm, Epot= -4.58727e+04 Fmax= 2.04077e+02, atom= 339\n", + "Step= 750, Dmax= 9.9e-03 nm, Epot= -4.58758e+04 Fmax= 3.01696e+01, atom= 626\n", + "Step= 751, Dmax= 1.2e-02 nm, Epot= -4.58782e+04 Fmax= 2.29559e+02, atom= 626\n", + "Step= 752, Dmax= 1.4e-02 nm, Epot= -4.58808e+04 Fmax= 1.07844e+02, atom= 339\n", + "Step= 754, Dmax= 8.5e-03 nm, Epot= -4.58820e+04 Fmax= 8.79604e+01, atom= 339\n", + "Step= 755, Dmax= 1.0e-02 nm, Epot= -4.58826e+04 Fmax= 1.49108e+02, atom= 339\n", + "Step= 756, Dmax= 1.2e-02 nm, Epot= -4.58838e+04 Fmax= 1.38957e+02, atom= 339\n", + "Step= 757, Dmax= 1.5e-02 nm, Epot= -4.58838e+04 Fmax= 2.02099e+02, atom= 339\n", + "Step= 758, Dmax= 1.8e-02 nm, Epot= -4.58845e+04 Fmax= 2.17486e+02, atom= 339\n", + "Step= 760, Dmax= 1.1e-02 nm, Epot= -4.58880e+04 Fmax= 3.34163e+01, atom= 626\n", + "Step= 761, Dmax= 1.3e-02 nm, Epot= -4.58900e+04 Fmax= 2.47808e+02, atom= 626\n", + "Step= 762, Dmax= 1.5e-02 nm, Epot= -4.58930e+04 Fmax= 1.16214e+02, atom= 339\n", + "Step= 764, Dmax= 9.2e-03 nm, Epot= -4.58942e+04 Fmax= 9.36903e+01, atom= 339\n", + "Step= 765, Dmax= 1.1e-02 nm, Epot= -4.58947e+04 Fmax= 1.61052e+02, atom= 339\n", + "Step= 766, Dmax= 1.3e-02 nm, Epot= -4.58960e+04 Fmax= 1.47897e+02, atom= 339\n", + "Step= 768, Dmax= 7.9e-03 nm, Epot= -4.58980e+04 Fmax= 3.58704e+01, atom= 626\n", + "Step= 769, Dmax= 9.5e-03 nm, Epot= -4.58997e+04 Fmax= 1.83300e+02, atom= 339\n", + "Step= 770, Dmax= 1.1e-02 nm, Epot= -4.59019e+04 Fmax= 8.29662e+01, atom= 339\n", + "Step= 772, Dmax= 6.8e-03 nm, Epot= -4.59031e+04 Fmax= 7.23602e+01, atom= 339\n", + "Step= 773, Dmax= 8.2e-03 nm, Epot= -4.59041e+04 Fmax= 1.17845e+02, atom= 339\n", + "Step= 774, Dmax= 9.8e-03 nm, Epot= -4.59053e+04 Fmax= 1.11226e+02, atom= 339\n", + "Step= 775, Dmax= 1.2e-02 nm, Epot= -4.59059e+04 Fmax= 1.61287e+02, atom= 339\n", + "Step= 776, Dmax= 1.4e-02 nm, Epot= -4.59068e+04 Fmax= 1.70512e+02, atom= 339\n", + "Step= 777, Dmax= 1.7e-02 nm, Epot= -4.59069e+04 Fmax= 2.21020e+02, atom= 339\n", + "Step= 778, Dmax= 2.0e-02 nm, Epot= -4.59070e+04 Fmax= 2.63265e+02, atom= 339\n", + "Step= 780, Dmax= 1.2e-02 nm, Epot= -4.59118e+04 Fmax= 2.87628e+01, atom= 626\n", + "Step= 781, Dmax= 1.5e-02 nm, Epot= -4.59154e+04 Fmax= 2.75397e+02, atom= 626\n", + "Step= 782, Dmax= 1.8e-02 nm, Epot= -4.59182e+04 Fmax= 1.44366e+02, atom= 339\n", + "Step= 784, Dmax= 1.1e-02 nm, Epot= -4.59197e+04 Fmax= 1.03991e+02, atom= 339\n", + "Step= 785, Dmax= 1.3e-02 nm, Epot= -4.59198e+04 Fmax= 1.88353e+02, atom= 339\n", + "Step= 786, Dmax= 1.5e-02 nm, Epot= -4.59213e+04 Fmax= 1.68242e+02, atom= 339\n", + "Step= 788, Dmax= 9.1e-03 nm, Epot= -4.59236e+04 Fmax= 4.25005e+01, atom= 626\n", + "Step= 789, Dmax= 1.1e-02 nm, Epot= -4.59247e+04 Fmax= 2.08891e+02, atom= 339\n", + "Step= 790, Dmax= 1.3e-02 nm, Epot= -4.59273e+04 Fmax= 9.82721e+01, atom= 339\n", + "Step= 792, Dmax= 7.9e-03 nm, Epot= -4.59285e+04 Fmax= 7.88287e+01, atom= 339\n", + "Step= 793, Dmax= 9.5e-03 nm, Epot= -4.59292e+04 Fmax= 1.40228e+02, atom= 339\n", + "Step= 794, Dmax= 1.1e-02 nm, Epot= -4.59305e+04 Fmax= 1.23526e+02, atom= 339\n", + "Step= 795, Dmax= 1.4e-02 nm, Epot= -4.59306e+04 Fmax= 1.90196e+02, atom= 339\n", + "Step= 796, Dmax= 1.6e-02 nm, Epot= -4.59316e+04 Fmax= 1.92276e+02, atom= 339\n", + "Step= 798, Dmax= 9.8e-03 nm, Epot= -4.59345e+04 Fmax= 3.59415e+01, atom= 626\n", + "Step= 799, Dmax= 1.2e-02 nm, Epot= -4.59361e+04 Fmax= 2.22986e+02, atom= 626\n", + "Step= 800, Dmax= 1.4e-02 nm, Epot= -4.59388e+04 Fmax= 1.08835e+02, atom= 339\n", + "Step= 802, Dmax= 8.5e-03 nm, Epot= -4.59400e+04 Fmax= 8.22214e+01, atom= 339\n", + "Step= 803, Dmax= 1.0e-02 nm, Epot= -4.59405e+04 Fmax= 1.52607e+02, atom= 339\n", + "Step= 804, Dmax= 1.2e-02 nm, Epot= -4.59419e+04 Fmax= 1.30530e+02, atom= 339\n", + "Step= 806, Dmax= 7.3e-03 nm, Epot= -4.59436e+04 Fmax= 3.69766e+01, atom= 339\n", + "Step= 807, Dmax= 8.8e-03 nm, Epot= -4.59450e+04 Fmax= 1.64574e+02, atom= 339\n", + "Step= 808, Dmax= 1.1e-02 nm, Epot= -4.59470e+04 Fmax= 7.84499e+01, atom= 339\n", + "Step= 810, Dmax= 6.3e-03 nm, Epot= -4.59481e+04 Fmax= 6.38636e+01, atom= 339\n", + "Step= 811, Dmax= 7.6e-03 nm, Epot= -4.59490e+04 Fmax= 1.10600e+02, atom= 339\n", + "Step= 812, Dmax= 9.1e-03 nm, Epot= -4.59502e+04 Fmax= 9.94042e+01, atom= 339\n", + "Step= 813, Dmax= 1.1e-02 nm, Epot= -4.59508e+04 Fmax= 1.50806e+02, atom= 339\n", + "Step= 814, Dmax= 1.3e-02 nm, Epot= -4.59518e+04 Fmax= 1.53324e+02, atom= 339\n", + "Step= 815, Dmax= 1.6e-02 nm, Epot= -4.59519e+04 Fmax= 2.06270e+02, atom= 339\n", + "Step= 816, Dmax= 1.9e-02 nm, Epot= -4.59522e+04 Fmax= 2.35618e+02, atom= 339\n", + "Step= 818, Dmax= 1.1e-02 nm, Epot= -4.59562e+04 Fmax= 3.07404e+01, atom= 626\n", + "Step= 819, Dmax= 1.4e-02 nm, Epot= -4.59589e+04 Fmax= 2.49983e+02, atom= 626\n", + "Step= 820, Dmax= 1.6e-02 nm, Epot= -4.59615e+04 Fmax= 1.31232e+02, atom= 339\n", + "Step= 822, Dmax= 9.8e-03 nm, Epot= -4.59629e+04 Fmax= 9.17377e+01, atom= 339\n", + "Step= 823, Dmax= 1.2e-02 nm, Epot= -4.59630e+04 Fmax= 1.78002e+02, atom= 339\n", + "Step= 824, Dmax= 1.4e-02 nm, Epot= -4.59645e+04 Fmax= 1.47893e+02, atom= 339\n", + "Step= 826, Dmax= 8.5e-03 nm, Epot= -4.59665e+04 Fmax= 4.37481e+01, atom= 626\n", + "Step= 827, Dmax= 1.0e-02 nm, Epot= -4.59674e+04 Fmax= 1.88920e+02, atom= 339\n", + "Step= 828, Dmax= 1.2e-02 nm, Epot= -4.59697e+04 Fmax= 9.13859e+01, atom= 339\n", + "Step= 830, Dmax= 7.3e-03 nm, Epot= -4.59708e+04 Fmax= 7.08268e+01, atom= 339\n", + "Step= 831, Dmax= 8.8e-03 nm, Epot= -4.59716e+04 Fmax= 1.30459e+02, atom= 339\n", + "Step= 832, Dmax= 1.1e-02 nm, Epot= -4.59729e+04 Fmax= 1.10408e+02, atom= 339\n", + "Step= 833, Dmax= 1.3e-02 nm, Epot= -4.59731e+04 Fmax= 1.76787e+02, atom= 339\n", + "Step= 834, Dmax= 1.5e-02 nm, Epot= -4.59743e+04 Fmax= 1.72232e+02, atom= 339\n", + "Step= 836, Dmax= 9.1e-03 nm, Epot= -4.59767e+04 Fmax= 3.56087e+01, atom= 626\n", + "Step= 837, Dmax= 1.1e-02 nm, Epot= -4.59783e+04 Fmax= 2.02562e+02, atom= 339\n", + "Step= 838, Dmax= 1.3e-02 nm, Epot= -4.59807e+04 Fmax= 1.00461e+02, atom= 339\n", + "Step= 840, Dmax= 7.9e-03 nm, Epot= -4.59820e+04 Fmax= 7.41119e+01, atom= 339\n", + "Step= 841, Dmax= 9.4e-03 nm, Epot= -4.59826e+04 Fmax= 1.40962e+02, atom= 339\n", + "Step= 842, Dmax= 1.1e-02 nm, Epot= -4.59840e+04 Fmax= 1.17473e+02, atom= 339\n", + "Step= 843, Dmax= 1.4e-02 nm, Epot= -4.59841e+04 Fmax= 1.90774e+02, atom= 339\n", + "Step= 844, Dmax= 1.6e-02 nm, Epot= -4.59852e+04 Fmax= 1.83520e+02, atom= 339\n", + "Step= 846, Dmax= 9.8e-03 nm, Epot= -4.59879e+04 Fmax= 3.89524e+01, atom= 626\n", + "Step= 847, Dmax= 1.2e-02 nm, Epot= -4.59892e+04 Fmax= 2.14554e+02, atom= 626\n", + "Step= 848, Dmax= 1.4e-02 nm, Epot= -4.59918e+04 Fmax= 1.09660e+02, atom= 339\n", + "Step= 850, Dmax= 8.5e-03 nm, Epot= -4.59931e+04 Fmax= 7.67259e+01, atom= 339\n", + "Step= 851, Dmax= 1.0e-02 nm, Epot= -4.59936e+04 Fmax= 1.54610e+02, atom= 339\n", + "Step= 852, Dmax= 1.2e-02 nm, Epot= -4.59951e+04 Fmax= 1.22581e+02, atom= 339\n", + "Step= 854, Dmax= 7.3e-03 nm, Epot= -4.59967e+04 Fmax= 4.02329e+01, atom= 339\n", + "Step= 855, Dmax= 8.8e-03 nm, Epot= -4.59980e+04 Fmax= 1.57835e+02, atom= 339\n", + "Step= 856, Dmax= 1.1e-02 nm, Epot= -4.59999e+04 Fmax= 7.94969e+01, atom= 339\n", + "Step= 858, Dmax= 6.3e-03 nm, Epot= -4.60010e+04 Fmax= 5.93191e+01, atom= 339\n", + "Step= 859, Dmax= 7.6e-03 nm, Epot= -4.60020e+04 Fmax= 1.12260e+02, atom= 339\n", + "Step= 860, Dmax= 9.1e-03 nm, Epot= -4.60032e+04 Fmax= 9.29688e+01, atom= 339\n", + "Step= 861, Dmax= 1.1e-02 nm, Epot= -4.60037e+04 Fmax= 1.52243e+02, atom= 339\n", + "Step= 862, Dmax= 1.3e-02 nm, Epot= -4.60049e+04 Fmax= 1.44542e+02, atom= 339\n", + "Step= 864, Dmax= 7.9e-03 nm, Epot= -4.60067e+04 Fmax= 3.12378e+01, atom= 626\n", + "Step= 865, Dmax= 9.4e-03 nm, Epot= -4.60086e+04 Fmax= 1.74690e+02, atom= 339\n", + "Step= 866, Dmax= 1.1e-02 nm, Epot= -4.60107e+04 Fmax= 8.15345e+01, atom= 339\n", + "Step= 868, Dmax= 6.8e-03 nm, Epot= -4.60118e+04 Fmax= 6.76013e+01, atom= 339\n", + "Step= 869, Dmax= 8.1e-03 nm, Epot= -4.60127e+04 Fmax= 1.15008e+02, atom= 339\n", + "Step= 870, Dmax= 9.8e-03 nm, Epot= -4.60138e+04 Fmax= 1.04545e+02, atom= 339\n", + "Step= 871, Dmax= 1.2e-02 nm, Epot= -4.60143e+04 Fmax= 1.57190e+02, atom= 339\n", + "Step= 872, Dmax= 1.4e-02 nm, Epot= -4.60153e+04 Fmax= 1.59444e+02, atom= 339\n", + "Step= 874, Dmax= 8.4e-03 nm, Epot= -4.60175e+04 Fmax= 2.95869e+01, atom= 626\n", + "Step= 875, Dmax= 1.0e-02 nm, Epot= -4.60195e+04 Fmax= 1.82758e+02, atom= 626\n", + "Step= 876, Dmax= 1.2e-02 nm, Epot= -4.60217e+04 Fmax= 9.26096e+01, atom= 339\n", + "Step= 878, Dmax= 7.3e-03 nm, Epot= -4.60228e+04 Fmax= 6.74876e+01, atom= 339\n", + "Step= 879, Dmax= 8.8e-03 nm, Epot= -4.60236e+04 Fmax= 1.28510e+02, atom= 339\n", + "Step= 880, Dmax= 1.1e-02 nm, Epot= -4.60248e+04 Fmax= 1.06742e+02, atom= 339\n", + "Step= 881, Dmax= 1.3e-02 nm, Epot= -4.60250e+04 Fmax= 1.73983e+02, atom= 339\n", + "Step= 882, Dmax= 1.5e-02 nm, Epot= -4.60261e+04 Fmax= 1.64498e+02, atom= 339\n", + "Step= 884, Dmax= 9.1e-03 nm, Epot= -4.60284e+04 Fmax= 3.65172e+01, atom= 626\n", + "Step= 885, Dmax= 1.1e-02 nm, Epot= -4.60296e+04 Fmax= 1.93786e+02, atom= 626\n", + "Step= 886, Dmax= 1.3e-02 nm, Epot= -4.60320e+04 Fmax= 1.00589e+02, atom= 339\n", + "Step= 888, Dmax= 7.8e-03 nm, Epot= -4.60332e+04 Fmax= 6.96189e+01, atom= 339\n", + "Step= 889, Dmax= 9.4e-03 nm, Epot= -4.60338e+04 Fmax= 1.40895e+02, atom= 339\n", + "Step= 890, Dmax= 1.1e-02 nm, Epot= -4.60351e+04 Fmax= 1.09929e+02, atom= 339\n", + "Step= 892, Dmax= 6.8e-03 nm, Epot= -4.60365e+04 Fmax= 3.78470e+01, atom= 339\n", + "Step= 893, Dmax= 8.1e-03 nm, Epot= -4.60377e+04 Fmax= 1.40660e+02, atom= 339\n", + "Step= 894, Dmax= 9.8e-03 nm, Epot= -4.60393e+04 Fmax= 7.44084e+01, atom= 339\n", + "Step= 896, Dmax= 5.9e-03 nm, Epot= -4.60404e+04 Fmax= 5.29986e+01, atom= 339\n", + "Step= 897, Dmax= 7.0e-03 nm, Epot= -4.60413e+04 Fmax= 1.03341e+02, atom= 339\n", + "Step= 898, Dmax= 8.4e-03 nm, Epot= -4.60424e+04 Fmax= 8.34452e+01, atom= 339\n", + "Step= 899, Dmax= 1.0e-02 nm, Epot= -4.60430e+04 Fmax= 1.40299e+02, atom= 339\n", + "Step= 900, Dmax= 1.2e-02 nm, Epot= -4.60441e+04 Fmax= 1.27627e+02, atom= 339\n", + "Step= 902, Dmax= 7.3e-03 nm, Epot= -4.60457e+04 Fmax= 3.10242e+01, atom= 626\n", + "Step= 903, Dmax= 8.7e-03 nm, Epot= -4.60472e+04 Fmax= 1.59598e+02, atom= 339\n", + "Step= 904, Dmax= 1.0e-02 nm, Epot= -4.60491e+04 Fmax= 7.32902e+01, atom= 339\n", + "Step= 906, Dmax= 6.3e-03 nm, Epot= -4.60501e+04 Fmax= 6.22260e+01, atom= 339\n", + "Step= 907, Dmax= 7.6e-03 nm, Epot= -4.60509e+04 Fmax= 1.04430e+02, atom= 339\n", + "Step= 908, Dmax= 9.1e-03 nm, Epot= -4.60519e+04 Fmax= 9.36935e+01, atom= 339\n", + "Step= 909, Dmax= 1.1e-02 nm, Epot= -4.60524e+04 Fmax= 1.45083e+02, atom= 339\n", + "Step= 910, Dmax= 1.3e-02 nm, Epot= -4.60533e+04 Fmax= 1.42734e+02, atom= 339\n", + "Step= 912, Dmax= 7.8e-03 nm, Epot= -4.60551e+04 Fmax= 2.79819e+01, atom= 626\n", + "Step= 913, Dmax= 9.4e-03 nm, Epot= -4.60567e+04 Fmax= 1.69572e+02, atom= 339\n", + "Step= 914, Dmax= 1.1e-02 nm, Epot= -4.60587e+04 Fmax= 8.09347e+01, atom= 339\n", + "Step= 916, Dmax= 6.8e-03 nm, Epot= -4.60596e+04 Fmax= 6.40327e+01, atom= 339\n", + "Step= 917, Dmax= 8.1e-03 nm, Epot= -4.60603e+04 Fmax= 1.14264e+02, atom= 339\n", + "Step= 918, Dmax= 9.7e-03 nm, Epot= -4.60613e+04 Fmax= 9.81419e+01, atom= 339\n", + "Step= 919, Dmax= 1.2e-02 nm, Epot= -4.60614e+04 Fmax= 1.57401e+02, atom= 339\n", + "Step= 920, Dmax= 1.4e-02 nm, Epot= -4.60623e+04 Fmax= 1.50803e+02, atom= 339\n", + "Step= 922, Dmax= 8.4e-03 nm, Epot= -4.60642e+04 Fmax= 3.15662e+01, atom= 626\n", + "Step= 923, Dmax= 1.0e-02 nm, Epot= -4.60652e+04 Fmax= 1.80039e+02, atom= 339\n", + "Step= 924, Dmax= 1.2e-02 nm, Epot= -4.60673e+04 Fmax= 8.82780e+01, atom= 339\n", + "Step= 926, Dmax= 7.3e-03 nm, Epot= -4.60682e+04 Fmax= 6.53041e+01, atom= 339\n", + "Step= 927, Dmax= 8.7e-03 nm, Epot= -4.60686e+04 Fmax= 1.26425e+02, atom= 339\n", + "Step= 928, Dmax= 1.0e-02 nm, Epot= -4.60697e+04 Fmax= 1.01643e+02, atom= 339\n", + "Step= 930, Dmax= 6.3e-03 nm, Epot= -4.60708e+04 Fmax= 3.34565e+01, atom= 339\n", + "Step= 931, Dmax= 7.5e-03 nm, Epot= -4.60716e+04 Fmax= 1.28651e+02, atom= 339\n", + "Step= 932, Dmax= 9.1e-03 nm, Epot= -4.60731e+04 Fmax= 6.67952e+01, atom= 339\n", + "Step= 934, Dmax= 5.4e-03 nm, Epot= -4.60739e+04 Fmax= 4.89232e+01, atom= 339\n", + "Step= 935, Dmax= 6.5e-03 nm, Epot= -4.60745e+04 Fmax= 9.32006e+01, atom= 339\n", + "Step= 936, Dmax= 7.8e-03 nm, Epot= -4.60754e+04 Fmax= 7.53156e+01, atom= 339\n", + "Step= 937, Dmax= 9.4e-03 nm, Epot= -4.60754e+04 Fmax= 1.28261e+02, atom= 339\n", + "Step= 938, Dmax= 1.1e-02 nm, Epot= -4.60762e+04 Fmax= 1.16226e+02, atom= 339\n", + "Step= 940, Dmax= 6.8e-03 nm, Epot= -4.60780e+04 Fmax= 2.95041e+01, atom= 1368\n", + "Step= 942, Dmax= 4.1e-03 nm, Epot= -4.60788e+04 Fmax= 6.31746e+01, atom= 1368\n", + "Step= 943, Dmax= 4.9e-03 nm, Epot= -4.60796e+04 Fmax= 4.76729e+01, atom= 1368\n", + "Step= 944, Dmax= 5.8e-03 nm, Epot= -4.60802e+04 Fmax= 8.41276e+01, atom= 1368\n", + "Step= 945, Dmax= 7.0e-03 nm, Epot= -4.60810e+04 Fmax= 7.53131e+01, atom= 1368\n", + "Step= 946, Dmax= 8.4e-03 nm, Epot= -4.60814e+04 Fmax= 1.14408e+02, atom= 1368\n", + "Step= 947, Dmax= 1.0e-02 nm, Epot= -4.60821e+04 Fmax= 1.15662e+02, atom= 1368\n", + "Step= 948, Dmax= 1.2e-02 nm, Epot= -4.60822e+04 Fmax= 1.57248e+02, atom= 1368\n", + "Step= 949, Dmax= 1.5e-02 nm, Epot= -4.60828e+04 Fmax= 1.74987e+02, atom= 1368\n", + "Step= 951, Dmax= 8.7e-03 nm, Epot= -4.60848e+04 Fmax= 3.01782e+01, atom= 1345\n", + "Step= 952, Dmax= 1.0e-02 nm, Epot= -4.60855e+04 Fmax= 2.14247e+02, atom= 1368\n", + "Step= 953, Dmax= 1.3e-02 nm, Epot= -4.60876e+04 Fmax= 8.94970e+01, atom= 1368\n", + "Step= 955, Dmax= 7.5e-03 nm, Epot= -4.60883e+04 Fmax= 7.76314e+01, atom= 1368\n", + "Step= 956, Dmax= 9.0e-03 nm, Epot= -4.60887e+04 Fmax= 1.25467e+02, atom= 1368\n", + "Step= 957, Dmax= 1.1e-02 nm, Epot= -4.60894e+04 Fmax= 1.19966e+02, atom= 1368\n", + "Step= 959, Dmax= 6.5e-03 nm, Epot= -4.60905e+04 Fmax= 2.95166e+01, atom= 1368\n", + "Step= 960, Dmax= 7.8e-03 nm, Epot= -4.60914e+04 Fmax= 1.54612e+02, atom= 1368\n", + "Step= 961, Dmax= 9.4e-03 nm, Epot= -4.60927e+04 Fmax= 6.45018e+01, atom= 1368\n", + "Step= 963, Dmax= 5.6e-03 nm, Epot= -4.60933e+04 Fmax= 6.11630e+01, atom= 1368\n", + "Step= 964, Dmax= 6.7e-03 nm, Epot= -4.60939e+04 Fmax= 9.07986e+01, atom= 1368\n", + "Step= 965, Dmax= 8.1e-03 nm, Epot= -4.60945e+04 Fmax= 9.25017e+01, atom= 1368\n", + "Step= 966, Dmax= 9.7e-03 nm, Epot= -4.60949e+04 Fmax= 1.26024e+02, atom= 1368\n", + "Step= 967, Dmax= 1.2e-02 nm, Epot= -4.60954e+04 Fmax= 1.38783e+02, atom= 1368\n", + "Step= 968, Dmax= 1.4e-02 nm, Epot= -4.60955e+04 Fmax= 1.75522e+02, atom= 1368\n", + "Step= 969, Dmax= 1.7e-02 nm, Epot= -4.60957e+04 Fmax= 2.07413e+02, atom= 1368\n", + "Step= 971, Dmax= 1.0e-02 nm, Epot= -4.60980e+04 Fmax= 3.19811e+01, atom= 1345\n", + "Step= 972, Dmax= 1.2e-02 nm, Epot= -4.60984e+04 Fmax= 2.31645e+02, atom= 1368\n", + "Step= 973, Dmax= 1.5e-02 nm, Epot= -4.61004e+04 Fmax= 1.20309e+02, atom= 1368\n", + "Step= 975, Dmax= 8.7e-03 nm, Epot= -4.61013e+04 Fmax= 7.04173e+01, atom= 1368\n", + "Step= 977, Dmax= 5.2e-03 nm, Epot= -4.61019e+04 Fmax= 4.83563e+01, atom= 1368\n", + "Step= 978, Dmax= 6.3e-03 nm, Epot= -4.61025e+04 Fmax= 9.28116e+01, atom= 1368\n", + "Step= 979, Dmax= 7.5e-03 nm, Epot= -4.61032e+04 Fmax= 7.70792e+01, atom= 1368\n", + "Step= 980, Dmax= 9.0e-03 nm, Epot= -4.61035e+04 Fmax= 1.28397e+02, atom= 1368\n", + "Step= 981, Dmax= 1.1e-02 nm, Epot= -4.61042e+04 Fmax= 1.15731e+02, atom= 1368\n", + "Step= 983, Dmax= 6.5e-03 nm, Epot= -4.61052e+04 Fmax= 2.69529e+01, atom= 1368\n", + "Step= 984, Dmax= 7.8e-03 nm, Epot= -4.61059e+04 Fmax= 1.55765e+02, atom= 1368\n", + "Step= 985, Dmax= 9.4e-03 nm, Epot= -4.61074e+04 Fmax= 5.79249e+01, atom= 1368\n", + "Step= 987, Dmax= 5.6e-03 nm, Epot= -4.61079e+04 Fmax= 6.65819e+01, atom= 1368\n", + "Step= 988, Dmax= 6.7e-03 nm, Epot= -4.61084e+04 Fmax= 8.52191e+01, atom= 1368\n", + "Step= 989, Dmax= 8.1e-03 nm, Epot= -4.61090e+04 Fmax= 9.58728e+01, atom= 1368\n", + "Step= 990, Dmax= 9.7e-03 nm, Epot= -4.61093e+04 Fmax= 1.23232e+02, atom= 1368\n", + "Step= 991, Dmax= 1.2e-02 nm, Epot= -4.61097e+04 Fmax= 1.37459e+02, atom= 1368\n", + "Step= 992, Dmax= 1.4e-02 nm, Epot= -4.61098e+04 Fmax= 1.79358e+02, atom= 1368\n", + "Step= 993, Dmax= 1.7e-02 nm, Epot= -4.61099e+04 Fmax= 1.95544e+02, atom= 1368\n", + "Step= 995, Dmax= 1.0e-02 nm, Epot= -4.61122e+04 Fmax= 2.91625e+01, atom= 1076\n", + "Step= 996, Dmax= 1.2e-02 nm, Epot= -4.61123e+04 Fmax= 2.26608e+02, atom= 1368\n", + "Step= 997, Dmax= 1.4e-02 nm, Epot= -4.61145e+04 Fmax= 1.22948e+02, atom= 1368\n", + "Step= 999, Dmax= 8.7e-03 nm, Epot= -4.61154e+04 Fmax= 6.60313e+01, atom= 1368\n", + "Step= 1000, Dmax= 1.0e-02 nm, Epot= -4.61151e+04 Fmax= 1.79608e+02, atom= 1368\n", "Energy minimization reached the maximum number of steps before the forces\n", "reached the requested precision Fmax < 10.\n", "\n", "writing lowest energy coordinates.\n", "\n", + "Back Off! I just backed up em.pdb to ./#em.pdb.1#\n", + "\n", "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n", - "Potential Energy = -4.6114367e+04\n", - "Maximum force = 6.1517822e+01 on atom 1026\n", - "Norm of force = 3.0288026e+00\n", + "Potential Energy = -4.6115398e+04\n", + "Maximum force = 6.6031342e+01 on atom 1368\n", + "Norm of force = 3.1664403e+00\n", "\n", - "GROMACS reminds you: \"In the End Science Comes Down to Praying\" (P. v.d. Berg)\n", + "GROMACS reminds you: \"Everything's formed from particles\" (Van der Graaf Generator)\n", "\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -1520,9 +1513,13 @@ "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top\n", "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", - "GROMACS reminds you: \"In the End Science Comes Down to Praying\" (P. v.d. Berg)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Naive you are if you believe life favours those who aren't naive.\" (Piet Hein)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -1538,7 +1535,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -2343429\n", + "Setting the LD random seed to -1087517089\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -1570,7 +1567,7 @@ " '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top']}" ] }, - "execution_count": 5, + "execution_count": 38, "metadata": {}, "output_type": "execute_result" } @@ -1595,9 +1592,16 @@ "sim.MD_relaxed(runtime=1e3, dt=0.01)" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We can execute `mdrun` using `GromacsWrapper`:" + ] + }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 39, "metadata": {}, "outputs": [ { @@ -1614,7 +1618,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 10 to 50, rlist from 1.108 to 1.274\n", + "Changing nstlist from 10 to 50, rlist from 1.107 to 1.268\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -1625,22 +1629,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "100000 steps, 1000.0 ps.\n", - "\n", - "Step 0 Warning: pressure scaling more than 1%, mu: 0.98589 0.98589 0.98589\n", - "step 0\n", - "Step 50 Warning: pressure scaling more than 1%, mu: 1.02318 1.02318 1.02318\n", - "step 100, remaining wall clock time: 39 s \n", - "Step 150 Warning: pressure scaling more than 1%, mu: 1.0125 1.0125 1.0125\n", - "step 99900, remaining wall clock time: 0 s 700, remaining wall clock time: 38 s \n", + "100000 steps, 1000.0 ps (continuing from step 100000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 100000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 127.012 31.753 400.0\n", + " Time: 0.028 0.007 394.3\n", " (ns/day) (hour/ns)\n", - "Performance: 2721.028 0.009\n", + "Performance: 120.539 0.199\n", "\n", - "GROMACS reminds you: \"The Path Of the Righteous Man is Beset On All Sides With the Iniquities Of the Selfish and the Tyranny Of Evil Men.\" (Pulp Fiction)\n", + "GROMACS reminds you: \"I have noticed a large, negative correlation between having a well-defined mission workload and concern for the Top500. It's almost like LINPACK is what you focus on when you don't know what to focus on.\" (Jeff Hammond)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n" ] @@ -1651,14 +1651,12 @@ "0" ] }, - "execution_count": 6, + "execution_count": 39, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "import gromacs\n", - "\n", "r = gromacs.run.MDrunner(\n", " dirname=sim.dirs[\"MD_relaxed\"],\n", " deffnm=\"md\",\n", @@ -1669,9 +1667,16 @@ "r.run() # runs mdrun in the python shell" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now we do the same thing for a longer NPT run, with a longer timestep." + ] + }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 40, "metadata": {}, "outputs": [ { @@ -1681,7 +1686,6 @@ "mdpow.equil : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.gro').\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 't']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -1697,10 +1701,14 @@ "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -t /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt\n", "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "Last frame -1 time 1000.000 \n", "\n", - "GROMACS reminds you: \"The Path Of the Righteous Man is Beset On All Sides With the Iniquities Of the Selfish and the Tyranny Of Evil Men.\" (Pulp Fiction)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"This really is a pretty scene, could you ask your kid to smile please?\" (Joe Jackson)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -1725,7 +1733,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -100958209\n", + "Setting the LD random seed to -1880144435\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -1768,16 +1776,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "500000 steps, 10000.0 ps.\n", - "step 499900, remaining wall clock time: 0 s 443700, remaining wall clock time: 26 s 493000, remaining wall clock time: 3 s \n", + "500000 steps, 10000.0 ps (continuing from step 500000, 10000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 500000, remaining wall clock time: 0 s \n", + "NOTE: 19 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 942.251 235.563 400.0\n", + " Time: 0.053 0.013 397.2\n", " (ns/day) (hour/ns)\n", - "Performance: 3667.817 0.007\n", + "Performance: 129.150 0.186\n", "\n", - "GROMACS reminds you: \"Inventions have long since reached their limit, and I see no hope for further development.\" (Julius Sextus Frontinus, 1st century A.D.)\n", + "GROMACS reminds you: \"This really is a pretty scene, could you ask your kid to smile please?\" (Joe Jackson)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n" ] @@ -1788,7 +1801,7 @@ "0" ] }, - "execution_count": 7, + "execution_count": 40, "metadata": {}, "output_type": "execute_result" } @@ -1804,9 +1817,16 @@ "r.run() # runs mdrun in the python shell" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Finally, we can set up the thermodynamic integration files. The following will create several directories, one for each $\\lambda$ value:" + ] + }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 41, "metadata": {}, "outputs": [ { @@ -1861,13 +1881,17 @@ " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", "Number of degrees of freedom in T-Coupling group System is 4902.00\n", "\n", "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"What If None Of Your Dreams Come True ?\" (E. Costello)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"It's Bicycle Repair Man !\" (Monty Python)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -1881,7 +1905,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -1917,14 +1940,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1276686385\n", + "Setting the LD random seed to -176167043\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -1957,7 +1982,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Not to get technical... but according to chemistry, alcohol is a solution.\" (Anonymous)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"And It Goes a Little Something Like This\" (Tag Team)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -1971,7 +1998,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2007,14 +2033,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -313278573\n", + "Setting the LD random seed to 1878752383\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -2047,7 +2075,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Not to get technical... but according to chemistry, alcohol is a solution.\" (Anonymous)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"And It Goes a Little Something Like This\" (Tag Team)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2061,7 +2091,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2097,14 +2126,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -18777225\n", + "Setting the LD random seed to -279132165\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -2137,7 +2168,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"In science, truth always wins.\" (Max Perutz)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"The easiest way to scale well is to have bad single-core performance\" (Blind Freddie)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2151,7 +2184,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2187,14 +2219,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1187233801\n", + "Setting the LD random seed to 970913279\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -2227,7 +2261,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Your Bones Got a Little Machine\" (Pixies)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"The easiest way to scale well is to have bad single-core performance\" (Blind Freddie)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2243,7 +2279,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2279,14 +2314,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 2062417135\n", + "Setting the LD random seed to -277102597\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -2319,7 +2356,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Your Bones Got a Little Machine\" (Pixies)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Raw data is like raw sewage, it requires some processing before it can be spread around. The opposite is true of theories.\" (Jim Carr)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2333,7 +2372,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2369,14 +2407,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1225019537\n", + "Setting the LD random seed to -1125393\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2409,7 +2449,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Naive you are if you believe life favours those who aren't naive.\" (Piet Hein)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Millions saw the apple fall, Newton was the only one who asked why?\" (Bernard Baruch)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2423,7 +2465,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2459,14 +2500,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1203762038\n", + "Setting the LD random seed to -283645253\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2499,7 +2542,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Naive you are if you believe life favours those who aren't naive.\" (Piet Hein)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Millions saw the apple fall, Newton was the only one who asked why?\" (Bernard Baruch)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2513,7 +2558,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2549,14 +2593,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -369033\n", + "Setting the LD random seed to -33628482\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2589,7 +2635,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Shake Yourself\" (YES)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I never thought about breaking barriers, I was just interested in what I was doing and kept going.\" (Barbara Liskov)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2603,7 +2651,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2639,14 +2686,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1973943263\n", + "Setting the LD random seed to 2130180031\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2679,7 +2728,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Shake Yourself\" (YES)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Jesus Not Only Saves, He Also Frequently Makes Backups.\" (Myron Bradshaw)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2693,7 +2744,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2729,14 +2779,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -118815233\n", + "Setting the LD random seed to 2128084273\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2769,7 +2821,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Science, my lad, is made up of mistakes, but they are mistakes which it is useful to make, because they lead little by little to the truth.\" (Jules Verne)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Jesus Not Only Saves, He Also Frequently Makes Backups.\" (Myron Bradshaw)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2783,7 +2837,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2819,14 +2872,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1100921521\n", + "Setting the LD random seed to -1133076737\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2859,7 +2914,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"You Can Always Go On Ricky Lake\" (Offspring)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Numbers have life; they’re not just symbols on paper.\" (Shakuntala Devi)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2873,7 +2930,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2909,14 +2965,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1431325972\n", + "Setting the LD random seed to 1543503550\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -2949,7 +3007,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"You Can Always Go On Ricky Lake\" (Offspring)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Numbers have life; they’re not just symbols on paper.\" (Shakuntala Devi)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -2963,7 +3023,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -2999,14 +3058,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 522582511\n", + "Setting the LD random seed to -1283854372\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3039,7 +3100,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"As Always Your Logic Is Impeccable\" (Tuvok)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I Was Born to Have Adventure\" (F. Zappa)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3053,7 +3116,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3089,14 +3151,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1291878529\n", + "Setting the LD random seed to -1613856850\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3129,7 +3193,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"As Always Your Logic Is Impeccable\" (Tuvok)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I Was Born to Have Adventure\" (F. Zappa)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3143,7 +3209,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3179,14 +3244,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1568472927\n", + "Setting the LD random seed to -335680515\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3219,7 +3286,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Science Won't Change You\" (The Talking Heads)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"The Microsecond is Within Reach\" (P.J. Van Maaren)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3233,7 +3302,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3269,14 +3337,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -35946561\n", + "Setting the LD random seed to -811074625\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3309,7 +3379,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Computer system analysis is like child-rearing; you can do grievous damage, but you cannot ensure success.\" (Tom DeMarcho)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"A protein is a chain of letters.\" (Julie Bernauer)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3323,7 +3395,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3359,14 +3430,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -17572231\n", + "Setting the LD random seed to -206046313\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3399,7 +3472,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Computer system analysis is like child-rearing; you can do grievous damage, but you cannot ensure success.\" (Tom DeMarcho)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"A protein is a chain of letters.\" (Julie Bernauer)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3413,7 +3488,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3449,14 +3523,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1806893055\n", + "Setting the LD random seed to -1214978\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3489,7 +3565,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"The historical meaning of QM/MM: Quanto Mangi, Mamma Mia!\" (Attilio Vittorio Vargiu, at BioExcel 2022 Summer School in Sardinia)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"...sometimes a scream is better than a thesis.\" (Ralph Waldo Emerson)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3503,7 +3581,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3539,14 +3616,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1083769157\n", + "Setting the LD random seed to -1481185425\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3579,7 +3658,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"The historical meaning of QM/MM: Quanto Mangi, Mamma Mia!\" (Attilio Vittorio Vargiu, at BioExcel 2022 Summer School in Sardinia)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"...sometimes a scream is better than a thesis.\" (Ralph Waldo Emerson)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3593,7 +3674,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -3629,14 +3709,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -570441874\n", + "Setting the LD random seed to -549716569\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3669,7 +3751,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Beware of bugs in the above code; I have only proved it correct, not tried it.\" (Donald Knuth)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Sisters Have Always Fascinated Me\" (Speech)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -3689,7 +3773,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -311828649\n", + "Setting the LD random seed to -136445963\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -3739,7 +3823,7 @@ " 'calc_lambda_neighbors': -1}" ] }, - "execution_count": 10, + "execution_count": 41, "metadata": {}, "output_type": "execute_result" } @@ -3753,9 +3837,16 @@ "# run multiple simulations on cluster" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "These could be run on a cluster using the `local.sh` scripts, but with Martini they can be done on a local machine in a reasonable amount of time (10-15 minutes on a desktop machine with a GTX 1080). " + ] + }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 42, "metadata": {}, "outputs": [ { @@ -3783,16 +3874,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 112.406 28.102 400.0\n", + " Time: 0.025 0.006 396.8\n", " (ns/day) (hour/ns)\n", - "Performance: 3074.618 0.008\n", + "Performance: 272.359 0.088\n", "\n", - "GROMACS reminds you: \"Take Dehydrated Water On Your Desert Trips\" (Space Quest III)\n", + "GROMACS reminds you: \"I Caught It In the Face\" (P.J. Harvey)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -3805,7 +3898,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.261\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -3816,16 +3909,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 13 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 103.522 25.881 400.0\n", + " Time: 0.049 0.012 398.6\n", " (ns/day) (hour/ns)\n", - "Performance: 3338.469 0.007\n", + "Performance: 139.630 0.172\n", "\n", - "GROMACS reminds you: \"If everything seems under control, you're just not going fast enough.\" (Mario Andretti)\n", + "GROMACS reminds you: \"I Caught It In the Face\" (P.J. Harvey)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -3849,16 +3947,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 15 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 111.958 27.989 400.0\n", + " Time: 0.168 0.042 398.1\n", " (ns/day) (hour/ns)\n", - "Performance: 3086.935 0.008\n", + "Performance: 40.992 0.585\n", "\n", - "GROMACS reminds you: \"If all it takes to motivate you is a fancy picture and quote, you probably have a very easy job. The type of job computers will soon be doing.\" (Anonymous)\n", + "GROMACS reminds you: \"I was a bit of an artist, and somewhere along the way had gotten the idea that computers could be used for animation and artists, because in-betweening was so tedious... Of course, everyone thought I was nuts.\" (Carla Meninsky, Atari engineer)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -3882,16 +3985,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 20 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 91.919 22.980 400.0\n", + " Time: 0.031 0.008 397.9\n", " (ns/day) (hour/ns)\n", - "Performance: 3759.912 0.006\n", + "Performance: 218.840 0.110\n", "\n", - "GROMACS reminds you: \"We're having an information explosion, among others, and it's certainly obvious that information is of no use unless it's available.\" (Sister Mary Kenneth Keller)\n", + "GROMACS reminds you: \"Here's the Way It Might End\" (G. Michael)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -3915,16 +4023,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s 900, remaining wall clock time: 20 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 109.086 27.272 400.0\n", + " Time: 0.025 0.006 397.2\n", " (ns/day) (hour/ns)\n", - "Performance: 3168.202 0.008\n", + "Performance: 275.308 0.087\n", "\n", - "GROMACS reminds you: \"I used to be blond and stupid, but now I dyed it black\" (Miss Li)\n", + "GROMACS reminds you: \"Christianity may be OK between consenting adults in private but should not be taught to young children.\" (Francis Crick)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -3948,16 +4058,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s 10200, remaining wall clock time: 20 s , remaining wall clock time: 19 s 24900, remaining wall clock time: 14 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 106.914 26.729 400.0\n", + " Time: 0.031 0.008 397.4\n", " (ns/day) (hour/ns)\n", - "Performance: 3232.568 0.007\n", + "Performance: 224.333 0.107\n", "\n", - "GROMACS reminds you: \"Get Down In 3D\" (George Clinton)\n", + "GROMACS reminds you: \"Move about like a Scientist, lay down, get kissed\" (Red Hot Chili Peppars)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -3970,7 +4082,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "Changing nstlist from 20 to 25, rlist from 1.214 to 1.261\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -3981,16 +4093,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s remaining wall clock time: 22 s 19900, remaining wall clock time: 15 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 26 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 121.145 30.286 400.0\n", + " Time: 0.035 0.009 397.9\n", " (ns/day) (hour/ns)\n", - "Performance: 2852.835 0.008\n", + "Performance: 195.832 0.123\n", "\n", - "GROMACS reminds you: \"Come on boys, Let's push it hard\" (P.J. Harvey)\n", + "GROMACS reminds you: \"Move about like a Scientist, lay down, get kissed\" (Red Hot Chili Peppars)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4014,16 +4131,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 173.225 43.306 400.0\n", + " Time: 0.047 0.012 398.2\n", " (ns/day) (hour/ns)\n", - "Performance: 1995.128 0.012\n", + "Performance: 146.089 0.164\n", "\n", - "GROMACS reminds you: \"I can't help but think the model is ungrateful for all that nice data I gave it. Jerk.\" (Kate Stafford)\n", + "GROMACS reminds you: \"Restraint! What possible restraint?\" (Joseph Conrad)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4047,16 +4166,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 133.766 33.442 400.0\n", + " Time: 0.030 0.008 397.4\n", " (ns/day) (hour/ns)\n", - "Performance: 2583.656 0.009\n", + "Performance: 225.401 0.106\n", "\n", - "GROMACS reminds you: \"Don't waste pure thoughts on dirty enzymes.\" (Efraim Racker)\n", + "GROMACS reminds you: \"I'm a Jerk\" (F. Black)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4080,16 +4201,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 15 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 145.685 36.421 400.0\n", + " Time: 0.029 0.007 397.2\n", " (ns/day) (hour/ns)\n", - "Performance: 2372.278 0.010\n", + "Performance: 237.803 0.101\n", "\n", - "GROMACS reminds you: \"Here's something fun to do: Next time you approach a conversation say 'I want to talk to someone technical... Oh! There's a woman!' and walk straight over to her.\" (Patty Lopez)\n", + "GROMACS reminds you: \"Two chemists walk into a bar. The first one says, 'I'll have some H2O.'. The second one says, 'I'll have some H2O, too'. He dies.\" (Anonymous)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4113,16 +4239,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 24 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 119.297 29.824 400.0\n", + " Time: 0.056 0.014 398.6\n", " (ns/day) (hour/ns)\n", - "Performance: 2897.015 0.008\n", + "Performance: 121.934 0.197\n", "\n", - "GROMACS reminds you: \"It's Not Dark Yet, But It's Getting There\" (Bob Dylan)\n", + "GROMACS reminds you: \"Two chemists walk into a bar. The first one says, 'I'll have some H2O.'. The second one says, 'I'll have some H2O, too'. He dies.\" (Anonymous)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4146,16 +4277,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 30 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 127.291 31.823 400.0\n", + " Time: 0.047 0.012 398.3\n", " (ns/day) (hour/ns)\n", - "Performance: 2715.098 0.009\n", + "Performance: 145.534 0.165\n", "\n", - "GROMACS reminds you: \"Science is the record of dead religions.\" (Oscar Wilde)\n", + "GROMACS reminds you: \"Shake Yourself\" (YES)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4179,16 +4315,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 12 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 135.754 33.938 400.0\n", + " Time: 0.024 0.006 396.8\n", " (ns/day) (hour/ns)\n", - "Performance: 2545.836 0.009\n", + "Performance: 291.637 0.082\n", "\n", - "GROMACS reminds you: \"Everybody Wants to Be Naked and Famous\" (Tricky)\n", + "GROMACS reminds you: \"I think everybody should like everybody.\" (Andy Warhol)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4201,7 +4342,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -4212,16 +4353,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 26 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 139.214 34.804 400.0\n", + " Time: 0.044 0.011 398.4\n", " (ns/day) (hour/ns)\n", - "Performance: 2482.552 0.010\n", + "Performance: 155.175 0.155\n", "\n", - "GROMACS reminds you: \"You see it through a charmed medium: you can not discern that the gilding is slime and the silk draperies cobwebs; that the marble is sordid slate, and the polished woods mere refuse chips and scale bark.\" (Mr. Rochester in Jane Eyre by Charlotte Bronte)\n", + "GROMACS reminds you: \"Shit Happens\" (Pulp Fiction)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4234,7 +4380,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -4245,16 +4391,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 130.245 32.561 400.0\n", + " Time: 0.034 0.009 397.6\n", " (ns/day) (hour/ns)\n", - "Performance: 2653.511 0.009\n", + "Performance: 203.183 0.118\n", "\n", - "GROMACS reminds you: \"To survive science you have to become science.\" (Gerrit Groenhof)\n", + "GROMACS reminds you: \"A curious aspect of the theory of evolution is that everybody thinks he understands it.\" (Jacques Monod)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4278,16 +4426,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s , remaining wall clock time: 21 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 17 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 133.221 33.305 400.0\n", + " Time: 0.023 0.006 396.7\n", " (ns/day) (hour/ns)\n", - "Performance: 2594.232 0.009\n", + "Performance: 303.368 0.079\n", "\n", - "GROMACS reminds you: \"Your Proposal is Accepted\" (Men In Black)\n", + "GROMACS reminds you: \"If it weren't for bad luck, we'd have no luck at all\" (The Unthanks)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4311,16 +4464,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 36 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 132.336 33.084 400.0\n", + " Time: 0.045 0.011 398.3\n", " (ns/day) (hour/ns)\n", - "Performance: 2611.583 0.009\n", + "Performance: 152.222 0.158\n", "\n", - "GROMACS reminds you: \"Erwin with his psi can do / Calculations quite a few. / But one thing has not been seen / Just what psi really mean.\" (Felix Bloch)\n", + "GROMACS reminds you: \"If it weren't for bad luck, we'd have no luck at all\" (The Unthanks)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4344,16 +4502,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 11 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 118.261 29.565 400.0\n", + " Time: 0.029 0.007 397.4\n", " (ns/day) (hour/ns)\n", - "Performance: 2922.399 0.008\n", + "Performance: 233.731 0.103\n", "\n", - "GROMACS reminds you: \"Strength is just an accident arising from the weakness of others\" (Joseph Conrad)\n", + "GROMACS reminds you: \"Move Over Hogey Bear\" (Urban Dance Squad)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4377,16 +4540,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s 39500, remaining wall clock time: 10 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 12 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 187.262 46.815 400.0\n", + " Time: 0.029 0.007 397.6\n", " (ns/day) (hour/ns)\n", - "Performance: 1845.580 0.013\n", + "Performance: 233.889 0.103\n", "\n", - "GROMACS reminds you: \"Check Your Input\" (D. Van Der Spoel)\n", + "GROMACS reminds you: \"Scientists do not join hands every Sunday and sing \"Yes gravity is real! I know gravity is real! I will have faith! I believe in my heart that what goes up, up, up must come down, down, down. Amen!\" If they did, we would think they were pretty insecure about the concept.\" (Dan Barker)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4399,7 +4567,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -4410,16 +4578,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s 000, remaining wall clock time: 30 s 13200, remaining wall clock time: 22 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 15 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 137.558 34.390 400.0\n", + " Time: 0.024 0.006 396.9\n", " (ns/day) (hour/ns)\n", - "Performance: 2512.442 0.010\n", + "Performance: 283.481 0.085\n", "\n", - "GROMACS reminds you: \"When It Starts to Start It'll Never Stop\" (Magnapop)\n", + "GROMACS reminds you: \"Scientists do not join hands every Sunday and sing \"Yes gravity is real! I know gravity is real! I will have faith! I believe in my heart that what goes up, up, up must come down, down, down. Amen!\" If they did, we would think they were pretty insecure about the concept.\" (Dan Barker)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -4432,7 +4605,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n", + "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -4443,16 +4616,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 133.675 33.419 400.0\n", + " Time: 0.028 0.007 397.4\n", " (ns/day) (hour/ns)\n", - "Performance: 2585.423 0.009\n", + "Performance: 242.660 0.099\n", "\n", - "GROMACS reminds you: \"Perfect is the enemy of good.\" (Voltaire)\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n" ] @@ -4466,9 +4641,16 @@ " r.run() # runs mdrun in the python shell" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Finally, we read the `.edr` files from the disk to get the energy reported by Gromacs and use `alchemlyb` to determine the free energy of solvation." + ] + }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 43, "metadata": {}, "outputs": [ { @@ -4487,9 +4669,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4502,9 +4686,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4517,9 +4703,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4532,11 +4720,37 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n", "\n", - "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", @@ -4547,11 +4761,13 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/#md.xvg.1#\n", + "Reading energy frame 140 time 560.000 mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n", "\n", - "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", @@ -4562,37 +4778,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.tpr, VERSION 2023.2 (single precision)\n", - "Reading energy frame 130 time 520.000 " - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", "\n", - "\n", - "Wrote 8 lambda values with 5001 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n", - "\n", - "\n", - "Wrote 8 lambda values with 5001 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n", - "\n", - "\n", - "Wrote 8 lambda values with 5001 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n", - "\n", - "\n", - "Wrote 8 lambda values with 5001 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n", - "\n", - "\n", - "Wrote 8 lambda values with 5001 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Last energy frame read 250 time 1000.000 \n", - "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4605,9 +4795,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4620,22 +4812,9 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.tpr, VERSION 2023.2 (single precision)\n", - "Last energy frame read 250 time 1000.000 \n", - "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", - "\n", - "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", - " :-) GROMACS - gmx energy, 2023.2 (-:\n", - "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", - "Command line:\n", - " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", - "\n", - "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr as single precision energy file\n", - "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.tpr, VERSION 2023.2 (single precision)\n", - "Reading energy frame 0 time 0.000 " + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/#md.xvg.1#\n", + "Reading energy frame 13 time 52.000 " ] }, { @@ -4644,13 +4823,13 @@ "text": [ "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n", "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n", "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n" + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n" ] }, { @@ -4659,9 +4838,26 @@ "text": [ "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/#md.xvg.1#\n", + "Reading energy frame 200 time 800.000 mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", - "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", @@ -4672,9 +4868,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4687,22 +4885,13 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", - "\n", - "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n", - " :-) GROMACS - gmx energy, 2023.2 (-:\n", - "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", - "Command line:\n", - " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", - "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr as single precision energy file\n", - "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.tpr, VERSION 2023.2 (single precision)\n", - "Reading energy frame 200 time 800.000 " + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n" ] }, { @@ -4711,24 +4900,39 @@ "text": [ "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n", "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n", "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n" + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/#md.xvg.1#\n", + "Reading energy frame 200 time 800.000 mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", - "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", @@ -4739,9 +4943,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4754,9 +4960,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4769,7 +4977,13 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.tpr, VERSION 2023.2 (single precision)\n", - "Reading energy frame 140 time 560.000 " + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/#md.xvg.1#\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n" ] }, { @@ -4778,24 +4992,22 @@ "text": [ "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n", + "\n", "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n", "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n" + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "Last energy frame read 250 time 1000.000 \n", - "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", - "\n", - "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", @@ -4806,9 +5018,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4821,28 +5035,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.tpr, VERSION 2023.2 (single precision)\n", - "Reading energy frame 180 time 720.000 " - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n", - "\n", - "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4855,9 +5052,11 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4870,22 +5069,12 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", - "\n", - "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", - " :-) GROMACS - gmx energy, 2023.2 (-:\n", - "\n", - "Executable: /usr/local/gromacs/bin/gmx\n", - "Data prefix: /usr/local/gromacs\n", - "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", - "Command line:\n", - " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", - "\n", - "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr as single precision energy file\n", - "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.tpr, VERSION 2023.2 (single precision)\n", - "Reading energy frame 30 time 120.000 " + "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n", + "\n" ] }, { @@ -4894,22 +5083,35 @@ "text": [ "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n", "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n", "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n" + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "GROMACS reminds you: \"set: No match.\" (tcsh)\n", "\n", "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n", " :-) GROMACS - gmx energy, 2023.2 (-:\n", @@ -4922,16 +5124,16 @@ "\n", "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr as single precision energy file\n", "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 0 time 0.000 \n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/#md.xvg.1#\n", "Last energy frame read 250 time 1000.000 \n", "\n", - "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "GROMACS reminds you: \"set: No match.\" (tcsh)\n", "\n", "mdpow.fep : INFO Analysis stride is 1.\n", "mdpow.fep : INFO Analysis starts from frame 0.\n", "mdpow.fep : INFO Analysis stops at frame None.\n", - "mdpow.fep : INFO Analyzing stored data.\n", - "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/pymbar/other_estimators.py:510: RuntimeWarning: invalid value encountered in sqrt\n", - " dDeltaF = np.sqrt(variance)\n" + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg' with bzip2\n" ] }, { @@ -4940,29 +5142,200 @@ "text": [ "\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n", + "\n", "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n", "\n", - "Wrote 19 lambda values with 5001 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n" + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/water] Finding dgdl xvg files, reading with stride=1 permissive=False.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0000\n", + "\u001b[32m2023-09-04 22:40:31.863\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:31.865\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.78.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:31.866\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.9740.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0250\n", + "\u001b[32m2023-09-04 22:40:31.949\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:31.951\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 20.06.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:31.952\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 238.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 10.4664.\n", + "mdpow.fep : INFO The data are subsampled every 11 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0500\n", + "\u001b[32m2023-09-04 22:40:32.022\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.028\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 43.47.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.030\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 114.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 21.8509.\n", + "mdpow.fep : INFO The data are subsampled every 22 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0750\n", + "\u001b[32m2023-09-04 22:40:32.108\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.109\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 23.00.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.111\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 208.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 11.9760.\n", + "mdpow.fep : INFO The data are subsampled every 12 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 1000\n", + "\u001b[32m2023-09-04 22:40:32.180\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.182\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 33.72.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.184\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 147.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 16.9456.\n", + "mdpow.fep : INFO The data are subsampled every 17 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0000\n", + "\u001b[32m2023-09-04 22:40:32.400\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.402\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 34.54.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.403\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 143.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 17.4196.\n", + "mdpow.fep : INFO The data are subsampled every 18 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0050\n", + "\u001b[32m2023-09-04 22:40:32.612\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.615\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 20.10.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.616\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 238.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 10.4664.\n", + "mdpow.fep : INFO The data are subsampled every 11 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0100\n", + "\u001b[32m2023-09-04 22:40:32.824\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.825\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.47.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:32.826\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 11.4793.\n", + "mdpow.fep : INFO The data are subsampled every 12 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0200\n", + "\u001b[32m2023-09-04 22:40:33.054\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.056\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 27.85.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.057\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 178.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 13.9944.\n", + "mdpow.fep : INFO The data are subsampled every 14 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0300\n", + "\u001b[32m2023-09-04 22:40:33.298\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.300\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 27.51.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.302\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 178.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 13.9944.\n", + "mdpow.fep : INFO The data are subsampled every 14 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0400\n", + "\u001b[32m2023-09-04 22:40:33.555\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.557\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.25.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.558\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.9740.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0500\n", + "\u001b[32m2023-09-04 22:40:33.818\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.820\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 24.63.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:33.820\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 200.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.4550.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0600\n", + "\u001b[32m2023-09-04 22:40:34.042\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.047\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 42.95.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.048\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 116.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 21.4741.\n", + "mdpow.fep : INFO The data are subsampled every 22 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0650\n", + "\u001b[32m2023-09-04 22:40:34.274\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.276\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.73.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.277\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 11.4793.\n", + "mdpow.fep : INFO The data are subsampled every 12 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0700\n", + "\u001b[32m2023-09-04 22:40:34.611\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.616\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.96.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.617\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 11.4793.\n", + "mdpow.fep : INFO The data are subsampled every 12 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0750\n", + "\u001b[32m2023-09-04 22:40:34.863\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.865\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.68.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:34.866\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.9740.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0800\n", + "\u001b[32m2023-09-04 22:40:35.091\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.094\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 32.94.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.095\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 151.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 16.4967.\n", + "mdpow.fep : INFO The data are subsampled every 17 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0850\n", + "\u001b[32m2023-09-04 22:40:35.343\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.349\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 40.21.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.350\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 122.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 20.4180.\n", + "mdpow.fep : INFO The data are subsampled every 21 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0900\n", + "\u001b[32m2023-09-04 22:40:35.564\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.567\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 29.12.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.568\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 167.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 14.9162.\n", + "mdpow.fep : INFO The data are subsampled every 15 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0950\n", + "\u001b[32m2023-09-04 22:40:35.787\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.788\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.51.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.789\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 1000\n", + "\u001b[32m2023-09-04 22:40:35.996\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.998\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.19.\u001b[0m\n", + "\u001b[32m2023-09-04 22:40:35.999\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 11.4793.\n", + "mdpow.fep : INFO The data are subsampled every 12 frames.\n", "mdpow.fep : INFO DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n", - "mdpow.fep : INFO [BENZ] Water solvation free energy (coulomb) -1.10771e-15 (nan) kJ/mol\n", - "mdpow.fep : INFO [BENZ] Water solvation free energy (vdw) -6.88405 (0.28) kJ/mol\n", - "mdpow.fep : INFO [BENZ] Water solvation free energy (Gibbs) 6.88405 (nan) kJ/mol\n" + "mdpow.fep : INFO [BENZ] Water solvation free energy (coulomb) 1.10771e-15 (0.00) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (vdw) -6.74471 (0.27) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Water solvation free energy (Gibbs) 6.74471 (0.27) kJ/mol\n" ] }, { "data": { "text/plain": [ - "6.88405 (nan)" + "6.74471 (0.269555)" ] }, - "execution_count": 18, + "execution_count": 43, "metadata": {}, "output_type": "execute_result" } @@ -4973,55 +5346,24 @@ ] }, { - "cell_type": "code", - "execution_count": null, + "cell_type": "markdown", "metadata": {}, - "outputs": [], "source": [ - "import pandas as pd\n", - "import seaborn as sb\n", + "## Octanol solvation\n", "\n", - "def plot_results(gsolv: mdpow.fep.Gsolv):\n", - " \"\"\"Plot the results of thermodynamic integration.\"\"\"\n", - " fep_dfs: dict[str, pd.DataFrame] = {component: tuple_[1] for component, tuple_ in gsolv.results.xvg.items()}\n", - " \n", - " # Each df has one column for each lambda value\n", - " # We want several rows for each lambda value\n", - " formatted_data = {\"Component\": [], \"Lambda\": [], \"dvdl\": []}\n", - " for component, df in fep_dfs.items():\n", - " for lambda_ in df.columns:\n", - " entries = df.loc[:, lambda_].values\n", - " n_entries = len(entries)\n", - "\n", - " formatted_data[\"Component\"] += [component] * n_entries\n", - " formatted_data[\"Lambda\"] += [lambda_] * n_entries\n", - " formatted_data[\"dvdl\"].extend(entries)\n", - " \n", - " plot_df = pd.DataFrame(formatted_data)\n", - " return sb.catplot(data=plot_df, x=\"Lambda\", y=\"dvdl\", errorbar=\"se\", col=\"Component\")\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "plot_results(gwat)" + "Now, we repeat the exact same steps as above but using an `OctanolSimulation`." ] }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 44, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top' (newly created)...\n", "mdpow.equil : INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation' (newly created)...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/octanol.gro'...\n", " :-) GROMACS - gmx editconf, 2023.2 (-:\n", "\n", @@ -5032,7 +5374,9 @@ " gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 4.0\n", "\n", "\n", - "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "Back Off! I just backed up boxed.gro to ./#boxed.gro.1#\n", + "\n", + "GROMACS reminds you: \"Sir, spare your threats: The bug which you would fright me with I seek.\" (Hermione, Act III, scene II of Shakespeare's Winter's Tale)\n", "\n", " :-) GROMACS - gmx solvate, 2023.2 (-:\n", "\n", @@ -5057,6 +5401,8 @@ "Generated solvent containing 5112 atoms in 1704 residues\n", "Writing generated configuration to solvated.gro\n", "\n", + "Back Off! I just backed up solvated.gro to ./#solvated.gro.1#\n", + "\n", "Output configuration contains 5115 atoms in 1705 residues\n", "Volume : 399.981 (nm^3)\n", "Density : 389.199 (g/l)\n", @@ -5064,9 +5410,9 @@ "\n", "Processing topology\n", "\n", - "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/#system.top.1#\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/#system.top.2#\n", "\n", - "GROMACS reminds you: \"I Got a Forty Dollar Bill\" (F. Zappa)\n", + "GROMACS reminds you: \"Sir, spare your threats: The bug which you would fright me with I seek.\" (Hermione, Act III, scene II of Shakespeare's Winter's Tale)\n", "\n", "gromacs.setup: INFO Solvated system with /home/awsm/MDPOW/doc/examples/martini/octanol.gro\n" ] @@ -5134,7 +5480,9 @@ "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "\n", - "GROMACS reminds you: \"Welcome to the Power Age\" (2 Unlimited)\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.2#\n", + "\n", + "GROMACS reminds you: \"Sir, spare your threats: The bug which you would fright me with I seek.\" (Hermione, Act III, scene II of Shakespeare's Winter's Tale)\n", "\n", " :-) GROMACS - gmx make_ndx, 2023.2 (-:\n", "\n", @@ -5149,9 +5497,9 @@ "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n", "\n", - "Back Off! I just backed up main.ndx to ./#main.ndx.1#\n", + "Back Off! I just backed up main.ndx to ./#main.ndx.3#\n", "\n", - "GROMACS reminds you: \"Welcome to the Power Age\" (2 Unlimited)\n", + "GROMACS reminds you: \"The physical chemists never use their eyes and are most lamentably lacking in chemical culture. It is essential to cast out from our midst, root and branch, this physical element and return to our laboratories.\" (Henry Edward Armstrong)\n", "\n", " :-) GROMACS - gmx trjconv, 2023.2 (-:\n", "\n", @@ -5179,12 +5527,14 @@ "Select a group: Reading frames from gro file 'This is an auto generated system', 5115 atoms.\n", "Reading frame 0 time 0.000 \n", "Precision of ionized.gro is 0.001 (nm)\n", + "\n", + "Back Off! I just backed up compact.pdb to ./#compact.pdb.1#\n", "Last frame 0 time 0.000 \n", " -> frame 0 time 0.000 \n", "Last written: frame 0 time 0.000\n", "\n", "\n", - "GROMACS reminds you: \"Welcome to the Power Age\" (2 Unlimited)\n", + "GROMACS reminds you: \"The physical chemists never use their eyes and are most lamentably lacking in chemical culture. It is essential to cast out from our midst, root and branch, this physical element and return to our laboratories.\" (Henry Edward Armstrong)\n", "\n", " :-) GROMACS - gmx grompp, 2023.2 (-:\n", "\n", @@ -5192,13 +5542,15 @@ "Data prefix: /usr/local/gromacs\n", "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", "Command line:\n", - " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -f /tmp/tmp2_aikyq2.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -nov\n", + " gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -f /tmp/tmpxe8vdy7l.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -nov\n", "\n", "\n", - "NOTE 1 [file /tmp/tmp2_aikyq2.mdp]:\n", + "NOTE 1 [file /tmp/tmpxe8vdy7l.mdp]:\n", " For a correct single-point energy evaluation with nsteps = 0, use\n", " continuation = yes to avoid constraining the input coordinates.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/#pp_system.top.1#\n" ] }, { @@ -5224,17 +5576,16 @@ "Number of degrees of freedom in T-Coupling group rest is 15339.00\n", "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", "\n", - "NOTE 3 [file /tmp/tmp2_aikyq2.mdp]:\n", + "NOTE 3 [file /tmp/tmpxe8vdy7l.mdp]:\n", " NVE simulation with an initial temperature of zero: will use a Verlet\n", " buffer of 10%. Check your energy drift!\n", "\n", "\n", "There were 3 NOTEs\n", "\n", - "GROMACS reminds you: \"You should call it 'entropy'. No one knows what entropy really is, so in a debate you will always have the advantage.\" (John von Neumann to Claude Shannon, on why he should borrow the term for information theory)\n", + "GROMACS reminds you: \"The physical chemists never use their eyes and are most lamentably lacking in chemical culture. It is essential to cast out from our midst, root and branch, this physical element and return to our laboratories.\" (Henry Edward Armstrong)\n", "\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top', mdp='em.mdp' ...\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'em.mdp': ['maxwarn', 'pp']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -5251,14 +5602,16 @@ " gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -maxwarn 1 -pp processed.top\n", "\n", "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n", - "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n" + "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1669599249\n", + "Setting the LD random seed to -105579659\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -5279,7 +5632,9 @@ "Number of degrees of freedom in T-Coupling group rest is 15339.00\n", "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n", "\n", - "GROMACS reminds you: \"You should call it 'entropy'. No one knows what entropy really is, so in a debate you will always have the advantage.\" (John von Neumann to Claude Shannon, on why he should borrow the term for information theory)\n", + "Back Off! I just backed up em.tpr to ./#em.tpr.1#\n", + "\n", + "GROMACS reminds you: \"You Can Always Go On Ricky Lake\" (Offspring)\n", "\n", "gromacs.run : WARNING No 'mdrun_d' binary found so trying 'mdrun' instead.\n", "(Note that energy minimization runs better with mdrun_d.)\n", @@ -5300,7 +5655,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -538320998\n", + "Setting the LD random seed to 1459009023\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -5318,6 +5673,8 @@ "name": "stderr", "output_type": "stream", "text": [ + "\n", + "Back Off! I just backed up em.log to ./#em.log.1#\n", "Reading file em.tpr, VERSION 2023.2 (single precision)\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -5328,6 +5685,10 @@ "Using 4 OpenMP threads \n", "\n", "\n", + "Back Off! I just backed up em.trr to ./#em.trr.1#\n", + "\n", + "Back Off! I just backed up em.edr to ./#em.edr.1#\n", + "\n", "Steepest Descents:\n", " Tolerance (Fmax) = 1.00000e+01\n", " Number of steps = 1000\n", @@ -5344,804 +5705,804 @@ "Step= 10, Dmax= 5.2e-02 nm, Epot= 4.74060e+04 Fmax= 1.09883e+05, atom= 3020\n", "Step= 11, Dmax= 6.2e-02 nm, Epot= 3.89493e+04 Fmax= 1.54250e+04, atom= 1088\n", "Step= 12, Dmax= 7.4e-02 nm, Epot= 6.83725e+03 Fmax= 1.68745e+04, atom= 1088\n", - "Step= 13, Dmax= 8.9e-02 nm, Epot= -4.12859e+03 Fmax= 1.03437e+04, atom= 1088\n", - "Step= 14, Dmax= 1.1e-01 nm, Epot= -1.13033e+04 Fmax= 1.60187e+05, atom= 4\n", - "Step= 15, Dmax= 1.3e-01 nm, Epot= -1.48685e+04 Fmax= 1.22382e+04, atom= 4\n", - "Step= 16, Dmax= 1.5e-01 nm, Epot= -2.01120e+04 Fmax= 3.01354e+04, atom= 4\n", - "Step= 17, Dmax= 1.8e-01 nm, Epot= -2.17950e+04 Fmax= 4.10907e+04, atom= 2520\n", - "Step= 18, Dmax= 2.2e-01 nm, Epot= -2.41451e+04 Fmax= 2.58663e+04, atom= 4\n", - "Step= 19, Dmax= 2.7e-01 nm, Epot= -2.66228e+04 Fmax= 2.69286e+04, atom= 835\n", - "Step= 23, Dmax= 4.0e-02 nm, Epot= -2.72892e+04 Fmax= 1.12464e+04, atom= 5360\n", - "Step= 24, Dmax= 4.8e-02 nm, Epot= -2.82606e+04 Fmax= 8.89099e+03, atom= 3110\n", - "Step= 25, Dmax= 5.8e-02 nm, Epot= -2.94476e+04 Fmax= 7.02441e+03, atom= 835\n", - "Step= 26, Dmax= 6.9e-02 nm, Epot= -3.10712e+04 Fmax= 4.20767e+03, atom= 835\n", - "Step= 27, Dmax= 8.3e-02 nm, Epot= -3.33635e+04 Fmax= 1.18104e+04, atom= 835\n", - "Step= 28, Dmax= 9.9e-02 nm, Epot= -3.46017e+04 Fmax= 2.13437e+03, atom= 3110\n", - "Step= 29, Dmax= 1.2e-01 nm, Epot= -3.82056e+04 Fmax= 4.27338e+04, atom= 3110\n", - "Step= 30, Dmax= 1.4e-01 nm, Epot= -3.94374e+04 Fmax= 2.83113e+03, atom= 536\n", - "Step= 31, Dmax= 1.7e-01 nm, Epot= -3.95423e+04 Fmax= 1.29043e+05, atom= 413\n", - "Step= 33, Dmax= 1.0e-01 nm, Epot= -4.13777e+04 Fmax= 3.66374e+04, atom= 413\n", - "Step= 34, Dmax= 1.2e-01 nm, Epot= -4.20921e+04 Fmax= 3.45667e+03, atom= 5051\n", - "Step= 35, Dmax= 1.5e-01 nm, Epot= -4.35935e+04 Fmax= 9.64975e+03, atom= 5051\n", - "Step= 36, Dmax= 1.8e-01 nm, Epot= -4.38149e+04 Fmax= 8.18688e+03, atom= 413\n", - "Step= 38, Dmax= 1.1e-01 nm, Epot= -4.40733e+04 Fmax= 1.07000e+04, atom= 5050\n", - "Step= 39, Dmax= 1.3e-01 nm, Epot= -4.43300e+04 Fmax= 2.05335e+04, atom= 5113\n", - "Step= 40, Dmax= 1.5e-01 nm, Epot= -4.47992e+04 Fmax= 6.05413e+03, atom= 1883\n", - "Step= 41, Dmax= 1.8e-01 nm, Epot= -4.49074e+04 Fmax= 3.01743e+04, atom= 1883\n", - "Step= 43, Dmax= 1.1e-01 nm, Epot= -4.56484e+04 Fmax= 1.52506e+03, atom= 4743\n", - "Step= 44, Dmax= 1.3e-01 nm, Epot= -4.68200e+04 Fmax= 1.07854e+04, atom= 5051\n", - "Step= 46, Dmax= 8.0e-02 nm, Epot= -4.73751e+04 Fmax= 2.52220e+03, atom= 5051\n", - "Step= 47, Dmax= 9.6e-02 nm, Epot= -4.79770e+04 Fmax= 4.87343e+03, atom= 5051\n", - "Step= 48, Dmax= 1.1e-01 nm, Epot= -4.82572e+04 Fmax= 1.91275e+03, atom= 413\n", - "Step= 49, Dmax= 1.4e-01 nm, Epot= -4.89999e+04 Fmax= 8.15021e+03, atom= 413\n", - "Step= 50, Dmax= 1.7e-01 nm, Epot= -4.90237e+04 Fmax= 7.20306e+03, atom= 5050\n", - "Step= 52, Dmax= 9.9e-02 nm, Epot= -4.94243e+04 Fmax= 1.62333e+03, atom= 5113\n", - "Step= 53, Dmax= 1.2e-01 nm, Epot= -5.00761e+04 Fmax= 1.83149e+03, atom= 1883\n", - "Step= 54, Dmax= 1.4e-01 nm, Epot= -5.05800e+04 Fmax= 3.35992e+03, atom= 1883\n", - "Step= 55, Dmax= 1.7e-01 nm, Epot= -5.07979e+04 Fmax= 6.36579e+03, atom= 4743\n", - "Step= 56, Dmax= 2.1e-01 nm, Epot= -5.10603e+04 Fmax= 3.91558e+03, atom= 4743\n", - "Step= 58, Dmax= 1.2e-01 nm, Epot= -5.12744e+04 Fmax= 4.35122e+03, atom= 1361\n", - "Step= 59, Dmax= 1.5e-01 nm, Epot= -5.12777e+04 Fmax= 1.09249e+04, atom= 644\n", - "Step= 60, Dmax= 1.8e-01 nm, Epot= -5.13083e+04 Fmax= 1.53387e+04, atom= 4715\n", - "Step= 62, Dmax= 1.1e-01 nm, Epot= -5.16633e+04 Fmax= 9.15874e+02, atom= 4715\n", - "Step= 63, Dmax= 1.3e-01 nm, Epot= -5.22662e+04 Fmax= 2.03880e+03, atom= 1684\n", - "Step= 65, Dmax= 7.7e-02 nm, Epot= -5.24549e+04 Fmax= 2.91928e+03, atom= 1684\n", - "Step= 66, Dmax= 9.2e-02 nm, Epot= -5.26368e+04 Fmax= 1.72494e+03, atom= 5089\n", - "Step= 67, Dmax= 1.1e-01 nm, Epot= -5.27366e+04 Fmax= 5.74404e+03, atom= 1684\n", - "Step= 68, Dmax= 1.3e-01 nm, Epot= -5.28955e+04 Fmax= 4.63541e+03, atom= 1684\n", - "Step= 70, Dmax= 8.0e-02 nm, Epot= -5.29997e+04 Fmax= 1.91787e+03, atom= 5063\n", - "Step= 71, Dmax= 9.6e-02 nm, Epot= -5.32217e+04 Fmax= 6.49572e+02, atom= 431\n", - "Step= 72, Dmax= 1.1e-01 nm, Epot= -5.34501e+04 Fmax= 9.63944e+03, atom= 5063\n", - "Step= 73, Dmax= 1.4e-01 nm, Epot= -5.37606e+04 Fmax= 8.94016e+02, atom= 431\n", - "Step= 74, Dmax= 1.7e-01 nm, Epot= -5.39605e+04 Fmax= 2.52140e+03, atom= 1684\n", - "Step= 76, Dmax= 9.9e-02 nm, Epot= -5.42504e+04 Fmax= 6.83333e+02, atom= 1684\n", - "Step= 77, Dmax= 1.2e-01 nm, Epot= -5.42770e+04 Fmax= 8.26019e+03, atom= 1684\n", - "Step= 78, Dmax= 1.4e-01 nm, Epot= -5.45678e+04 Fmax= 2.83134e+03, atom= 5062\n", - "Step= 80, Dmax= 8.6e-02 nm, Epot= -5.46790e+04 Fmax= 2.38991e+03, atom= 5101\n", - "Step= 81, Dmax= 1.0e-01 nm, Epot= -5.47846e+04 Fmax= 7.86056e+02, atom= 413\n", - "Step= 82, Dmax= 1.2e-01 nm, Epot= -5.49908e+04 Fmax= 1.47592e+03, atom= 413\n", - "Step= 83, Dmax= 1.5e-01 nm, Epot= -5.50680e+04 Fmax= 1.37360e+03, atom= 5101\n", - "Step= 85, Dmax= 8.9e-02 nm, Epot= -5.52757e+04 Fmax= 8.87388e+02, atom= 5062\n", - "Step= 86, Dmax= 1.1e-01 nm, Epot= -5.53671e+04 Fmax= 3.01079e+03, atom= 1684\n", - "Step= 87, Dmax= 1.3e-01 nm, Epot= -5.53722e+04 Fmax= 4.76861e+03, atom= 14\n", - "Step= 89, Dmax= 7.7e-02 nm, Epot= -5.54904e+04 Fmax= 1.28290e+03, atom= 2172\n", - "Step= 90, Dmax= 9.2e-02 nm, Epot= -5.55903e+04 Fmax= 5.29342e+02, atom= 1967\n", - "Step= 91, Dmax= 1.1e-01 nm, Epot= -5.56311e+04 Fmax= 3.79409e+03, atom= 2172\n", - "Step= 92, Dmax= 1.3e-01 nm, Epot= -5.58242e+04 Fmax= 8.02267e+02, atom= 2172\n", - "Step= 93, Dmax= 1.6e-01 nm, Epot= -5.58868e+04 Fmax= 2.26917e+03, atom= 5084\n", - "Step= 95, Dmax= 9.5e-02 nm, Epot= -5.59963e+04 Fmax= 2.49396e+03, atom= 14\n", - "Step= 96, Dmax= 1.1e-01 nm, Epot= -5.60698e+04 Fmax= 1.52605e+03, atom= 2171\n", - "Step= 97, Dmax= 1.4e-01 nm, Epot= -5.61231e+04 Fmax= 1.90551e+03, atom= 1966\n", - "Step= 98, Dmax= 1.6e-01 nm, Epot= -5.61786e+04 Fmax= 1.84995e+03, atom= 661\n", - "Step= 100, Dmax= 9.9e-02 nm, Epot= -5.62628e+04 Fmax= 6.51040e+02, atom= 1622\n", - "Step= 101, Dmax= 1.2e-01 nm, Epot= -5.63016e+04 Fmax= 1.70613e+03, atom= 667\n", - "Step= 102, Dmax= 1.4e-01 nm, Epot= -5.64090e+04 Fmax= 1.54019e+03, atom= 881\n", - "Step= 103, Dmax= 1.7e-01 nm, Epot= -5.64727e+04 Fmax= 8.08136e+02, atom= 968\n", - "Step= 105, Dmax= 1.0e-01 nm, Epot= -5.65925e+04 Fmax= 8.57638e+02, atom= 968\n", - "Step= 106, Dmax= 1.2e-01 nm, Epot= -5.66342e+04 Fmax= 9.91126e+02, atom= 968\n", - "Step= 108, Dmax= 7.4e-02 nm, Epot= -5.67794e+04 Fmax= 2.13723e+02, atom= 968\n", - "Step= 109, Dmax= 8.9e-02 nm, Epot= -5.67891e+04 Fmax= 1.98010e+03, atom= 969\n", - "Step= 110, Dmax= 1.1e-01 nm, Epot= -5.70265e+04 Fmax= 3.42698e+02, atom= 589\n", - "Step= 112, Dmax= 6.4e-02 nm, Epot= -5.71025e+04 Fmax= 5.63475e+02, atom= 590\n", - "Step= 113, Dmax= 7.7e-02 nm, Epot= -5.71615e+04 Fmax= 5.79251e+02, atom= 590\n", - "Step= 114, Dmax= 9.2e-02 nm, Epot= -5.71927e+04 Fmax= 8.66274e+02, atom= 590\n", - "Step= 115, Dmax= 1.1e-01 nm, Epot= -5.72416e+04 Fmax= 8.34020e+02, atom= 590\n", - "Step= 117, Dmax= 6.6e-02 nm, Epot= -5.73480e+04 Fmax= 1.76306e+02, atom= 590\n", - "Step= 119, Dmax= 4.0e-02 nm, Epot= -5.74114e+04 Fmax= 3.97555e+02, atom= 590\n", - "Step= 120, Dmax= 4.8e-02 nm, Epot= -5.74583e+04 Fmax= 3.61480e+02, atom= 590\n", - "Step= 121, Dmax= 5.7e-02 nm, Epot= -5.74646e+04 Fmax= 5.43998e+02, atom= 1268\n", - "Step= 122, Dmax= 6.9e-02 nm, Epot= -5.74734e+04 Fmax= 6.51600e+02, atom= 2750\n", - "Step= 124, Dmax= 4.1e-02 nm, Epot= -5.76075e+04 Fmax= 1.62744e+02, atom= 3420\n", - "Step= 125, Dmax= 4.9e-02 nm, Epot= -5.76634e+04 Fmax= 9.86603e+02, atom= 1037\n", - "Step= 126, Dmax= 5.9e-02 nm, Epot= -5.77230e+04 Fmax= 2.50357e+02, atom= 1037\n", - "Step= 127, Dmax= 7.1e-02 nm, Epot= -5.77331e+04 Fmax= 2.54090e+03, atom= 1037\n", - "Step= 128, Dmax= 8.5e-02 nm, Epot= -5.78134e+04 Fmax= 3.28038e+02, atom= 342\n", - "Step= 130, Dmax= 5.1e-02 nm, Epot= -5.78580e+04 Fmax= 3.56783e+02, atom= 1037\n", - "Step= 131, Dmax= 6.1e-02 nm, Epot= -5.78686e+04 Fmax= 6.76955e+02, atom= 1037\n", - "Step= 132, Dmax= 7.4e-02 nm, Epot= -5.79020e+04 Fmax= 5.59506e+02, atom= 1037\n", - "Step= 134, Dmax= 4.4e-02 nm, Epot= -5.79598e+04 Fmax= 2.36282e+02, atom= 1037\n", - "Step= 136, Dmax= 2.7e-02 nm, Epot= -5.79889e+04 Fmax= 2.18827e+02, atom= 4446\n", - "Step= 137, Dmax= 3.2e-02 nm, Epot= -5.80023e+04 Fmax= 5.21913e+02, atom= 444\n", - "Step= 138, Dmax= 3.8e-02 nm, Epot= -5.80462e+04 Fmax= 2.84451e+02, atom= 2366\n", - "Step= 139, Dmax= 4.6e-02 nm, Epot= -5.80608e+04 Fmax= 8.97149e+02, atom= 2366\n", - "Step= 140, Dmax= 5.5e-02 nm, Epot= -5.80975e+04 Fmax= 3.42887e+02, atom= 2366\n", - "Step= 142, Dmax= 3.3e-02 nm, Epot= -5.81282e+04 Fmax= 1.36145e+02, atom= 3046\n", - "Step= 143, Dmax= 4.0e-02 nm, Epot= -5.81573e+04 Fmax= 6.49999e+02, atom= 444\n", - "Step= 144, Dmax= 4.8e-02 nm, Epot= -5.81985e+04 Fmax= 5.85509e+02, atom= 444\n", - "Step= 145, Dmax= 5.7e-02 nm, Epot= -5.82168e+04 Fmax= 5.20569e+02, atom= 2366\n", - "Step= 146, Dmax= 6.8e-02 nm, Epot= -5.82348e+04 Fmax= 7.49805e+02, atom= 2366\n", - "Step= 147, Dmax= 8.2e-02 nm, Epot= -5.82399e+04 Fmax= 8.13908e+02, atom= 444\n", - "Step= 149, Dmax= 4.9e-02 nm, Epot= -5.82909e+04 Fmax= 1.92976e+02, atom= 3046\n", - "Step= 150, Dmax= 5.9e-02 nm, Epot= -5.83183e+04 Fmax= 7.54840e+02, atom= 3046\n", - "Step= 151, Dmax= 7.1e-02 nm, Epot= -5.83438e+04 Fmax= 7.57133e+02, atom= 444\n", - "Step= 152, Dmax= 8.5e-02 nm, Epot= -5.83492e+04 Fmax= 1.18558e+03, atom= 2366\n", - "Step= 153, Dmax= 1.0e-01 nm, Epot= -5.83833e+04 Fmax= 6.94247e+02, atom= 1079\n", - "Step= 155, Dmax= 6.1e-02 nm, Epot= -5.84236e+04 Fmax= 2.60608e+02, atom= 2759\n", - "Step= 156, Dmax= 7.4e-02 nm, Epot= -5.84247e+04 Fmax= 1.01250e+03, atom= 1079\n", - "Step= 157, Dmax= 8.8e-02 nm, Epot= -5.84664e+04 Fmax= 7.38344e+02, atom= 1079\n", - "Step= 159, Dmax= 5.3e-02 nm, Epot= -5.85081e+04 Fmax= 3.14148e+02, atom= 2366\n", - "Step= 160, Dmax= 6.4e-02 nm, Epot= -5.85283e+04 Fmax= 4.62261e+02, atom= 2366\n", - "Step= 162, Dmax= 3.8e-02 nm, Epot= -5.85613e+04 Fmax= 1.20716e+02, atom= 2056\n", - "Step= 163, Dmax= 4.6e-02 nm, Epot= -5.85799e+04 Fmax= 5.28588e+02, atom= 2056\n", - "Step= 164, Dmax= 5.5e-02 nm, Epot= -5.86070e+04 Fmax= 6.41145e+02, atom= 444\n", - "Step= 165, Dmax= 6.6e-02 nm, Epot= -5.86313e+04 Fmax= 6.33683e+02, atom= 2366\n", - "Step= 166, Dmax= 7.9e-02 nm, Epot= -5.86481e+04 Fmax= 4.59080e+02, atom= 2366\n", - "Step= 168, Dmax= 4.7e-02 nm, Epot= -5.86816e+04 Fmax= 2.75045e+02, atom= 4446\n", - "Step= 170, Dmax= 2.8e-02 nm, Epot= -5.87073e+04 Fmax= 1.67651e+02, atom= 2567\n", - "Step= 172, Dmax= 1.7e-02 nm, Epot= -5.87271e+04 Fmax= 1.31748e+02, atom= 1088\n", - "Step= 173, Dmax= 2.1e-02 nm, Epot= -5.87449e+04 Fmax= 2.22822e+02, atom= 1088\n", - "Step= 174, Dmax= 2.5e-02 nm, Epot= -5.87632e+04 Fmax= 2.10901e+02, atom= 2558\n", - "Step= 175, Dmax= 3.0e-02 nm, Epot= -5.87758e+04 Fmax= 3.27185e+02, atom= 2558\n", - "Step= 176, Dmax= 3.5e-02 nm, Epot= -5.87944e+04 Fmax= 3.08317e+02, atom= 2558\n", - "Step= 177, Dmax= 4.3e-02 nm, Epot= -5.88020e+04 Fmax= 4.61500e+02, atom= 2558\n", - "Step= 178, Dmax= 5.1e-02 nm, Epot= -5.88195e+04 Fmax= 4.45693e+02, atom= 2558\n", - "Step= 180, Dmax= 3.1e-02 nm, Epot= -5.88535e+04 Fmax= 8.54541e+01, atom= 2558\n", - "Step= 181, Dmax= 3.7e-02 nm, Epot= -5.88827e+04 Fmax= 5.40215e+02, atom= 2558\n", - "Step= 182, Dmax= 4.4e-02 nm, Epot= -5.89190e+04 Fmax= 2.35271e+02, atom= 2558\n", - "Step= 184, Dmax= 2.6e-02 nm, Epot= -5.89342e+04 Fmax= 2.30083e+02, atom= 2558\n", - "Step= 185, Dmax= 3.2e-02 nm, Epot= -5.89464e+04 Fmax= 3.31008e+02, atom= 2558\n", - "Step= 186, Dmax= 3.8e-02 nm, Epot= -5.89608e+04 Fmax= 3.34787e+02, atom= 2558\n", - "Step= 187, Dmax= 4.6e-02 nm, Epot= -5.89667e+04 Fmax= 4.70588e+02, atom= 2558\n", - "Step= 188, Dmax= 5.5e-02 nm, Epot= -5.89793e+04 Fmax= 4.82120e+02, atom= 2558\n", - "Step= 190, Dmax= 3.3e-02 nm, Epot= -5.90132e+04 Fmax= 7.92084e+01, atom= 2750\n", - "Step= 192, Dmax= 2.0e-02 nm, Epot= -5.90341e+04 Fmax= 3.02839e+02, atom= 2750\n", - "Step= 193, Dmax= 2.4e-02 nm, Epot= -5.90526e+04 Fmax= 1.38626e+02, atom= 2750\n", - "Step= 194, Dmax= 2.8e-02 nm, Epot= -5.90647e+04 Fmax= 4.28440e+02, atom= 2750\n", - "Step= 195, Dmax= 3.4e-02 nm, Epot= -5.90850e+04 Fmax= 2.04448e+02, atom= 2750\n", - "Step= 196, Dmax= 4.1e-02 nm, Epot= -5.90885e+04 Fmax= 6.34782e+02, atom= 2750\n", - "Step= 197, Dmax= 4.9e-02 nm, Epot= -5.91141e+04 Fmax= 2.81753e+02, atom= 2750\n", - "Step= 199, Dmax= 2.9e-02 nm, Epot= -5.91302e+04 Fmax= 1.71736e+02, atom= 2750\n", - "Step= 200, Dmax= 3.5e-02 nm, Epot= -5.91366e+04 Fmax= 4.23679e+02, atom= 1037\n", - "Step= 201, Dmax= 4.2e-02 nm, Epot= -5.91595e+04 Fmax= 3.24522e+02, atom= 1037\n", - "Step= 203, Dmax= 2.5e-02 nm, Epot= -5.91755e+04 Fmax= 1.34946e+02, atom= 2750\n", - "Step= 204, Dmax= 3.1e-02 nm, Epot= -5.91877e+04 Fmax= 4.69017e+02, atom= 2750\n", - "Step= 205, Dmax= 3.7e-02 nm, Epot= -5.92069e+04 Fmax= 2.09146e+02, atom= 2750\n", - "Step= 206, Dmax= 4.4e-02 nm, Epot= -5.92081e+04 Fmax= 6.84871e+02, atom= 2750\n", - "Step= 207, Dmax= 5.3e-02 nm, Epot= -5.92339e+04 Fmax= 2.91752e+02, atom= 2750\n", - "Step= 209, Dmax= 3.2e-02 nm, Epot= -5.92494e+04 Fmax= 1.91073e+02, atom= 1037\n", - "Step= 210, Dmax= 3.8e-02 nm, Epot= -5.92536e+04 Fmax= 4.45564e+02, atom= 1037\n", - "Step= 211, Dmax= 4.6e-02 nm, Epot= -5.92755e+04 Fmax= 3.48115e+02, atom= 1037\n", - "Step= 213, Dmax= 2.7e-02 nm, Epot= -5.92914e+04 Fmax= 1.36146e+02, atom= 2750\n", - "Step= 214, Dmax= 3.3e-02 nm, Epot= -5.93009e+04 Fmax= 5.12191e+02, atom= 2750\n", - "Step= 215, Dmax= 3.9e-02 nm, Epot= -5.93214e+04 Fmax= 2.14140e+02, atom= 2750\n", - "Step= 217, Dmax= 2.4e-02 nm, Epot= -5.93342e+04 Fmax= 1.60744e+02, atom= 1037\n", - "Step= 218, Dmax= 2.8e-02 nm, Epot= -5.93443e+04 Fmax= 3.17338e+02, atom= 1037\n", - "Step= 219, Dmax= 3.4e-02 nm, Epot= -5.93589e+04 Fmax= 2.73929e+02, atom= 1037\n", - "Step= 220, Dmax= 4.1e-02 nm, Epot= -5.93638e+04 Fmax= 4.06981e+02, atom= 1037\n", - "Step= 221, Dmax= 4.9e-02 nm, Epot= -5.93762e+04 Fmax= 4.42758e+02, atom= 1037\n", - "Step= 222, Dmax= 5.9e-02 nm, Epot= -5.93764e+04 Fmax= 5.38567e+02, atom= 1037\n", - "Step= 223, Dmax= 7.1e-02 nm, Epot= -5.93817e+04 Fmax= 6.85024e+02, atom= 1037\n", - "Step= 225, Dmax= 4.2e-02 nm, Epot= -5.94210e+04 Fmax= 1.13595e+02, atom= 2750\n", - "Step= 226, Dmax= 5.1e-02 nm, Epot= -5.94264e+04 Fmax= 1.12021e+03, atom= 2750\n", - "Step= 227, Dmax= 6.1e-02 nm, Epot= -5.94648e+04 Fmax= 2.13155e+02, atom= 2750\n", - "Step= 229, Dmax= 3.7e-02 nm, Epot= -5.94763e+04 Fmax= 3.40382e+02, atom= 2750\n", - "Step= 230, Dmax= 4.4e-02 nm, Epot= -5.94846e+04 Fmax= 3.72517e+02, atom= 2750\n", - "Step= 231, Dmax= 5.3e-02 nm, Epot= -5.94899e+04 Fmax= 5.17229e+02, atom= 2750\n", - "Step= 232, Dmax= 6.3e-02 nm, Epot= -5.94943e+04 Fmax= 5.04661e+02, atom= 2750\n", - "Step= 234, Dmax= 3.8e-02 nm, Epot= -5.95260e+04 Fmax= 1.10726e+02, atom= 1037\n", - "Step= 235, Dmax= 4.6e-02 nm, Epot= -5.95365e+04 Fmax= 5.90053e+02, atom= 1037\n", - "Step= 236, Dmax= 5.5e-02 nm, Epot= -5.95637e+04 Fmax= 3.74966e+02, atom= 1037\n", - "Step= 238, Dmax= 3.3e-02 nm, Epot= -5.95763e+04 Fmax= 1.82726e+02, atom= 1037\n", - "Step= 239, Dmax= 3.9e-02 nm, Epot= -5.95772e+04 Fmax= 5.49092e+02, atom= 1037\n", - "Step= 240, Dmax= 4.7e-02 nm, Epot= -5.95973e+04 Fmax= 2.75807e+02, atom= 2750\n", - "Step= 242, Dmax= 2.8e-02 nm, Epot= -5.96106e+04 Fmax= 1.84392e+02, atom= 1037\n", - "Step= 243, Dmax= 3.4e-02 nm, Epot= -5.96163e+04 Fmax= 3.79298e+02, atom= 1037\n", - "Step= 244, Dmax= 4.1e-02 nm, Epot= -5.96307e+04 Fmax= 3.13443e+02, atom= 1037\n", - "Step= 246, Dmax= 2.4e-02 nm, Epot= -5.96435e+04 Fmax= 1.07066e+02, atom= 1037\n", - "Step= 247, Dmax= 2.9e-02 nm, Epot= -5.96536e+04 Fmax= 4.31069e+02, atom= 1037\n", - "Step= 248, Dmax= 3.5e-02 nm, Epot= -5.96701e+04 Fmax= 1.86394e+02, atom= 2750\n", - "Step= 250, Dmax= 2.1e-02 nm, Epot= -5.96802e+04 Fmax= 1.64083e+02, atom= 1037\n", - "Step= 251, Dmax= 2.5e-02 nm, Epot= -5.96885e+04 Fmax= 2.59689e+02, atom= 1037\n", - "Step= 252, Dmax= 3.0e-02 nm, Epot= -5.96985e+04 Fmax= 2.61649e+02, atom= 1037\n", - "Step= 253, Dmax= 3.7e-02 nm, Epot= -5.97040e+04 Fmax= 3.45406e+02, atom= 1037\n", - "Step= 254, Dmax= 4.4e-02 nm, Epot= -5.97120e+04 Fmax= 4.06156e+02, atom= 1037\n", - "Step= 255, Dmax= 5.3e-02 nm, Epot= -5.97147e+04 Fmax= 4.66646e+02, atom= 1037\n", - "Step= 256, Dmax= 6.3e-02 nm, Epot= -5.97166e+04 Fmax= 6.15389e+02, atom= 1037\n", - "Step= 258, Dmax= 3.8e-02 nm, Epot= -5.97483e+04 Fmax= 8.18105e+01, atom= 2750\n", - "Step= 259, Dmax= 4.5e-02 nm, Epot= -5.97598e+04 Fmax= 9.54914e+02, atom= 2750\n", - "Step= 260, Dmax= 5.5e-02 nm, Epot= -5.97904e+04 Fmax= 1.91853e+02, atom= 2750\n", - "Step= 262, Dmax= 3.3e-02 nm, Epot= -5.97985e+04 Fmax= 3.15322e+02, atom= 2750\n", - "Step= 263, Dmax= 3.9e-02 nm, Epot= -5.98056e+04 Fmax= 3.21297e+02, atom= 2750\n", - "Step= 264, Dmax= 4.7e-02 nm, Epot= -5.98084e+04 Fmax= 4.68174e+02, atom= 2750\n", - "Step= 265, Dmax= 5.7e-02 nm, Epot= -5.98132e+04 Fmax= 4.44374e+02, atom= 2750\n", - "Step= 267, Dmax= 3.4e-02 nm, Epot= -5.98370e+04 Fmax= 1.04068e+02, atom= 1037\n", - "Step= 268, Dmax= 4.1e-02 nm, Epot= -5.98418e+04 Fmax= 5.35238e+02, atom= 1037\n", - "Step= 269, Dmax= 4.9e-02 nm, Epot= -5.98648e+04 Fmax= 2.99566e+02, atom= 1037\n", - "Step= 271, Dmax= 2.9e-02 nm, Epot= -5.98739e+04 Fmax= 1.89412e+02, atom= 1037\n", - "Step= 272, Dmax= 3.5e-02 nm, Epot= -5.98761e+04 Fmax= 4.27339e+02, atom= 1037\n", - "Step= 273, Dmax= 4.2e-02 nm, Epot= -5.98881e+04 Fmax= 2.85161e+02, atom= 1037\n", - "Step= 275, Dmax= 2.5e-02 nm, Epot= -5.98998e+04 Fmax= 1.31589e+02, atom= 1037\n", - "Step= 276, Dmax= 3.0e-02 nm, Epot= -5.99052e+04 Fmax= 3.66594e+02, atom= 1037\n", - "Step= 277, Dmax= 3.6e-02 nm, Epot= -5.99179e+04 Fmax= 2.45938e+02, atom= 1037\n", - "Step= 279, Dmax= 2.2e-02 nm, Epot= -5.99266e+04 Fmax= 1.22527e+02, atom= 1037\n", - "Step= 280, Dmax= 2.6e-02 nm, Epot= -5.99331e+04 Fmax= 3.36093e+02, atom= 1037\n", - "Step= 281, Dmax= 3.2e-02 nm, Epot= -5.99436e+04 Fmax= 1.97719e+02, atom= 1037\n", - "Step= 283, Dmax= 1.9e-02 nm, Epot= -5.99518e+04 Fmax= 1.17503e+02, atom= 1037\n", - "Step= 284, Dmax= 2.3e-02 nm, Epot= -5.99593e+04 Fmax= 2.56680e+02, atom= 1037\n", - "Step= 285, Dmax= 2.7e-02 nm, Epot= -5.99681e+04 Fmax= 2.03015e+02, atom= 1037\n", - "Step= 286, Dmax= 3.3e-02 nm, Epot= -5.99718e+04 Fmax= 3.34761e+02, atom= 1037\n", - "Step= 287, Dmax= 3.9e-02 nm, Epot= -5.99802e+04 Fmax= 3.27429e+02, atom= 1037\n", - "Step= 289, Dmax= 2.4e-02 nm, Epot= -5.99916e+04 Fmax= 7.51183e+01, atom= 1037\n", - "Step= 290, Dmax= 2.8e-02 nm, Epot= -6.00004e+04 Fmax= 4.44159e+02, atom= 1037\n", - "Step= 291, Dmax= 3.4e-02 nm, Epot= -6.00164e+04 Fmax= 1.52832e+02, atom= 2750\n", - "Step= 293, Dmax= 2.0e-02 nm, Epot= -6.00233e+04 Fmax= 1.84184e+02, atom= 1037\n", - "Step= 294, Dmax= 2.4e-02 nm, Epot= -6.00292e+04 Fmax= 2.23600e+02, atom= 1037\n", - "Step= 295, Dmax= 2.9e-02 nm, Epot= -6.00352e+04 Fmax= 2.76996e+02, atom= 1037\n", - "Step= 296, Dmax= 3.5e-02 nm, Epot= -6.00399e+04 Fmax= 3.08297e+02, atom= 1037\n", - "Step= 297, Dmax= 4.2e-02 nm, Epot= -6.00432e+04 Fmax= 4.13042e+02, atom= 1037\n", - "Step= 298, Dmax= 5.1e-02 nm, Epot= -6.00467e+04 Fmax= 4.27370e+02, atom= 1037\n", - "Step= 300, Dmax= 3.0e-02 nm, Epot= -6.00665e+04 Fmax= 6.86301e+01, atom= 1037\n", - "Step= 301, Dmax= 3.6e-02 nm, Epot= -6.00790e+04 Fmax= 4.94901e+02, atom= 1037\n", - "Step= 302, Dmax= 4.4e-02 nm, Epot= -6.00971e+04 Fmax= 2.47767e+02, atom= 1037\n", - "Step= 304, Dmax= 2.6e-02 nm, Epot= -6.01039e+04 Fmax= 1.85350e+02, atom= 1037\n", - "Step= 305, Dmax= 3.1e-02 nm, Epot= -6.01068e+04 Fmax= 3.56989e+02, atom= 1037\n", - "Step= 306, Dmax= 3.8e-02 nm, Epot= -6.01148e+04 Fmax= 2.75919e+02, atom= 1037\n", - "Step= 308, Dmax= 2.3e-02 nm, Epot= -6.01246e+04 Fmax= 9.78715e+01, atom= 1037\n", - "Step= 309, Dmax= 2.7e-02 nm, Epot= -6.01309e+04 Fmax= 3.46739e+02, atom= 1037\n", - "Step= 310, Dmax= 3.3e-02 nm, Epot= -6.01421e+04 Fmax= 1.98503e+02, atom= 1037\n", - "Step= 312, Dmax= 2.0e-02 nm, Epot= -6.01487e+04 Fmax= 1.28477e+02, atom= 1037\n", - "Step= 313, Dmax= 2.3e-02 nm, Epot= -6.01540e+04 Fmax= 2.75405e+02, atom= 1037\n", - "Step= 314, Dmax= 2.8e-02 nm, Epot= -6.01613e+04 Fmax= 1.98013e+02, atom= 1037\n", - "Step= 315, Dmax= 3.4e-02 nm, Epot= -6.01626e+04 Fmax= 3.86317e+02, atom= 1037\n", - "Step= 316, Dmax= 4.1e-02 nm, Epot= -6.01711e+04 Fmax= 2.95692e+02, atom= 1037\n", - "Step= 318, Dmax= 2.4e-02 nm, Epot= -6.01816e+04 Fmax= 1.05991e+02, atom= 1037\n", - "Step= 319, Dmax= 2.9e-02 nm, Epot= -6.01859e+04 Fmax= 3.70320e+02, atom= 1037\n", - "Step= 320, Dmax= 3.5e-02 nm, Epot= -6.01977e+04 Fmax= 2.15025e+02, atom= 1037\n", - "Step= 322, Dmax= 2.1e-02 nm, Epot= -6.02042e+04 Fmax= 1.36626e+02, atom= 1037\n", - "Step= 323, Dmax= 2.5e-02 nm, Epot= -6.02085e+04 Fmax= 2.97344e+02, atom= 1037\n", - "Step= 324, Dmax= 3.0e-02 nm, Epot= -6.02160e+04 Fmax= 2.11920e+02, atom= 1037\n", - "Step= 326, Dmax= 1.8e-02 nm, Epot= -6.02232e+04 Fmax= 9.05070e+01, atom= 1037\n", - "Step= 327, Dmax= 2.2e-02 nm, Epot= -6.02299e+04 Fmax= 2.67235e+02, atom= 1037\n", - "Step= 328, Dmax= 2.6e-02 nm, Epot= -6.02379e+04 Fmax= 1.71430e+02, atom= 1037\n", - "Step= 329, Dmax= 3.1e-02 nm, Epot= -6.02398e+04 Fmax= 3.43862e+02, atom= 1037\n", - "Step= 330, Dmax= 3.8e-02 nm, Epot= -6.02481e+04 Fmax= 2.87984e+02, atom= 1037\n", - "Step= 332, Dmax= 2.3e-02 nm, Epot= -6.02567e+04 Fmax= 9.48735e+01, atom= 1037\n", - "Step= 333, Dmax= 2.7e-02 nm, Epot= -6.02606e+04 Fmax= 3.83167e+02, atom= 1037\n", - "Step= 334, Dmax= 3.3e-02 nm, Epot= -6.02722e+04 Fmax= 1.74631e+02, atom= 1037\n", - "Step= 336, Dmax= 2.0e-02 nm, Epot= -6.02781e+04 Fmax= 1.53774e+02, atom= 1037\n", - "Step= 337, Dmax= 2.3e-02 nm, Epot= -6.02825e+04 Fmax= 2.35394e+02, atom= 1037\n", - "Step= 338, Dmax= 2.8e-02 nm, Epot= -6.02882e+04 Fmax= 2.40650e+02, atom= 1037\n", - "Step= 339, Dmax= 3.4e-02 nm, Epot= -6.02907e+04 Fmax= 3.19053e+02, atom= 1037\n", - "Step= 340, Dmax= 4.1e-02 nm, Epot= -6.02951e+04 Fmax= 3.67076e+02, atom= 1037\n", - "Step= 341, Dmax= 4.9e-02 nm, Epot= -6.02952e+04 Fmax= 4.37482e+02, atom= 1037\n", - "Step= 342, Dmax= 5.8e-02 nm, Epot= -6.02956e+04 Fmax= 5.51808e+02, atom= 1037\n", - "Step= 344, Dmax= 3.5e-02 nm, Epot= -6.03189e+04 Fmax= 6.47657e+01, atom= 2750\n", - "Step= 346, Dmax= 2.1e-02 nm, Epot= -6.03278e+04 Fmax= 2.65796e+02, atom= 1037\n", - "Step= 347, Dmax= 2.5e-02 nm, Epot= -6.03354e+04 Fmax= 1.68249e+02, atom= 1037\n", - "Step= 348, Dmax= 3.0e-02 nm, Epot= -6.03359e+04 Fmax= 3.57357e+02, atom= 1037\n", - "Step= 349, Dmax= 3.6e-02 nm, Epot= -6.03444e+04 Fmax= 2.56839e+02, atom= 1037\n", - "Step= 351, Dmax= 2.2e-02 nm, Epot= -6.03533e+04 Fmax= 1.03634e+02, atom= 1037\n", - "Step= 352, Dmax= 2.6e-02 nm, Epot= -6.03569e+04 Fmax= 3.24418e+02, atom= 1037\n", - "Step= 353, Dmax= 3.1e-02 nm, Epot= -6.03665e+04 Fmax= 1.99515e+02, atom= 1037\n", - "Step= 355, Dmax= 1.9e-02 nm, Epot= -6.03724e+04 Fmax= 1.16216e+02, atom= 1037\n", - "Step= 356, Dmax= 2.3e-02 nm, Epot= -6.03766e+04 Fmax= 2.72102e+02, atom= 1037\n", - "Step= 357, Dmax= 2.7e-02 nm, Epot= -6.03834e+04 Fmax= 1.84755e+02, atom= 1037\n", - "Step= 358, Dmax= 3.3e-02 nm, Epot= -6.03837e+04 Fmax= 3.76645e+02, atom= 1037\n", - "Step= 359, Dmax= 3.9e-02 nm, Epot= -6.03916e+04 Fmax= 2.81100e+02, atom= 1037\n", - "Step= 361, Dmax= 2.3e-02 nm, Epot= -6.04007e+04 Fmax= 1.05848e+02, atom= 1037\n", - "Step= 362, Dmax= 2.8e-02 nm, Epot= -6.04037e+04 Fmax= 3.52774e+02, atom= 1037\n", - "Step= 363, Dmax= 3.4e-02 nm, Epot= -6.04139e+04 Fmax= 2.08901e+02, atom= 1037\n", - "Step= 365, Dmax= 2.0e-02 nm, Epot= -6.04196e+04 Fmax= 1.29971e+02, atom= 1037\n", - "Step= 366, Dmax= 2.4e-02 nm, Epot= -6.04232e+04 Fmax= 2.86343e+02, atom= 1037\n", - "Step= 367, Dmax= 2.9e-02 nm, Epot= -6.04299e+04 Fmax= 2.03936e+02, atom= 1037\n", - "Step= 369, Dmax= 1.7e-02 nm, Epot= -6.04360e+04 Fmax= 8.72055e+01, atom= 1037\n", - "Step= 370, Dmax= 2.1e-02 nm, Epot= -6.04418e+04 Fmax= 2.56841e+02, atom= 1037\n", - "Step= 371, Dmax= 2.5e-02 nm, Epot= -6.04488e+04 Fmax= 1.64364e+02, atom= 1037\n", - "Step= 372, Dmax= 3.0e-02 nm, Epot= -6.04502e+04 Fmax= 3.31834e+02, atom= 1037\n", - "Step= 373, Dmax= 3.6e-02 nm, Epot= -6.04576e+04 Fmax= 2.75539e+02, atom= 1037\n", - "Step= 375, Dmax= 2.2e-02 nm, Epot= -6.04652e+04 Fmax= 9.25214e+01, atom= 1037\n", - "Step= 376, Dmax= 2.6e-02 nm, Epot= -6.04683e+04 Fmax= 3.64517e+02, atom= 1037\n", - "Step= 377, Dmax= 3.1e-02 nm, Epot= -6.04785e+04 Fmax= 1.71353e+02, atom= 1037\n", - "Step= 379, Dmax= 1.9e-02 nm, Epot= -6.04837e+04 Fmax= 1.44810e+02, atom= 1037\n", - "Step= 380, Dmax= 2.3e-02 nm, Epot= -6.04875e+04 Fmax= 2.28991e+02, atom= 1037\n", - "Step= 381, Dmax= 2.7e-02 nm, Epot= -6.04926e+04 Fmax= 2.27742e+02, atom= 1037\n", - "Step= 382, Dmax= 3.2e-02 nm, Epot= -6.04946e+04 Fmax= 3.10242e+02, atom= 1037\n", - "Step= 383, Dmax= 3.9e-02 nm, Epot= -6.04986e+04 Fmax= 3.48585e+02, atom= 1037\n", - "Step= 385, Dmax= 2.3e-02 nm, Epot= -6.05092e+04 Fmax= 5.26484e+01, atom= 1037\n", - "Step= 386, Dmax= 2.8e-02 nm, Epot= -6.05155e+04 Fmax= 4.62501e+02, atom= 1037\n", - "Step= 387, Dmax= 3.4e-02 nm, Epot= -6.05316e+04 Fmax= 1.34614e+02, atom= 1037\n", - "Step= 389, Dmax= 2.0e-02 nm, Epot= -6.05356e+04 Fmax= 2.10017e+02, atom= 1037\n", - "Step= 390, Dmax= 2.4e-02 nm, Epot= -6.05402e+04 Fmax= 1.97335e+02, atom= 1037\n", - "Step= 391, Dmax= 2.9e-02 nm, Epot= -6.05424e+04 Fmax= 3.00593e+02, atom= 1037\n", - "Step= 392, Dmax= 3.5e-02 nm, Epot= -6.05469e+04 Fmax= 2.84566e+02, atom= 1037\n", - "Step= 394, Dmax= 2.1e-02 nm, Epot= -6.05561e+04 Fmax= 6.08198e+01, atom= 1037\n", - "Step= 395, Dmax= 2.5e-02 nm, Epot= -6.05637e+04 Fmax= 3.46049e+02, atom= 1037\n", - "Step= 396, Dmax= 3.0e-02 nm, Epot= -6.05739e+04 Fmax= 1.55490e+02, atom= 1037\n", - "Step= 398, Dmax= 1.8e-02 nm, Epot= -6.05785e+04 Fmax= 1.45502e+02, atom= 1037\n", - "Step= 399, Dmax= 2.2e-02 nm, Epot= -6.05822e+04 Fmax= 2.23874e+02, atom= 1037\n", - "Step= 400, Dmax= 2.6e-02 nm, Epot= -6.05867e+04 Fmax= 2.11393e+02, atom= 1037\n", - "Step= 401, Dmax= 3.1e-02 nm, Epot= -6.05885e+04 Fmax= 3.21945e+02, atom= 1037\n", - "Step= 402, Dmax= 3.8e-02 nm, Epot= -6.05929e+04 Fmax= 3.04826e+02, atom= 1037\n", - "Step= 404, Dmax= 2.3e-02 nm, Epot= -6.06024e+04 Fmax= 6.54186e+01, atom= 1037\n", - "Step= 405, Dmax= 2.7e-02 nm, Epot= -6.06084e+04 Fmax= 3.72286e+02, atom= 1037\n", - "Step= 406, Dmax= 3.2e-02 nm, Epot= -6.06196e+04 Fmax= 1.65258e+02, atom= 1037\n", - "Step= 408, Dmax= 1.9e-02 nm, Epot= -6.06240e+04 Fmax= 1.58314e+02, atom= 1037\n", - "Step= 409, Dmax= 2.3e-02 nm, Epot= -6.06274e+04 Fmax= 2.38066e+02, atom= 1037\n", - "Step= 410, Dmax= 2.8e-02 nm, Epot= -6.06317e+04 Fmax= 2.29244e+02, atom= 1037\n", - "Step= 411, Dmax= 3.4e-02 nm, Epot= -6.06331e+04 Fmax= 3.43271e+02, atom= 1037\n", - "Step= 412, Dmax= 4.0e-02 nm, Epot= -6.06371e+04 Fmax= 3.29533e+02, atom= 1037\n", - "Step= 414, Dmax= 2.4e-02 nm, Epot= -6.06478e+04 Fmax= 6.72159e+01, atom= 1037\n", - "Step= 415, Dmax= 2.9e-02 nm, Epot= -6.06522e+04 Fmax= 4.02576e+02, atom= 1037\n", - "Step= 416, Dmax= 3.5e-02 nm, Epot= -6.06652e+04 Fmax= 1.74136e+02, atom= 1037\n", - "Step= 418, Dmax= 2.1e-02 nm, Epot= -6.06694e+04 Fmax= 1.73671e+02, atom= 1037\n", - "Step= 419, Dmax= 2.5e-02 nm, Epot= -6.06725e+04 Fmax= 2.51593e+02, atom= 1037\n", - "Step= 420, Dmax= 3.0e-02 nm, Epot= -6.06764e+04 Fmax= 2.50038e+02, atom= 1037\n", - "Step= 421, Dmax= 3.6e-02 nm, Epot= -6.06770e+04 Fmax= 3.64277e+02, atom= 1037\n", - "Step= 422, Dmax= 4.3e-02 nm, Epot= -6.06804e+04 Fmax= 3.57519e+02, atom= 1037\n", - "Step= 424, Dmax= 2.6e-02 nm, Epot= -6.06932e+04 Fmax= 6.74370e+01, atom= 1037\n", - "Step= 425, Dmax= 3.1e-02 nm, Epot= -6.06943e+04 Fmax= 4.36958e+02, atom= 1037\n", - "Step= 426, Dmax= 3.7e-02 nm, Epot= -6.07107e+04 Fmax= 1.81910e+02, atom= 1037\n", - "Step= 428, Dmax= 2.2e-02 nm, Epot= -6.07146e+04 Fmax= 1.91709e+02, atom= 1037\n", - "Step= 429, Dmax= 2.7e-02 nm, Epot= -6.07168e+04 Fmax= 2.64640e+02, atom= 1037\n", - "Step= 430, Dmax= 3.2e-02 nm, Epot= -6.07201e+04 Fmax= 2.73523e+02, atom= 1037\n", - "Step= 432, Dmax= 1.9e-02 nm, Epot= -6.07298e+04 Fmax= 4.56656e+01, atom= 1037\n", - "Step= 433, Dmax= 2.3e-02 nm, Epot= -6.07352e+04 Fmax= 3.31970e+02, atom= 1037\n", - "Step= 434, Dmax= 2.8e-02 nm, Epot= -6.07491e+04 Fmax= 1.31192e+02, atom= 1037\n", - "Step= 436, Dmax= 1.7e-02 nm, Epot= -6.07529e+04 Fmax= 1.47563e+02, atom= 1037\n", - "Step= 437, Dmax= 2.0e-02 nm, Epot= -6.07555e+04 Fmax= 1.93043e+02, atom= 1037\n", - "Step= 438, Dmax= 2.4e-02 nm, Epot= -6.07585e+04 Fmax= 2.08789e+02, atom= 1037\n", - "Step= 440, Dmax= 1.4e-02 nm, Epot= -6.07676e+04 Fmax= 3.43850e+01, atom= 1223\n", - "Step= 441, Dmax= 1.7e-02 nm, Epot= -6.07744e+04 Fmax= 2.64587e+02, atom= 1223\n", - "Step= 442, Dmax= 2.1e-02 nm, Epot= -6.07872e+04 Fmax= 1.03972e+02, atom= 1223\n", - "Step= 444, Dmax= 1.3e-02 nm, Epot= -6.07913e+04 Fmax= 1.04103e+02, atom= 1223\n", - "Step= 445, Dmax= 1.5e-02 nm, Epot= -6.07947e+04 Fmax= 1.53758e+02, atom= 1223\n", - "Step= 446, Dmax= 1.8e-02 nm, Epot= -6.07989e+04 Fmax= 1.50513e+02, atom= 1223\n", - "Step= 447, Dmax= 2.2e-02 nm, Epot= -6.08002e+04 Fmax= 2.19039e+02, atom= 1223\n", - "Step= 448, Dmax= 2.6e-02 nm, Epot= -6.08041e+04 Fmax= 2.22060e+02, atom= 1223\n", - "Step= 450, Dmax= 1.6e-02 nm, Epot= -6.08135e+04 Fmax= 4.75881e+01, atom= 1223\n", - "Step= 451, Dmax= 1.9e-02 nm, Epot= -6.08187e+04 Fmax= 2.76175e+02, atom= 1223\n", - "Step= 452, Dmax= 2.2e-02 nm, Epot= -6.08289e+04 Fmax= 1.20156e+02, atom= 1223\n", - "Step= 454, Dmax= 1.3e-02 nm, Epot= -6.08331e+04 Fmax= 1.02000e+02, atom= 1223\n", - "Step= 455, Dmax= 1.6e-02 nm, Epot= -6.08363e+04 Fmax= 1.75351e+02, atom= 1223\n", - "Step= 456, Dmax= 1.9e-02 nm, Epot= -6.08409e+04 Fmax= 1.50898e+02, atom= 1223\n", - "Step= 457, Dmax= 2.3e-02 nm, Epot= -6.08416e+04 Fmax= 2.46299e+02, atom= 1223\n", - "Step= 458, Dmax= 2.8e-02 nm, Epot= -6.08464e+04 Fmax= 2.26878e+02, atom= 1223\n", - "Step= 460, Dmax= 1.7e-02 nm, Epot= -6.08549e+04 Fmax= 6.13702e+01, atom= 1223\n", - "Step= 461, Dmax= 2.0e-02 nm, Epot= -6.08577e+04 Fmax= 2.86679e+02, atom= 1223\n", - "Step= 462, Dmax= 2.4e-02 nm, Epot= -6.08675e+04 Fmax= 1.36801e+02, atom= 1223\n", - "Step= 464, Dmax= 1.4e-02 nm, Epot= -6.08718e+04 Fmax= 1.01521e+02, atom= 1223\n", - "Step= 465, Dmax= 1.7e-02 nm, Epot= -6.08744e+04 Fmax= 1.97236e+02, atom= 1223\n", - "Step= 466, Dmax= 2.1e-02 nm, Epot= -6.08796e+04 Fmax= 1.53329e+02, atom= 1223\n", - "Step= 468, Dmax= 1.3e-02 nm, Epot= -6.08847e+04 Fmax= 6.19772e+01, atom= 1223\n", - "Step= 469, Dmax= 1.5e-02 nm, Epot= -6.08891e+04 Fmax= 1.90634e+02, atom= 1223\n", - "Step= 470, Dmax= 1.8e-02 nm, Epot= -6.08948e+04 Fmax= 1.21095e+02, atom= 1223\n", - "Step= 471, Dmax= 2.2e-02 nm, Epot= -6.08957e+04 Fmax= 2.47276e+02, atom= 1223\n", - "Step= 472, Dmax= 2.6e-02 nm, Epot= -6.09016e+04 Fmax= 1.96336e+02, atom= 1223\n", - "Step= 474, Dmax= 1.6e-02 nm, Epot= -6.09080e+04 Fmax= 6.02448e+01, atom= 1223\n", - "Step= 475, Dmax= 1.9e-02 nm, Epot= -6.09096e+04 Fmax= 2.75479e+02, atom= 1223\n", - "Step= 476, Dmax= 2.2e-02 nm, Epot= -6.09199e+04 Fmax= 1.08913e+02, atom= 1223\n", - "Step= 478, Dmax= 1.3e-02 nm, Epot= -6.09237e+04 Fmax= 1.19632e+02, atom= 1223\n", - "Step= 479, Dmax= 1.6e-02 nm, Epot= -6.09268e+04 Fmax= 1.52513e+02, atom= 1223\n", - "Step= 480, Dmax= 1.9e-02 nm, Epot= -6.09299e+04 Fmax= 1.80940e+02, atom= 1223\n", - "Step= 481, Dmax= 2.3e-02 nm, Epot= -6.09323e+04 Fmax= 2.13340e+02, atom= 1223\n", - "Step= 482, Dmax= 2.8e-02 nm, Epot= -6.09336e+04 Fmax= 2.63215e+02, atom= 1223\n", - "Step= 483, Dmax= 3.3e-02 nm, Epot= -6.09343e+04 Fmax= 3.06582e+02, atom= 1223\n", - "Step= 485, Dmax= 2.0e-02 nm, Epot= -6.09489e+04 Fmax= 4.04548e+01, atom= 1223\n", - "Step= 486, Dmax= 2.4e-02 nm, Epot= -6.09537e+04 Fmax= 3.76858e+02, atom= 1223\n", - "Step= 487, Dmax= 2.9e-02 nm, Epot= -6.09692e+04 Fmax= 1.55120e+02, atom= 1223\n", - "Step= 489, Dmax= 1.7e-02 nm, Epot= -6.09732e+04 Fmax= 1.25488e+02, atom= 1223\n", - "Step= 490, Dmax= 2.1e-02 nm, Epot= -6.09748e+04 Fmax= 2.29167e+02, atom= 1223\n", - "Step= 491, Dmax= 2.5e-02 nm, Epot= -6.09798e+04 Fmax= 1.88647e+02, atom= 1223\n", - "Step= 493, Dmax= 1.5e-02 nm, Epot= -6.09860e+04 Fmax= 6.73851e+01, atom= 1223\n", - "Step= 494, Dmax= 1.8e-02 nm, Epot= -6.09887e+04 Fmax= 2.36720e+02, atom= 1223\n", - "Step= 495, Dmax= 2.2e-02 nm, Epot= -6.09961e+04 Fmax= 1.36557e+02, atom= 1223\n", - "Step= 497, Dmax= 1.3e-02 nm, Epot= -6.10005e+04 Fmax= 7.65016e+01, atom= 1223\n", - "Step= 498, Dmax= 1.6e-02 nm, Epot= -6.10031e+04 Fmax= 1.94286e+02, atom= 1223\n", - "Step= 499, Dmax= 1.9e-02 nm, Epot= -6.10091e+04 Fmax= 1.19070e+02, atom= 1223\n", - "Step= 501, Dmax= 1.1e-02 nm, Epot= -6.10134e+04 Fmax= 7.30174e+01, atom= 1223\n", - "Step= 502, Dmax= 1.3e-02 nm, Epot= -6.10168e+04 Fmax= 1.51189e+02, atom= 1223\n", - "Step= 503, Dmax= 1.6e-02 nm, Epot= -6.10214e+04 Fmax= 1.26629e+02, atom= 1223\n", - "Step= 504, Dmax= 1.9e-02 nm, Epot= -6.10226e+04 Fmax= 1.99469e+02, atom= 1223\n", - "Step= 505, Dmax= 2.3e-02 nm, Epot= -6.10264e+04 Fmax= 1.97282e+02, atom= 1223\n", - "Step= 507, Dmax= 1.4e-02 nm, Epot= -6.10345e+04 Fmax= 3.68117e+01, atom= 2326\n", - "Step= 508, Dmax= 1.7e-02 nm, Epot= -6.10375e+04 Fmax= 2.67975e+02, atom= 1223\n", - "Step= 509, Dmax= 2.0e-02 nm, Epot= -6.10507e+04 Fmax= 8.53279e+01, atom= 1223\n", - "Step= 511, Dmax= 1.2e-02 nm, Epot= -6.10542e+04 Fmax= 1.17067e+02, atom= 1223\n", - "Step= 512, Dmax= 1.4e-02 nm, Epot= -6.10576e+04 Fmax= 1.24958e+02, atom= 1223\n", - "Step= 513, Dmax= 1.7e-02 nm, Epot= -6.10595e+04 Fmax= 1.74918e+02, atom= 1223\n", - "Step= 514, Dmax= 2.1e-02 nm, Epot= -6.10629e+04 Fmax= 1.76175e+02, atom= 1223\n", - "Step= 516, Dmax= 1.2e-02 nm, Epot= -6.10707e+04 Fmax= 3.64384e+01, atom= 1223\n", - "Step= 517, Dmax= 1.5e-02 nm, Epot= -6.10747e+04 Fmax= 2.13923e+02, atom= 1223\n", - "Step= 518, Dmax= 1.8e-02 nm, Epot= -6.10846e+04 Fmax= 1.01816e+02, atom= 1223\n", - "Step= 520, Dmax= 1.1e-02 nm, Epot= -6.10887e+04 Fmax= 8.20037e+01, atom= 3536\n", - "Step= 521, Dmax= 1.3e-02 nm, Epot= -6.10910e+04 Fmax= 1.41798e+02, atom= 3536\n", - "Step= 522, Dmax= 1.6e-02 nm, Epot= -6.10953e+04 Fmax= 1.25890e+02, atom= 3536\n", - "Step= 523, Dmax= 1.9e-02 nm, Epot= -6.10957e+04 Fmax= 1.95616e+02, atom= 3536\n", - "Step= 524, Dmax= 2.2e-02 nm, Epot= -6.10998e+04 Fmax= 1.90703e+02, atom= 3536\n", - "Step= 526, Dmax= 1.3e-02 nm, Epot= -6.11084e+04 Fmax= 4.56537e+01, atom= 3536\n", - "Step= 527, Dmax= 1.6e-02 nm, Epot= -6.11114e+04 Fmax= 2.35867e+02, atom= 3536\n", - "Step= 528, Dmax= 1.9e-02 nm, Epot= -6.11206e+04 Fmax= 1.05585e+02, atom= 3536\n", - "Step= 530, Dmax= 1.2e-02 nm, Epot= -6.11243e+04 Fmax= 9.42027e+01, atom= 3536\n", - "Step= 531, Dmax= 1.4e-02 nm, Epot= -6.11271e+04 Fmax= 1.46164e+02, atom= 3536\n", - "Step= 532, Dmax= 1.7e-02 nm, Epot= -6.11308e+04 Fmax= 1.41635e+02, atom= 3536\n", - "Step= 533, Dmax= 2.0e-02 nm, Epot= -6.11321e+04 Fmax= 2.03785e+02, atom= 3536\n", - "Step= 534, Dmax= 2.4e-02 nm, Epot= -6.11353e+04 Fmax= 2.11627e+02, atom= 3536\n", - "Step= 536, Dmax= 1.4e-02 nm, Epot= -6.11433e+04 Fmax= 4.28999e+01, atom= 3536\n", - "Step= 537, Dmax= 1.7e-02 nm, Epot= -6.11476e+04 Fmax= 2.60986e+02, atom= 3536\n", - "Step= 538, Dmax= 2.1e-02 nm, Epot= -6.11565e+04 Fmax= 1.08001e+02, atom= 3536\n", - "Step= 540, Dmax= 1.2e-02 nm, Epot= -6.11600e+04 Fmax= 1.07247e+02, atom= 3536\n", - "Step= 541, Dmax= 1.5e-02 nm, Epot= -6.11628e+04 Fmax= 1.50989e+02, atom= 3536\n", - "Step= 542, Dmax= 1.8e-02 nm, Epot= -6.11661e+04 Fmax= 1.58614e+02, atom= 3536\n", - "Step= 543, Dmax= 2.2e-02 nm, Epot= -6.11676e+04 Fmax= 2.12372e+02, atom= 3536\n", - "Step= 544, Dmax= 2.6e-02 nm, Epot= -6.11702e+04 Fmax= 2.34395e+02, atom= 3536\n", - "Step= 546, Dmax= 1.5e-02 nm, Epot= -6.11784e+04 Fmax= 3.97968e+01, atom= 3536\n", - "Step= 547, Dmax= 1.9e-02 nm, Epot= -6.11834e+04 Fmax= 2.88808e+02, atom= 3536\n", - "Step= 548, Dmax= 2.2e-02 nm, Epot= -6.11931e+04 Fmax= 1.10823e+02, atom= 3536\n", - "Step= 550, Dmax= 1.3e-02 nm, Epot= -6.11964e+04 Fmax= 1.21323e+02, atom= 3536\n", - "Step= 551, Dmax= 1.6e-02 nm, Epot= -6.11991e+04 Fmax= 1.56086e+02, atom= 3536\n", - "Step= 552, Dmax= 1.9e-02 nm, Epot= -6.12021e+04 Fmax= 1.77007e+02, atom= 3536\n", - "Step= 553, Dmax= 2.3e-02 nm, Epot= -6.12037e+04 Fmax= 2.21460e+02, atom= 3536\n", - "Step= 554, Dmax= 2.8e-02 nm, Epot= -6.12055e+04 Fmax= 2.59053e+02, atom= 3536\n", - "Step= 556, Dmax= 1.7e-02 nm, Epot= -6.12147e+04 Fmax= 3.63356e+01, atom= 3536\n", - "Step= 557, Dmax= 2.0e-02 nm, Epot= -6.12201e+04 Fmax= 3.20579e+02, atom= 3536\n", - "Step= 558, Dmax= 2.4e-02 nm, Epot= -6.12315e+04 Fmax= 1.14052e+02, atom= 3536\n", - "Step= 560, Dmax= 1.4e-02 nm, Epot= -6.12346e+04 Fmax= 1.36861e+02, atom= 3536\n", - "Step= 561, Dmax= 1.7e-02 nm, Epot= -6.12374e+04 Fmax= 1.61623e+02, atom= 3536\n", - "Step= 562, Dmax= 2.1e-02 nm, Epot= -6.12398e+04 Fmax= 1.96946e+02, atom= 3536\n", - "Step= 563, Dmax= 2.5e-02 nm, Epot= -6.12415e+04 Fmax= 2.30953e+02, atom= 3536\n", - "Step= 564, Dmax= 3.0e-02 nm, Epot= -6.12423e+04 Fmax= 2.85884e+02, atom= 3536\n", - "Step= 566, Dmax= 1.8e-02 nm, Epot= -6.12531e+04 Fmax= 3.24288e+01, atom= 3536\n", - "Step= 567, Dmax= 2.1e-02 nm, Epot= -6.12590e+04 Fmax= 3.56015e+02, atom= 3536\n", - "Step= 568, Dmax= 2.6e-02 nm, Epot= -6.12726e+04 Fmax= 1.30569e+02, atom= 3535\n", - "Step= 570, Dmax= 1.5e-02 nm, Epot= -6.12759e+04 Fmax= 1.28331e+02, atom= 3536\n", - "Step= 571, Dmax= 1.9e-02 nm, Epot= -6.12777e+04 Fmax= 1.91110e+02, atom= 3536\n", - "Step= 572, Dmax= 2.2e-02 nm, Epot= -6.12810e+04 Fmax= 1.93296e+02, atom= 3536\n", - "Step= 574, Dmax= 1.3e-02 nm, Epot= -6.12870e+04 Fmax= 4.14069e+01, atom= 3536\n", - "Step= 575, Dmax= 1.6e-02 nm, Epot= -6.12918e+04 Fmax= 2.40806e+02, atom= 3536\n", - "Step= 576, Dmax= 1.9e-02 nm, Epot= -6.12992e+04 Fmax= 9.95260e+01, atom= 3536\n", - "Step= 578, Dmax= 1.2e-02 nm, Epot= -6.13025e+04 Fmax= 1.00033e+02, atom= 3536\n", - "Step= 579, Dmax= 1.4e-02 nm, Epot= -6.13053e+04 Fmax= 1.38688e+02, atom= 3536\n", - "Step= 580, Dmax= 1.7e-02 nm, Epot= -6.13084e+04 Fmax= 1.48428e+02, atom= 3536\n", - "Step= 581, Dmax= 2.0e-02 nm, Epot= -6.13101e+04 Fmax= 1.94908e+02, atom= 3536\n", - "Step= 582, Dmax= 2.4e-02 nm, Epot= -6.13125e+04 Fmax= 2.19067e+02, atom= 3536\n", - "Step= 584, Dmax= 1.4e-02 nm, Epot= -6.13201e+04 Fmax= 3.48821e+01, atom= 3536\n", - "Step= 585, Dmax= 1.7e-02 nm, Epot= -6.13257e+04 Fmax= 2.71266e+02, atom= 3536\n", - "Step= 586, Dmax= 2.1e-02 nm, Epot= -6.13351e+04 Fmax= 1.01484e+02, atom= 3535\n", - "Step= 588, Dmax= 1.2e-02 nm, Epot= -6.13383e+04 Fmax= 1.12499e+02, atom= 3536\n", - "Step= 589, Dmax= 1.5e-02 nm, Epot= -6.13410e+04 Fmax= 1.44481e+02, atom= 3536\n", - "Step= 590, Dmax= 1.8e-02 nm, Epot= -6.13438e+04 Fmax= 1.64689e+02, atom= 3536\n", - "Step= 591, Dmax= 2.1e-02 nm, Epot= -6.13454e+04 Fmax= 2.04446e+02, atom= 3536\n", - "Step= 592, Dmax= 2.6e-02 nm, Epot= -6.13470e+04 Fmax= 2.40872e+02, atom= 3536\n", - "Step= 594, Dmax= 1.5e-02 nm, Epot= -6.13561e+04 Fmax= 3.26409e+01, atom= 3536\n", - "Step= 595, Dmax= 1.9e-02 nm, Epot= -6.13617e+04 Fmax= 2.99428e+02, atom= 3536\n", - "Step= 596, Dmax= 2.2e-02 nm, Epot= -6.13730e+04 Fmax= 1.16821e+02, atom= 3535\n", - "Step= 598, Dmax= 1.3e-02 nm, Epot= -6.13765e+04 Fmax= 1.02805e+02, atom= 3536\n", - "Step= 599, Dmax= 1.6e-02 nm, Epot= -6.13782e+04 Fmax= 1.72226e+02, atom= 3536\n", - "Step= 600, Dmax= 1.9e-02 nm, Epot= -6.13820e+04 Fmax= 1.59228e+02, atom= 3536\n", - "Step= 602, Dmax= 1.2e-02 nm, Epot= -6.13872e+04 Fmax= 4.27717e+01, atom= 3536\n", - "Step= 603, Dmax= 1.4e-02 nm, Epot= -6.13915e+04 Fmax= 1.99919e+02, atom= 3536\n", - "Step= 604, Dmax= 1.7e-02 nm, Epot= -6.13979e+04 Fmax= 9.18379e+01, atom= 3536\n", - "Step= 606, Dmax= 1.0e-02 nm, Epot= -6.14012e+04 Fmax= 8.02773e+01, atom= 3536\n", - "Step= 607, Dmax= 1.2e-02 nm, Epot= -6.14041e+04 Fmax= 1.25358e+02, atom= 3536\n", - "Step= 608, Dmax= 1.4e-02 nm, Epot= -6.14075e+04 Fmax= 1.22421e+02, atom= 3536\n", - "Step= 609, Dmax= 1.7e-02 nm, Epot= -6.14092e+04 Fmax= 1.76739e+02, atom= 1040\n", - "Step= 610, Dmax= 2.1e-02 nm, Epot= -6.14124e+04 Fmax= 1.79814e+02, atom= 1040\n", - "Step= 612, Dmax= 1.2e-02 nm, Epot= -6.14186e+04 Fmax= 3.79408e+01, atom= 3536\n", - "Step= 613, Dmax= 1.5e-02 nm, Epot= -6.14233e+04 Fmax= 2.24755e+02, atom= 3536\n", - "Step= 614, Dmax= 1.8e-02 nm, Epot= -6.14311e+04 Fmax= 9.76453e+01, atom= 3535\n", - "Step= 616, Dmax= 1.1e-02 nm, Epot= -6.14345e+04 Fmax= 8.28804e+01, atom= 3536\n", - "Step= 617, Dmax= 1.3e-02 nm, Epot= -6.14371e+04 Fmax= 1.39041e+02, atom= 1040\n", - "Step= 618, Dmax= 1.5e-02 nm, Epot= -6.14408e+04 Fmax= 1.27000e+02, atom= 1040\n", - "Step= 619, Dmax= 1.8e-02 nm, Epot= -6.14418e+04 Fmax= 1.95549e+02, atom= 1040\n", - "Step= 620, Dmax= 2.2e-02 nm, Epot= -6.14455e+04 Fmax= 1.87765e+02, atom= 1040\n", - "Step= 622, Dmax= 1.3e-02 nm, Epot= -6.14524e+04 Fmax= 4.56862e+01, atom= 3536\n", - "Step= 623, Dmax= 1.6e-02 nm, Epot= -6.14549e+04 Fmax= 2.36901e+02, atom= 3536\n", - "Step= 624, Dmax= 1.9e-02 nm, Epot= -6.14635e+04 Fmax= 1.11614e+02, atom= 3535\n", - "Step= 626, Dmax= 1.2e-02 nm, Epot= -6.14672e+04 Fmax= 8.07026e+01, atom= 3536\n", - "Step= 627, Dmax= 1.4e-02 nm, Epot= -6.14694e+04 Fmax= 1.59835e+02, atom= 3535\n", - "Step= 628, Dmax= 1.7e-02 nm, Epot= -6.14738e+04 Fmax= 1.25099e+02, atom= 1040\n", - "Step= 630, Dmax= 9.9e-03 nm, Epot= -6.14782e+04 Fmax= 4.88771e+01, atom= 1040\n", - "Step= 631, Dmax= 1.2e-02 nm, Epot= -6.14820e+04 Fmax= 1.57882e+02, atom= 1040\n", - "Step= 632, Dmax= 1.4e-02 nm, Epot= -6.14870e+04 Fmax= 9.52265e+01, atom= 3535\n", - "Step= 633, Dmax= 1.7e-02 nm, Epot= -6.14876e+04 Fmax= 2.02487e+02, atom= 3535\n", - "Step= 634, Dmax= 2.1e-02 nm, Epot= -6.14928e+04 Fmax= 1.59548e+02, atom= 3535\n", - "Step= 636, Dmax= 1.2e-02 nm, Epot= -6.14985e+04 Fmax= 5.32573e+01, atom= 1040\n", - "Step= 637, Dmax= 1.5e-02 nm, Epot= -6.15012e+04 Fmax= 2.01872e+02, atom= 1040\n", - "Step= 638, Dmax= 1.8e-02 nm, Epot= -6.15081e+04 Fmax= 1.09783e+02, atom= 3535\n", - "Step= 640, Dmax= 1.1e-02 nm, Epot= -6.15119e+04 Fmax= 7.39377e+01, atom= 3535\n", - "Step= 641, Dmax= 1.3e-02 nm, Epot= -6.15145e+04 Fmax= 1.46850e+02, atom= 3535\n", - "Step= 642, Dmax= 1.5e-02 nm, Epot= -6.15186e+04 Fmax= 1.24426e+02, atom= 3535\n", - "Step= 643, Dmax= 1.8e-02 nm, Epot= -6.15197e+04 Fmax= 1.94596e+02, atom= 3535\n", - "Step= 644, Dmax= 2.2e-02 nm, Epot= -6.15230e+04 Fmax= 1.94441e+02, atom= 3535\n", - "Step= 646, Dmax= 1.3e-02 nm, Epot= -6.15306e+04 Fmax= 3.85532e+01, atom= 3152\n", - "Step= 647, Dmax= 1.6e-02 nm, Epot= -6.15364e+04 Fmax= 2.25046e+02, atom= 3535\n", - "Step= 648, Dmax= 1.9e-02 nm, Epot= -6.15440e+04 Fmax= 1.18780e+02, atom= 3535\n", - "Step= 650, Dmax= 1.1e-02 nm, Epot= -6.15479e+04 Fmax= 7.42152e+01, atom= 3535\n", - "Step= 651, Dmax= 1.4e-02 nm, Epot= -6.15502e+04 Fmax= 1.63515e+02, atom= 3535\n", - "Step= 652, Dmax= 1.7e-02 nm, Epot= -6.15549e+04 Fmax= 1.27170e+02, atom= 3535\n", - "Step= 653, Dmax= 2.0e-02 nm, Epot= -6.15549e+04 Fmax= 2.15525e+02, atom= 3535\n", - "Step= 654, Dmax= 2.4e-02 nm, Epot= -6.15589e+04 Fmax= 2.02478e+02, atom= 3535\n", - "Step= 656, Dmax= 1.4e-02 nm, Epot= -6.15670e+04 Fmax= 4.80192e+01, atom= 3152\n", - "Step= 657, Dmax= 1.7e-02 nm, Epot= -6.15703e+04 Fmax= 2.35520e+02, atom= 3535\n", - "Step= 658, Dmax= 2.1e-02 nm, Epot= -6.15783e+04 Fmax= 1.31697e+02, atom= 3535\n", - "Step= 660, Dmax= 1.2e-02 nm, Epot= -6.15824e+04 Fmax= 7.52233e+01, atom= 3535\n", - "Step= 661, Dmax= 1.5e-02 nm, Epot= -6.15840e+04 Fmax= 1.82022e+02, atom= 3535\n", - "Step= 662, Dmax= 1.8e-02 nm, Epot= -6.15894e+04 Fmax= 1.31556e+02, atom= 3535\n", - "Step= 664, Dmax= 1.1e-02 nm, Epot= -6.15939e+04 Fmax= 5.10321e+01, atom= 3152\n", - "Step= 665, Dmax= 1.3e-02 nm, Epot= -6.15972e+04 Fmax= 1.74469e+02, atom= 3535\n", - "Step= 666, Dmax= 1.5e-02 nm, Epot= -6.16031e+04 Fmax= 9.24820e+01, atom= 3535\n", - "Step= 668, Dmax= 9.2e-03 nm, Epot= -6.16065e+04 Fmax= 6.65004e+01, atom= 3535\n", - "Step= 669, Dmax= 1.1e-02 nm, Epot= -6.16097e+04 Fmax= 1.22253e+02, atom= 3535\n", - "Step= 670, Dmax= 1.3e-02 nm, Epot= -6.16133e+04 Fmax= 1.12178e+02, atom= 3535\n", - "Step= 671, Dmax= 1.6e-02 nm, Epot= -6.16153e+04 Fmax= 1.61177e+02, atom= 3535\n", - "Step= 672, Dmax= 1.9e-02 nm, Epot= -6.16182e+04 Fmax= 1.75494e+02, atom= 3535\n", - "Step= 673, Dmax= 2.3e-02 nm, Epot= -6.16192e+04 Fmax= 2.19201e+02, atom= 3535\n", - "Step= 674, Dmax= 2.8e-02 nm, Epot= -6.16196e+04 Fmax= 2.65133e+02, atom= 3535\n", - "Step= 675, Dmax= 3.3e-02 nm, Epot= -6.16197e+04 Fmax= 3.02379e+02, atom= 3535\n", - "Step= 677, Dmax= 2.0e-02 nm, Epot= -6.16353e+04 Fmax= 5.31556e+01, atom= 1039\n", - "Step= 679, Dmax= 1.2e-02 nm, Epot= -6.16397e+04 Fmax= 1.29421e+02, atom= 1040\n", - "Step= 680, Dmax= 1.4e-02 nm, Epot= -6.16433e+04 Fmax= 1.18995e+02, atom= 1040\n", - "Step= 681, Dmax= 1.7e-02 nm, Epot= -6.16449e+04 Fmax= 1.73260e+02, atom= 1040\n", - "Step= 682, Dmax= 2.1e-02 nm, Epot= -6.16476e+04 Fmax= 1.83415e+02, atom= 3535\n", - "Step= 684, Dmax= 1.2e-02 nm, Epot= -6.16548e+04 Fmax= 3.27409e+01, atom= 3152\n", - "Step= 685, Dmax= 1.5e-02 nm, Epot= -6.16621e+04 Fmax= 2.04349e+02, atom= 3535\n", - "Step= 686, Dmax= 1.8e-02 nm, Epot= -6.16687e+04 Fmax= 1.11196e+02, atom= 3535\n", - "Step= 688, Dmax= 1.1e-02 nm, Epot= -6.16724e+04 Fmax= 6.89311e+01, atom= 3535\n", - "Step= 689, Dmax= 1.3e-02 nm, Epot= -6.16748e+04 Fmax= 1.49800e+02, atom= 3535\n", - "Step= 690, Dmax= 1.5e-02 nm, Epot= -6.16790e+04 Fmax= 1.19317e+02, atom= 3535\n", - "Step= 691, Dmax= 1.8e-02 nm, Epot= -6.16796e+04 Fmax= 1.96283e+02, atom= 3535\n", - "Step= 692, Dmax= 2.2e-02 nm, Epot= -6.16831e+04 Fmax= 1.90789e+02, atom= 3535\n", - "Step= 694, Dmax= 1.3e-02 nm, Epot= -6.16906e+04 Fmax= 4.29290e+01, atom= 3152\n", - "Step= 695, Dmax= 1.6e-02 nm, Epot= -6.16950e+04 Fmax= 2.15578e+02, atom= 3152\n", - "Step= 696, Dmax= 1.9e-02 nm, Epot= -6.17018e+04 Fmax= 1.18125e+02, atom= 3535\n", - "Step= 698, Dmax= 1.1e-02 nm, Epot= -6.17055e+04 Fmax= 7.49041e+01, atom= 3535\n", - "Step= 699, Dmax= 1.4e-02 nm, Epot= -6.17074e+04 Fmax= 1.60538e+02, atom= 3535\n", - "Step= 700, Dmax= 1.6e-02 nm, Epot= -6.17118e+04 Fmax= 1.28790e+02, atom= 3535\n", - "Step= 702, Dmax= 9.9e-03 nm, Epot= -6.17163e+04 Fmax= 4.33085e+01, atom= 3152\n", - "Step= 703, Dmax= 1.2e-02 nm, Epot= -6.17206e+04 Fmax= 1.55624e+02, atom= 3535\n", - "Step= 704, Dmax= 1.4e-02 nm, Epot= -6.17256e+04 Fmax= 9.05495e+01, atom= 3535\n", - "Step= 706, Dmax= 8.5e-03 nm, Epot= -6.17289e+04 Fmax= 5.71328e+01, atom= 3535\n", - "Step= 707, Dmax= 1.0e-02 nm, Epot= -6.17322e+04 Fmax= 1.16949e+02, atom= 3535\n", - "Step= 708, Dmax= 1.2e-02 nm, Epot= -6.17359e+04 Fmax= 1.00195e+02, atom= 3535\n", - "Step= 709, Dmax= 1.5e-02 nm, Epot= -6.17378e+04 Fmax= 1.51963e+02, atom= 3535\n", - "Step= 710, Dmax= 1.8e-02 nm, Epot= -6.17408e+04 Fmax= 1.59449e+02, atom= 3535\n", - "Step= 711, Dmax= 2.1e-02 nm, Epot= -6.17417e+04 Fmax= 2.04817e+02, atom= 3535\n", - "Step= 712, Dmax= 2.6e-02 nm, Epot= -6.17427e+04 Fmax= 2.43150e+02, atom= 3535\n", - "Step= 714, Dmax= 1.5e-02 nm, Epot= -6.17536e+04 Fmax= 3.42329e+01, atom= 4321\n", - "Step= 715, Dmax= 1.8e-02 nm, Epot= -6.17636e+04 Fmax= 2.31897e+02, atom= 3152\n", - "Step= 716, Dmax= 2.2e-02 nm, Epot= -6.17686e+04 Fmax= 1.42026e+02, atom= 3535\n", - "Step= 718, Dmax= 1.3e-02 nm, Epot= -6.17727e+04 Fmax= 8.02666e+01, atom= 3152\n", - "Step= 719, Dmax= 1.6e-02 nm, Epot= -6.17736e+04 Fmax= 1.90428e+02, atom= 3152\n", - "Step= 720, Dmax= 1.9e-02 nm, Epot= -6.17787e+04 Fmax= 1.39559e+02, atom= 3152\n", - "Step= 722, Dmax= 1.1e-02 nm, Epot= -6.17833e+04 Fmax= 6.06141e+01, atom= 3152\n", - "Step= 723, Dmax= 1.4e-02 nm, Epot= -6.17858e+04 Fmax= 1.69710e+02, atom= 3152\n", - "Step= 724, Dmax= 1.6e-02 nm, Epot= -6.17906e+04 Fmax= 1.12501e+02, atom= 3152\n", - "Step= 726, Dmax= 9.9e-03 nm, Epot= -6.17943e+04 Fmax= 5.36911e+01, atom= 3535\n", - "Step= 727, Dmax= 1.2e-02 nm, Epot= -6.17967e+04 Fmax= 1.49719e+02, atom= 3535\n", - "Step= 728, Dmax= 1.4e-02 nm, Epot= -6.18015e+04 Fmax= 1.01397e+02, atom= 3535\n", - "Step= 729, Dmax= 1.7e-02 nm, Epot= -6.18016e+04 Fmax= 1.90520e+02, atom= 3535\n", - "Step= 730, Dmax= 2.0e-02 nm, Epot= -6.18058e+04 Fmax= 1.67668e+02, atom= 3535\n", - "Step= 732, Dmax= 1.2e-02 nm, Epot= -6.18119e+04 Fmax= 4.75691e+01, atom= 3152\n", - "Step= 733, Dmax= 1.5e-02 nm, Epot= -6.18147e+04 Fmax= 1.96121e+02, atom= 3152\n", - "Step= 734, Dmax= 1.8e-02 nm, Epot= -6.18208e+04 Fmax= 1.07648e+02, atom= 3152\n", - "Step= 736, Dmax= 1.1e-02 nm, Epot= -6.18243e+04 Fmax= 7.27536e+01, atom= 3535\n", - "Step= 737, Dmax= 1.3e-02 nm, Epot= -6.18262e+04 Fmax= 1.44440e+02, atom= 3535\n", - "Step= 738, Dmax= 1.5e-02 nm, Epot= -6.18300e+04 Fmax= 1.23070e+02, atom= 3535\n", - "Step= 739, Dmax= 1.8e-02 nm, Epot= -6.18303e+04 Fmax= 1.90369e+02, atom= 3535\n", - "Step= 740, Dmax= 2.2e-02 nm, Epot= -6.18331e+04 Fmax= 1.93885e+02, atom= 3535\n", - "Step= 742, Dmax= 1.3e-02 nm, Epot= -6.18408e+04 Fmax= 3.97379e+01, atom= 3152\n", - "Step= 743, Dmax= 1.6e-02 nm, Epot= -6.18453e+04 Fmax= 2.14565e+02, atom= 3152\n", - "Step= 744, Dmax= 1.9e-02 nm, Epot= -6.18517e+04 Fmax= 1.10914e+02, atom= 3535\n", - "Step= 746, Dmax= 1.1e-02 nm, Epot= -6.18550e+04 Fmax= 8.17804e+01, atom= 3152\n", - "Step= 747, Dmax= 1.4e-02 nm, Epot= -6.18565e+04 Fmax= 1.51966e+02, atom= 3152\n", - "Step= 748, Dmax= 1.6e-02 nm, Epot= -6.18602e+04 Fmax= 1.31997e+02, atom= 3535\n", - "Step= 750, Dmax= 9.9e-03 nm, Epot= -6.18648e+04 Fmax= 4.06369e+01, atom= 3152\n", - "Step= 751, Dmax= 1.2e-02 nm, Epot= -6.18686e+04 Fmax= 1.55739e+02, atom= 3152\n", - "Step= 752, Dmax= 1.4e-02 nm, Epot= -6.18733e+04 Fmax= 8.78158e+01, atom= 3152\n", - "Step= 754, Dmax= 8.5e-03 nm, Epot= -6.18764e+04 Fmax= 5.63439e+01, atom= 3535\n", - "Step= 755, Dmax= 1.0e-02 nm, Epot= -6.18791e+04 Fmax= 1.17904e+02, atom= 3152\n", - "Step= 756, Dmax= 1.2e-02 nm, Epot= -6.18825e+04 Fmax= 9.56329e+01, atom= 3535\n", - "Step= 757, Dmax= 1.5e-02 nm, Epot= -6.18836e+04 Fmax= 1.54804e+02, atom= 3535\n", - "Step= 758, Dmax= 1.8e-02 nm, Epot= -6.18867e+04 Fmax= 1.53237e+02, atom= 3535\n", - "Step= 760, Dmax= 1.1e-02 nm, Epot= -6.18922e+04 Fmax= 3.31460e+01, atom= 3152\n", - "Step= 761, Dmax= 1.3e-02 nm, Epot= -6.18975e+04 Fmax= 1.73636e+02, atom= 3152\n", - "Step= 762, Dmax= 1.5e-02 nm, Epot= -6.19028e+04 Fmax= 8.76914e+01, atom= 3152\n", - "Step= 764, Dmax= 9.2e-03 nm, Epot= -6.19058e+04 Fmax= 6.73964e+01, atom= 3152\n", - "Step= 765, Dmax= 1.1e-02 nm, Epot= -6.19080e+04 Fmax= 1.20765e+02, atom= 3152\n", - "Step= 766, Dmax= 1.3e-02 nm, Epot= -6.19113e+04 Fmax= 1.05827e+02, atom= 3152\n", - "Step= 767, Dmax= 1.6e-02 nm, Epot= -6.19121e+04 Fmax= 1.64467e+02, atom= 3152\n", - "Step= 768, Dmax= 1.9e-02 nm, Epot= -6.19149e+04 Fmax= 1.64561e+02, atom= 3535\n", - "Step= 770, Dmax= 1.1e-02 nm, Epot= -6.19211e+04 Fmax= 3.64448e+01, atom= 3152\n", - "Step= 771, Dmax= 1.4e-02 nm, Epot= -6.19256e+04 Fmax= 1.85661e+02, atom= 3152\n", - "Step= 772, Dmax= 1.6e-02 nm, Epot= -6.19312e+04 Fmax= 9.48668e+01, atom= 3152\n", - "Step= 774, Dmax= 9.8e-03 nm, Epot= -6.19342e+04 Fmax= 7.16065e+01, atom= 3152\n", - "Step= 775, Dmax= 1.2e-02 nm, Epot= -6.19363e+04 Fmax= 1.30276e+02, atom= 3152\n", - "Step= 776, Dmax= 1.4e-02 nm, Epot= -6.19396e+04 Fmax= 1.12993e+02, atom= 3152\n", - "Step= 777, Dmax= 1.7e-02 nm, Epot= -6.19399e+04 Fmax= 1.76969e+02, atom= 3152\n", - "Step= 778, Dmax= 2.0e-02 nm, Epot= -6.19428e+04 Fmax= 1.76224e+02, atom= 3152\n", - "Step= 780, Dmax= 1.2e-02 nm, Epot= -6.19497e+04 Fmax= 3.93834e+01, atom= 3152\n", - "Step= 781, Dmax= 1.5e-02 nm, Epot= -6.19534e+04 Fmax= 2.00393e+02, atom= 3152\n", - "Step= 782, Dmax= 1.8e-02 nm, Epot= -6.19595e+04 Fmax= 1.01110e+02, atom= 3152\n", - "Step= 784, Dmax= 1.1e-02 nm, Epot= -6.19627e+04 Fmax= 7.74010e+01, atom= 3152\n", - "Step= 785, Dmax= 1.3e-02 nm, Epot= -6.19644e+04 Fmax= 1.39127e+02, atom= 3152\n", - "Step= 786, Dmax= 1.5e-02 nm, Epot= -6.19678e+04 Fmax= 1.22153e+02, atom= 3152\n", - "Step= 788, Dmax= 9.1e-03 nm, Epot= -6.19720e+04 Fmax= 3.89169e+01, atom= 4122\n", - "Step= 789, Dmax= 1.1e-02 nm, Epot= -6.19761e+04 Fmax= 1.36355e+02, atom= 3152\n", - "Step= 790, Dmax= 1.3e-02 nm, Epot= -6.19800e+04 Fmax= 8.85624e+01, atom= 3152\n", - "Step= 791, Dmax= 1.6e-02 nm, Epot= -6.19801e+04 Fmax= 1.86158e+02, atom= 3152\n", - "Step= 792, Dmax= 1.9e-02 nm, Epot= -6.19849e+04 Fmax= 1.38396e+02, atom= 3152\n", - "Step= 794, Dmax= 1.1e-02 nm, Epot= -6.19895e+04 Fmax= 5.09696e+01, atom= 1040\n", - "Step= 795, Dmax= 1.4e-02 nm, Epot= -6.19897e+04 Fmax= 1.86002e+02, atom= 3152\n", - "Step= 796, Dmax= 1.6e-02 nm, Epot= -6.19966e+04 Fmax= 1.01536e+02, atom= 3535\n", - "Step= 798, Dmax= 9.8e-03 nm, Epot= -6.20000e+04 Fmax= 6.64572e+01, atom= 3152\n", - "Step= 799, Dmax= 1.2e-02 nm, Epot= -6.20016e+04 Fmax= 1.33691e+02, atom= 3152\n", - "Step= 800, Dmax= 1.4e-02 nm, Epot= -6.20052e+04 Fmax= 1.08370e+02, atom= 3152\n", - "Step= 802, Dmax= 8.5e-03 nm, Epot= -6.20089e+04 Fmax= 3.70154e+01, atom= 1040\n", - "Step= 803, Dmax= 1.0e-02 nm, Epot= -6.20119e+04 Fmax= 1.35100e+02, atom= 1040\n", - "Step= 804, Dmax= 1.2e-02 nm, Epot= -6.20164e+04 Fmax= 7.73837e+01, atom= 3535\n", - "Step= 806, Dmax= 7.3e-03 nm, Epot= -6.20193e+04 Fmax= 4.72407e+01, atom= 3152\n", - "Step= 807, Dmax= 8.8e-03 nm, Epot= -6.20219e+04 Fmax= 1.05023e+02, atom= 1040\n", - "Step= 808, Dmax= 1.1e-02 nm, Epot= -6.20252e+04 Fmax= 7.44326e+01, atom= 3152\n", - "Step= 809, Dmax= 1.3e-02 nm, Epot= -6.20261e+04 Fmax= 1.44141e+02, atom= 3152\n", - "Step= 810, Dmax= 1.5e-02 nm, Epot= -6.20299e+04 Fmax= 1.16531e+02, atom= 3152\n", - "Step= 812, Dmax= 9.1e-03 nm, Epot= -6.20341e+04 Fmax= 4.05647e+01, atom= 1040\n", - "Step= 813, Dmax= 1.1e-02 nm, Epot= -6.20362e+04 Fmax= 1.44984e+02, atom= 1040\n", - "Step= 814, Dmax= 1.3e-02 nm, Epot= -6.20412e+04 Fmax= 8.27354e+01, atom= 1040\n", - "Step= 816, Dmax= 7.9e-03 nm, Epot= -6.20442e+04 Fmax= 5.09708e+01, atom= 1040\n", - "Step= 817, Dmax= 9.5e-03 nm, Epot= -6.20462e+04 Fmax= 1.13030e+02, atom= 1040\n", - "Step= 818, Dmax= 1.1e-02 nm, Epot= -6.20498e+04 Fmax= 7.92451e+01, atom= 1040\n", - "Step= 820, Dmax= 6.8e-03 nm, Epot= -6.20529e+04 Fmax= 3.87388e+01, atom= 1040\n", - "Step= 821, Dmax= 8.2e-03 nm, Epot= -6.20556e+04 Fmax= 9.87226e+01, atom= 1040\n", - "Step= 822, Dmax= 9.8e-03 nm, Epot= -6.20590e+04 Fmax= 7.10804e+01, atom= 1040\n", - "Step= 823, Dmax= 1.2e-02 nm, Epot= -6.20598e+04 Fmax= 1.28394e+02, atom= 1040\n", - "Step= 824, Dmax= 1.4e-02 nm, Epot= -6.20629e+04 Fmax= 1.15790e+02, atom= 1040\n", - "Step= 826, Dmax= 8.5e-03 nm, Epot= -6.20679e+04 Fmax= 2.99533e+01, atom= 3152\n", - "Step= 827, Dmax= 1.0e-02 nm, Epot= -6.20707e+04 Fmax= 1.38865e+02, atom= 4937\n", - "Step= 828, Dmax= 1.2e-02 nm, Epot= -6.20765e+04 Fmax= 7.09483e+01, atom= 4937\n", - "Step= 830, Dmax= 7.3e-03 nm, Epot= -6.20792e+04 Fmax= 5.78147e+01, atom= 4937\n", - "Step= 831, Dmax= 8.8e-03 nm, Epot= -6.20813e+04 Fmax= 9.70556e+01, atom= 4937\n", - "Step= 832, Dmax= 1.1e-02 nm, Epot= -6.20842e+04 Fmax= 8.95919e+01, atom= 4937\n", - "Step= 833, Dmax= 1.3e-02 nm, Epot= -6.20856e+04 Fmax= 1.33092e+02, atom= 4937\n", - "Step= 834, Dmax= 1.5e-02 nm, Epot= -6.20881e+04 Fmax= 1.36257e+02, atom= 4937\n", - "Step= 835, Dmax= 1.8e-02 nm, Epot= -6.20887e+04 Fmax= 1.83325e+02, atom= 4937\n", - "Step= 836, Dmax= 2.2e-02 nm, Epot= -6.20901e+04 Fmax= 2.04424e+02, atom= 4937\n", - "Step= 838, Dmax= 1.3e-02 nm, Epot= -6.20986e+04 Fmax= 2.09576e+01, atom= 4957\n", - "Step= 839, Dmax= 1.6e-02 nm, Epot= -6.21079e+04 Fmax= 2.04645e+02, atom= 4937\n", - "Step= 840, Dmax= 1.9e-02 nm, Epot= -6.21149e+04 Fmax= 1.09620e+02, atom= 4937\n", - "Step= 842, Dmax= 1.1e-02 nm, Epot= -6.21180e+04 Fmax= 9.83847e+01, atom= 4937\n", - "Step= 843, Dmax= 1.4e-02 nm, Epot= -6.21195e+04 Fmax= 1.38212e+02, atom= 4937\n", - "Step= 844, Dmax= 1.6e-02 nm, Epot= -6.21216e+04 Fmax= 1.52302e+02, atom= 4937\n", - "Step= 845, Dmax= 2.0e-02 nm, Epot= -6.21227e+04 Fmax= 1.89961e+02, atom= 4937\n", - "Step= 846, Dmax= 2.4e-02 nm, Epot= -6.21232e+04 Fmax= 2.26308e+02, atom= 4937\n", - "Step= 847, Dmax= 2.8e-02 nm, Epot= -6.21239e+04 Fmax= 2.63974e+02, atom= 4937\n", - "Step= 849, Dmax= 1.7e-02 nm, Epot= -6.21349e+04 Fmax= 5.16396e+01, atom= 4938\n", - "Step= 851, Dmax= 1.0e-02 nm, Epot= -6.21380e+04 Fmax= 1.14491e+02, atom= 4232\n", - "Step= 852, Dmax= 1.2e-02 nm, Epot= -6.21406e+04 Fmax= 1.03019e+02, atom= 4937\n", - "Step= 853, Dmax= 1.5e-02 nm, Epot= -6.21424e+04 Fmax= 1.56752e+02, atom= 4937\n", - "Step= 854, Dmax= 1.8e-02 nm, Epot= -6.21448e+04 Fmax= 1.55059e+02, atom= 4937\n", - "Step= 855, Dmax= 2.1e-02 nm, Epot= -6.21458e+04 Fmax= 2.15500e+02, atom= 4937\n", - "Step= 856, Dmax= 2.5e-02 nm, Epot= -6.21471e+04 Fmax= 2.33906e+02, atom= 4937\n", - "Step= 857, Dmax= 3.0e-02 nm, Epot= -6.21476e+04 Fmax= 2.95153e+02, atom= 4937\n", - "Step= 859, Dmax= 1.8e-02 nm, Epot= -6.21568e+04 Fmax= 5.16491e+01, atom= 4938\n", - "Step= 860, Dmax= 2.2e-02 nm, Epot= -6.21577e+04 Fmax= 3.69765e+02, atom= 4938\n", - "Step= 861, Dmax= 2.6e-02 nm, Epot= -6.21660e+04 Fmax= 1.30235e+02, atom= 4232\n", - "Step= 863, Dmax= 1.6e-02 nm, Epot= -6.21685e+04 Fmax= 1.33596e+02, atom= 4937\n", - "Step= 864, Dmax= 1.9e-02 nm, Epot= -6.21693e+04 Fmax= 1.92062e+02, atom= 4937\n", - "Step= 865, Dmax= 2.3e-02 nm, Epot= -6.21719e+04 Fmax= 2.03022e+02, atom= 4937\n", - "Step= 867, Dmax= 1.4e-02 nm, Epot= -6.21768e+04 Fmax= 4.63918e+01, atom= 4938\n", - "Step= 868, Dmax= 1.6e-02 nm, Epot= -6.21792e+04 Fmax= 2.57323e+02, atom= 4232\n", - "Step= 869, Dmax= 2.0e-02 nm, Epot= -6.21849e+04 Fmax= 1.05312e+02, atom= 4232\n", - "Step= 871, Dmax= 1.2e-02 nm, Epot= -6.21875e+04 Fmax= 9.94924e+01, atom= 4937\n", - "Step= 872, Dmax= 1.4e-02 nm, Epot= -6.21893e+04 Fmax= 1.43631e+02, atom= 4937\n", - "Step= 873, Dmax= 1.7e-02 nm, Epot= -6.21916e+04 Fmax= 1.52428e+02, atom= 4937\n", - "Step= 874, Dmax= 2.0e-02 nm, Epot= -6.21925e+04 Fmax= 2.03846e+02, atom= 4937\n", - "Step= 875, Dmax= 2.4e-02 nm, Epot= -6.21947e+04 Fmax= 2.19780e+02, atom= 4937\n", - "Step= 877, Dmax= 1.5e-02 nm, Epot= -6.22001e+04 Fmax= 4.90004e+01, atom= 4938\n", - "Step= 878, Dmax= 1.8e-02 nm, Epot= -6.22015e+04 Fmax= 2.84363e+02, atom= 4938\n", - "Step= 879, Dmax= 2.1e-02 nm, Epot= -6.22080e+04 Fmax= 1.09517e+02, atom= 4232\n", - "Step= 881, Dmax= 1.3e-02 nm, Epot= -6.22105e+04 Fmax= 1.08670e+02, atom= 4937\n", - "Step= 882, Dmax= 1.5e-02 nm, Epot= -6.22121e+04 Fmax= 1.53289e+02, atom= 4937\n", - "Step= 883, Dmax= 1.8e-02 nm, Epot= -6.22145e+04 Fmax= 1.64962e+02, atom= 4937\n", - "Step= 884, Dmax= 2.2e-02 nm, Epot= -6.22149e+04 Fmax= 2.18569e+02, atom= 4937\n", - "Step= 885, Dmax= 2.6e-02 nm, Epot= -6.22171e+04 Fmax= 2.36531e+02, atom= 4937\n", - "Step= 887, Dmax= 1.6e-02 nm, Epot= -6.22231e+04 Fmax= 5.39146e+01, atom= 4938\n", - "Step= 888, Dmax= 1.9e-02 nm, Epot= -6.22235e+04 Fmax= 3.07840e+02, atom= 4938\n", - "Step= 889, Dmax= 2.3e-02 nm, Epot= -6.22306e+04 Fmax= 1.17751e+02, atom= 4232\n", - "Step= 891, Dmax= 1.4e-02 nm, Epot= -6.22331e+04 Fmax= 1.15136e+02, atom= 4937\n", - "Step= 892, Dmax= 1.6e-02 nm, Epot= -6.22345e+04 Fmax= 1.65697e+02, atom= 4937\n", - "Step= 893, Dmax= 2.0e-02 nm, Epot= -6.22368e+04 Fmax= 1.75996e+02, atom= 4937\n", - "Step= 894, Dmax= 2.3e-02 nm, Epot= -6.22368e+04 Fmax= 2.36080e+02, atom= 4937\n", - "Step= 895, Dmax= 2.8e-02 nm, Epot= -6.22392e+04 Fmax= 2.52428e+02, atom= 4937\n", - "Step= 897, Dmax= 1.7e-02 nm, Epot= -6.22458e+04 Fmax= 6.01755e+01, atom= 4938\n", - "Step= 899, Dmax= 1.0e-02 nm, Epot= -6.22484e+04 Fmax= 1.10379e+02, atom= 4937\n", - "Step= 900, Dmax= 1.2e-02 nm, Epot= -6.22507e+04 Fmax= 1.04268e+02, atom= 4937\n", - "Step= 901, Dmax= 1.5e-02 nm, Epot= -6.22525e+04 Fmax= 1.54957e+02, atom= 4937\n", - "Step= 902, Dmax= 1.7e-02 nm, Epot= -6.22546e+04 Fmax= 1.55216e+02, atom= 4937\n", - "Step= 903, Dmax= 2.1e-02 nm, Epot= -6.22555e+04 Fmax= 2.14527e+02, atom= 4937\n", - "Step= 904, Dmax= 2.5e-02 nm, Epot= -6.22567e+04 Fmax= 2.33947e+02, atom= 4937\n", - "Step= 905, Dmax= 3.0e-02 nm, Epot= -6.22571e+04 Fmax= 2.94030e+02, atom= 4937\n", - "Step= 907, Dmax= 1.8e-02 nm, Epot= -6.22658e+04 Fmax= 5.29294e+01, atom= 4938\n", - "Step= 908, Dmax= 2.2e-02 nm, Epot= -6.22661e+04 Fmax= 3.67976e+02, atom= 4938\n", - "Step= 909, Dmax= 2.6e-02 nm, Epot= -6.22742e+04 Fmax= 1.31871e+02, atom= 4232\n", - "Step= 911, Dmax= 1.6e-02 nm, Epot= -6.22766e+04 Fmax= 1.29504e+02, atom= 4937\n", - "Step= 912, Dmax= 1.9e-02 nm, Epot= -6.22773e+04 Fmax= 1.94701e+02, atom= 4937\n", - "Step= 913, Dmax= 2.3e-02 nm, Epot= -6.22799e+04 Fmax= 1.98946e+02, atom= 4937\n", - "Step= 915, Dmax= 1.4e-02 nm, Epot= -6.22847e+04 Fmax= 4.96305e+01, atom= 4232\n", - "Step= 916, Dmax= 1.6e-02 nm, Epot= -6.22864e+04 Fmax= 2.57197e+02, atom= 4232\n", - "Step= 917, Dmax= 1.9e-02 nm, Epot= -6.22921e+04 Fmax= 1.04687e+02, atom= 4232\n", - "Step= 919, Dmax= 1.2e-02 nm, Epot= -6.22946e+04 Fmax= 9.76861e+01, atom= 4937\n", - "Step= 920, Dmax= 1.4e-02 nm, Epot= -6.22963e+04 Fmax= 1.44921e+02, atom= 4937\n", - "Step= 921, Dmax= 1.7e-02 nm, Epot= -6.22986e+04 Fmax= 1.50378e+02, atom= 4937\n", - "Step= 922, Dmax= 2.0e-02 nm, Epot= -6.22993e+04 Fmax= 2.05034e+02, atom= 4937\n", - "Step= 923, Dmax= 2.4e-02 nm, Epot= -6.23016e+04 Fmax= 2.17295e+02, atom= 4937\n", - "Step= 925, Dmax= 1.5e-02 nm, Epot= -6.23069e+04 Fmax= 5.08132e+01, atom= 4938\n", - "Step= 926, Dmax= 1.7e-02 nm, Epot= -6.23079e+04 Fmax= 2.83090e+02, atom= 4232\n", - "Step= 927, Dmax= 2.1e-02 nm, Epot= -6.23144e+04 Fmax= 1.09743e+02, atom= 4232\n", - "Step= 929, Dmax= 1.3e-02 nm, Epot= -6.23168e+04 Fmax= 1.06751e+02, atom= 4937\n", - "Step= 930, Dmax= 1.5e-02 nm, Epot= -6.23184e+04 Fmax= 1.54097e+02, atom= 4937\n", - "Step= 931, Dmax= 1.8e-02 nm, Epot= -6.23207e+04 Fmax= 1.63148e+02, atom= 4937\n", - "Step= 932, Dmax= 2.2e-02 nm, Epot= -6.23211e+04 Fmax= 2.18825e+02, atom= 4937\n", - "Step= 933, Dmax= 2.6e-02 nm, Epot= -6.23234e+04 Fmax= 2.35013e+02, atom= 4937\n", - "Step= 935, Dmax= 1.6e-02 nm, Epot= -6.23294e+04 Fmax= 5.38731e+01, atom= 4938\n", - "Step= 936, Dmax= 1.9e-02 nm, Epot= -6.23296e+04 Fmax= 3.05935e+02, atom= 4938\n", - "Step= 937, Dmax= 2.3e-02 nm, Epot= -6.23368e+04 Fmax= 1.17233e+02, atom= 4232\n", - "Step= 939, Dmax= 1.4e-02 nm, Epot= -6.23394e+04 Fmax= 1.15950e+02, atom= 4937\n", - "Step= 940, Dmax= 1.6e-02 nm, Epot= -6.23408e+04 Fmax= 1.63323e+02, atom= 4937\n", - "Step= 941, Dmax= 1.9e-02 nm, Epot= -6.23431e+04 Fmax= 1.77603e+02, atom= 4937\n", - "Step= 942, Dmax= 2.3e-02 nm, Epot= -6.23434e+04 Fmax= 2.32006e+02, atom= 4937\n", - "Step= 943, Dmax= 2.8e-02 nm, Epot= -6.23454e+04 Fmax= 2.55754e+02, atom= 4937\n", - "Step= 945, Dmax= 1.7e-02 nm, Epot= -6.23523e+04 Fmax= 5.46636e+01, atom= 4938\n", - "Step= 947, Dmax= 1.0e-02 nm, Epot= -6.23551e+04 Fmax= 1.16453e+02, atom= 4937\n", - "Step= 948, Dmax= 1.2e-02 nm, Epot= -6.23577e+04 Fmax= 9.75498e+01, atom= 4937\n", - "Step= 949, Dmax= 1.5e-02 nm, Epot= -6.23594e+04 Fmax= 1.61479e+02, atom= 4937\n", - "Step= 950, Dmax= 1.7e-02 nm, Epot= -6.23620e+04 Fmax= 1.46492e+02, atom= 4937\n", - "Step= 951, Dmax= 2.1e-02 nm, Epot= -6.23628e+04 Fmax= 2.23226e+02, atom= 4937\n", - "Step= 952, Dmax= 2.5e-02 nm, Epot= -6.23647e+04 Fmax= 2.21822e+02, atom= 4937\n", - "Step= 954, Dmax= 1.5e-02 nm, Epot= -6.23709e+04 Fmax= 3.62247e+01, atom= 4937\n", - "Step= 955, Dmax= 1.8e-02 nm, Epot= -6.23769e+04 Fmax= 2.36117e+02, atom= 4937\n", - "Step= 956, Dmax= 2.2e-02 nm, Epot= -6.23821e+04 Fmax= 1.31344e+02, atom= 4937\n", - "Step= 958, Dmax= 1.3e-02 nm, Epot= -6.23848e+04 Fmax= 1.01966e+02, atom= 4937\n", - "Step= 959, Dmax= 1.6e-02 nm, Epot= -6.23866e+04 Fmax= 1.73325e+02, atom= 4937\n", - "Step= 960, Dmax= 1.9e-02 nm, Epot= -6.23892e+04 Fmax= 1.58116e+02, atom= 4937\n", - "Step= 961, Dmax= 2.2e-02 nm, Epot= -6.23898e+04 Fmax= 2.38437e+02, atom= 4937\n", - "Step= 962, Dmax= 2.7e-02 nm, Epot= -6.23918e+04 Fmax= 2.37452e+02, atom= 4937\n", - "Step= 964, Dmax= 1.6e-02 nm, Epot= -6.23984e+04 Fmax= 3.79664e+01, atom= 4937\n", - "Step= 965, Dmax= 1.9e-02 nm, Epot= -6.24038e+04 Fmax= 2.57519e+02, atom= 4937\n", - "Step= 966, Dmax= 2.3e-02 nm, Epot= -6.24099e+04 Fmax= 1.38387e+02, atom= 4937\n", - "Step= 968, Dmax= 1.4e-02 nm, Epot= -6.24127e+04 Fmax= 1.11199e+02, atom= 4937\n", - "Step= 969, Dmax= 1.7e-02 nm, Epot= -6.24143e+04 Fmax= 1.84605e+02, atom= 4937\n", - "Step= 970, Dmax= 2.0e-02 nm, Epot= -6.24169e+04 Fmax= 1.70377e+02, atom= 4937\n", - "Step= 971, Dmax= 2.4e-02 nm, Epot= -6.24173e+04 Fmax= 2.55060e+02, atom= 4937\n", - "Step= 972, Dmax= 2.9e-02 nm, Epot= -6.24192e+04 Fmax= 2.54829e+02, atom= 4937\n", - "Step= 974, Dmax= 1.7e-02 nm, Epot= -6.24265e+04 Fmax= 3.89337e+01, atom= 4937\n", - "Step= 975, Dmax= 2.1e-02 nm, Epot= -6.24311e+04 Fmax= 2.82097e+02, atom= 4937\n", - "Step= 976, Dmax= 2.5e-02 nm, Epot= -6.24384e+04 Fmax= 1.42949e+02, atom= 4937\n", - "Step= 978, Dmax= 1.5e-02 nm, Epot= -6.24412e+04 Fmax= 1.25817e+02, atom= 4937\n", - "Step= 979, Dmax= 1.8e-02 nm, Epot= -6.24426e+04 Fmax= 1.90537e+02, atom= 4937\n", - "Step= 980, Dmax= 2.2e-02 nm, Epot= -6.24449e+04 Fmax= 1.90014e+02, atom= 4937\n", - "Step= 981, Dmax= 2.6e-02 nm, Epot= -6.24452e+04 Fmax= 2.65050e+02, atom= 4937\n", - "Step= 982, Dmax= 3.1e-02 nm, Epot= -6.24462e+04 Fmax= 2.81059e+02, atom= 4937\n", - "Step= 984, Dmax= 1.9e-02 nm, Epot= -6.24552e+04 Fmax= 3.23257e+01, atom= 4937\n", - "Step= 985, Dmax= 2.2e-02 nm, Epot= -6.24587e+04 Fmax= 3.07773e+02, atom= 4937\n", - "Step= 986, Dmax= 2.7e-02 nm, Epot= -6.24693e+04 Fmax= 1.49570e+02, atom= 4937\n", - "Step= 988, Dmax= 1.6e-02 nm, Epot= -6.24721e+04 Fmax= 1.44218e+02, atom= 4937\n", - "Step= 989, Dmax= 1.9e-02 nm, Epot= -6.24728e+04 Fmax= 1.93622e+02, atom= 4937\n", - "Step= 990, Dmax= 2.3e-02 nm, Epot= -6.24739e+04 Fmax= 2.15334e+02, atom= 4937\n", - "Step= 992, Dmax= 1.4e-02 nm, Epot= -6.24818e+04 Fmax= 3.12608e+01, atom= 4100\n", - "Step= 993, Dmax= 1.7e-02 nm, Epot= -6.24872e+04 Fmax= 2.83895e+02, atom= 4100\n", - "Step= 994, Dmax= 2.0e-02 nm, Epot= -6.24945e+04 Fmax= 8.68751e+01, atom= 4100\n", - "Step= 996, Dmax= 1.2e-02 nm, Epot= -6.24970e+04 Fmax= 1.27709e+02, atom= 4100\n", - "Step= 997, Dmax= 1.4e-02 nm, Epot= -6.24995e+04 Fmax= 1.28375e+02, atom= 4100\n", - "Step= 998, Dmax= 1.7e-02 nm, Epot= -6.25014e+04 Fmax= 1.81174e+02, atom= 4100\n", - "Step= 999, Dmax= 2.1e-02 nm, Epot= -6.25038e+04 Fmax= 1.87428e+02, atom= 4100\n", - "Step= 1000, Dmax= 2.5e-02 nm, Epot= -6.25048e+04 Fmax= 2.56882e+02, atom= 4100\n", - "\n", + "Step= 13, Dmax= 8.9e-02 nm, Epot= -4.12860e+03 Fmax= 1.03436e+04, atom= 1088\n", + "Step= 14, Dmax= 1.1e-01 nm, Epot= -1.13031e+04 Fmax= 1.60202e+05, atom= 4\n", + "Step= 15, Dmax= 1.3e-01 nm, Epot= -1.48685e+04 Fmax= 1.22373e+04, atom= 4\n", + "Step= 16, Dmax= 1.5e-01 nm, Epot= -2.01121e+04 Fmax= 3.01368e+04, atom= 4\n", + "Step= 17, Dmax= 1.8e-01 nm, Epot= -2.17951e+04 Fmax= 4.10915e+04, atom= 2520\n", + "Step= 18, Dmax= 2.2e-01 nm, Epot= -2.41457e+04 Fmax= 2.58494e+04, atom= 4\n", + "Step= 19, Dmax= 2.7e-01 nm, Epot= -2.66241e+04 Fmax= 2.69426e+04, atom= 835\n", + "Step= 23, Dmax= 4.0e-02 nm, Epot= -2.72906e+04 Fmax= 1.12460e+04, atom= 5360\n", + "Step= 24, Dmax= 4.8e-02 nm, Epot= -2.82619e+04 Fmax= 8.89296e+03, atom= 3110\n", + "Step= 25, Dmax= 5.8e-02 nm, Epot= -2.94485e+04 Fmax= 7.02511e+03, atom= 835\n", + "Step= 26, Dmax= 6.9e-02 nm, Epot= -3.10719e+04 Fmax= 4.20729e+03, atom= 835\n", + "Step= 27, Dmax= 8.3e-02 nm, Epot= -3.33641e+04 Fmax= 1.18154e+04, atom= 835\n", + "Step= 28, Dmax= 9.9e-02 nm, Epot= -3.46020e+04 Fmax= 2.13219e+03, atom= 3110\n", + "Step= 29, Dmax= 1.2e-01 nm, Epot= -3.82089e+04 Fmax= 4.27789e+04, atom= 3110\n", + "Step= 30, Dmax= 1.4e-01 nm, Epot= -3.94414e+04 Fmax= 2.82683e+03, atom= 536\n", + "Step= 31, Dmax= 1.7e-01 nm, Epot= -3.96515e+04 Fmax= 1.23669e+05, atom= 413\n", + "Step= 33, Dmax= 1.0e-01 nm, Epot= -4.13623e+04 Fmax= 3.78120e+04, atom= 413\n", + "Step= 34, Dmax= 1.2e-01 nm, Epot= -4.20929e+04 Fmax= 3.45758e+03, atom= 5051\n", + "Step= 35, Dmax= 1.5e-01 nm, Epot= -4.35947e+04 Fmax= 9.20874e+03, atom= 5051\n", + "Step= 36, Dmax= 1.8e-01 nm, Epot= -4.39134e+04 Fmax= 4.39989e+03, atom= 413\n", + "Step= 37, Dmax= 2.1e-01 nm, Epot= -4.44859e+04 Fmax= 2.43471e+04, atom= 5050\n", + "Step= 39, Dmax= 1.3e-01 nm, Epot= -4.46805e+04 Fmax= 3.27215e+04, atom= 5113\n", + "Step= 40, Dmax= 1.5e-01 nm, Epot= -4.53859e+04 Fmax= 6.23654e+03, atom= 1883\n", + "Step= 42, Dmax= 9.2e-02 nm, Epot= -4.59237e+04 Fmax= 1.73940e+03, atom= 1883\n", + "Step= 43, Dmax= 1.1e-01 nm, Epot= -4.70801e+04 Fmax= 2.89875e+03, atom= 1883\n", + "Step= 44, Dmax= 1.3e-01 nm, Epot= -4.77589e+04 Fmax= 3.05609e+03, atom= 1360\n", + "Step= 45, Dmax= 1.6e-01 nm, Epot= -4.80474e+04 Fmax= 1.33101e+04, atom= 1360\n", + "Step= 46, Dmax= 1.9e-01 nm, Epot= -4.84228e+04 Fmax= 6.33088e+03, atom= 567\n", + "Step= 48, Dmax= 1.1e-01 nm, Epot= -4.88170e+04 Fmax= 1.25395e+03, atom= 1608\n", + "Step= 49, Dmax= 1.4e-01 nm, Epot= -4.97575e+04 Fmax= 4.33496e+03, atom= 693\n", + "Step= 50, Dmax= 1.7e-01 nm, Epot= -5.01312e+04 Fmax= 3.75784e+03, atom= 1338\n", + "Step= 52, Dmax= 9.9e-02 nm, Epot= -5.02226e+04 Fmax= 9.33880e+03, atom= 2954\n", + "Step= 54, Dmax= 6.0e-02 nm, Epot= -5.04442e+04 Fmax= 1.97341e+03, atom= 144\n", + "Step= 55, Dmax= 7.1e-02 nm, Epot= -5.07143e+04 Fmax= 1.32154e+03, atom= 144\n", + "Step= 56, Dmax= 8.6e-02 nm, Epot= -5.11246e+04 Fmax= 1.28381e+03, atom= 144\n", + "Step= 57, Dmax= 1.0e-01 nm, Epot= -5.15390e+04 Fmax= 2.41925e+03, atom= 144\n", + "Step= 58, Dmax= 1.2e-01 nm, Epot= -5.18157e+04 Fmax= 1.10336e+03, atom= 2954\n", + "Step= 60, Dmax= 7.4e-02 nm, Epot= -5.21376e+04 Fmax= 1.22571e+03, atom= 3046\n", + "Step= 62, Dmax= 4.4e-02 nm, Epot= -5.22802e+04 Fmax= 1.99710e+03, atom= 3046\n", + "Step= 63, Dmax= 5.3e-02 nm, Epot= -5.24430e+04 Fmax= 1.13368e+03, atom= 444\n", + "Step= 64, Dmax= 6.4e-02 nm, Epot= -5.26101e+04 Fmax= 2.51858e+03, atom= 444\n", + "Step= 65, Dmax= 7.7e-02 nm, Epot= -5.27376e+04 Fmax= 1.69816e+03, atom= 3046\n", + "Step= 66, Dmax= 9.2e-02 nm, Epot= -5.27505e+04 Fmax= 4.60827e+03, atom= 3046\n", + "Step= 67, Dmax= 1.1e-01 nm, Epot= -5.29464e+04 Fmax= 2.66046e+03, atom= 444\n", + "Step= 68, Dmax= 1.3e-01 nm, Epot= -5.30886e+04 Fmax= 3.10115e+03, atom= 1079\n", + "Step= 70, Dmax= 8.0e-02 nm, Epot= -5.32855e+04 Fmax= 8.36880e+02, atom= 1079\n", + "Step= 72, Dmax= 4.8e-02 nm, Epot= -5.34753e+04 Fmax= 1.52218e+03, atom= 2567\n", + "Step= 73, Dmax= 5.7e-02 nm, Epot= -5.35846e+04 Fmax= 9.08475e+02, atom= 3179\n", + "Step= 74, Dmax= 6.9e-02 nm, Epot= -5.37531e+04 Fmax= 3.31739e+03, atom= 2567\n", + "Step= 75, Dmax= 8.3e-02 nm, Epot= -5.38422e+04 Fmax= 8.90771e+02, atom= 3179\n", + "Step= 76, Dmax= 9.9e-02 nm, Epot= -5.39374e+04 Fmax= 7.71798e+03, atom= 2567\n", + "Step= 77, Dmax= 1.2e-01 nm, Epot= -5.41298e+04 Fmax= 1.05874e+03, atom= 2567\n", + "Step= 79, Dmax= 7.1e-02 nm, Epot= -5.43156e+04 Fmax= 5.14630e+02, atom= 4622\n", + "Step= 80, Dmax= 8.6e-02 nm, Epot= -5.43995e+04 Fmax= 1.02555e+04, atom= 4622\n", + "Step= 81, Dmax= 1.0e-01 nm, Epot= -5.46246e+04 Fmax= 1.13109e+03, atom= 3179\n", + "Step= 82, Dmax= 1.2e-01 nm, Epot= -5.48060e+04 Fmax= 1.37699e+03, atom= 2567\n", + "Step= 83, Dmax= 1.5e-01 nm, Epot= -5.48334e+04 Fmax= 2.05696e+03, atom= 2567\n", + "Step= 84, Dmax= 1.8e-01 nm, Epot= -5.49886e+04 Fmax= 2.14840e+03, atom= 2567\n", + "Step= 85, Dmax= 2.1e-01 nm, Epot= -5.50857e+04 Fmax= 2.05082e+03, atom= 2567\n", + "Step= 87, Dmax= 1.3e-01 nm, Epot= -5.52320e+04 Fmax= 9.84210e+02, atom= 2567\n", + "Step= 89, Dmax= 7.7e-02 nm, Epot= -5.54016e+04 Fmax= 7.76042e+02, atom= 4623\n", + "Step= 90, Dmax= 9.2e-02 nm, Epot= -5.54718e+04 Fmax= 2.97639e+03, atom= 3180\n", + "Step= 91, Dmax= 1.1e-01 nm, Epot= -5.55854e+04 Fmax= 7.51557e+02, atom= 3180\n", + "Step= 93, Dmax= 6.6e-02 nm, Epot= -5.57277e+04 Fmax= 5.56224e+02, atom= 2566\n", + "Step= 94, Dmax= 7.9e-02 nm, Epot= -5.58208e+04 Fmax= 8.09355e+02, atom= 3568\n", + "Step= 95, Dmax= 9.5e-02 nm, Epot= -5.58278e+04 Fmax= 3.70043e+03, atom= 3015\n", + "Step= 96, Dmax= 1.1e-01 nm, Epot= -5.59803e+04 Fmax= 7.92915e+02, atom= 3015\n", + "Step= 97, Dmax= 1.4e-01 nm, Epot= -5.60522e+04 Fmax= 1.74485e+03, atom= 3528\n", + "Step= 99, Dmax= 8.2e-02 nm, Epot= -5.61793e+04 Fmax= 1.30159e+03, atom= 3207\n", + "Step= 100, Dmax= 9.9e-02 nm, Epot= -5.62395e+04 Fmax= 1.73043e+03, atom= 3306\n", + "Step= 101, Dmax= 1.2e-01 nm, Epot= -5.63205e+04 Fmax= 3.38021e+02, atom= 2922\n", + "Step= 102, Dmax= 1.4e-01 nm, Epot= -5.63321e+04 Fmax= 3.14597e+03, atom= 3306\n", + "Step= 103, Dmax= 1.7e-01 nm, Epot= -5.66195e+04 Fmax= 9.63577e+02, atom= 3306\n", + "Step= 105, Dmax= 1.0e-01 nm, Epot= -5.66649e+04 Fmax= 2.46338e+03, atom= 3207\n", + "Step= 106, Dmax= 1.2e-01 nm, Epot= -5.66681e+04 Fmax= 2.93470e+03, atom= 3528\n", + "Step= 107, Dmax= 1.5e-01 nm, Epot= -5.67116e+04 Fmax= 9.98182e+02, atom= 3015\n", + "Step= 108, Dmax= 1.8e-01 nm, Epot= -5.67160e+04 Fmax= 4.01710e+03, atom= 3568\n", + "Step= 109, Dmax= 2.1e-01 nm, Epot= -5.67314e+04 Fmax= 2.60014e+03, atom= 4623\n", + "Step= 110, Dmax= 2.6e-01 nm, Epot= -5.68128e+04 Fmax= 1.55369e+03, atom= 4632\n", + "Step= 112, Dmax= 1.5e-01 nm, Epot= -5.69097e+04 Fmax= 9.06986e+02, atom= 4624\n", + "Step= 114, Dmax= 9.2e-02 nm, Epot= -5.70090e+04 Fmax= 5.23911e+02, atom= 4624\n", + "Step= 116, Dmax= 5.5e-02 nm, Epot= -5.70881e+04 Fmax= 4.07709e+02, atom= 4625\n", + "Step= 117, Dmax= 6.6e-02 nm, Epot= -5.71193e+04 Fmax= 7.37738e+02, atom= 4625\n", + "Step= 118, Dmax= 7.9e-02 nm, Epot= -5.71803e+04 Fmax= 7.59541e+02, atom= 4625\n", + "Step= 119, Dmax= 9.5e-02 nm, Epot= -5.72119e+04 Fmax= 8.99682e+02, atom= 4625\n", + "Step= 121, Dmax= 5.7e-02 nm, Epot= -5.73265e+04 Fmax= 2.51483e+02, atom= 2558\n", + "Step= 123, Dmax= 3.4e-02 nm, Epot= -5.73747e+04 Fmax= 4.44440e+02, atom= 2558\n", + "Step= 124, Dmax= 4.1e-02 nm, Epot= -5.74121e+04 Fmax= 3.55337e+02, atom= 4635\n", + "Step= 125, Dmax= 4.9e-02 nm, Epot= -5.74287e+04 Fmax= 1.20535e+03, atom= 285\n", + "Step= 126, Dmax= 5.9e-02 nm, Epot= -5.74910e+04 Fmax= 3.55226e+02, atom= 285\n", + "Step= 127, Dmax= 7.1e-02 nm, Epot= -5.75302e+04 Fmax= 1.48864e+03, atom= 285\n", + "Step= 128, Dmax= 8.5e-02 nm, Epot= -5.75701e+04 Fmax= 6.22858e+02, atom= 4635\n", + "Step= 130, Dmax= 5.1e-02 nm, Epot= -5.76114e+04 Fmax= 3.83218e+02, atom= 5043\n", + "Step= 131, Dmax= 6.1e-02 nm, Epot= -5.76603e+04 Fmax= 4.35957e+02, atom= 5043\n", + "Step= 133, Dmax= 3.7e-02 nm, Epot= -5.76969e+04 Fmax= 3.00286e+02, atom= 4635\n", + "Step= 134, Dmax= 4.4e-02 nm, Epot= -5.77359e+04 Fmax= 3.85366e+02, atom= 285\n", + "Step= 135, Dmax= 5.3e-02 nm, Epot= -5.77624e+04 Fmax= 7.50828e+02, atom= 285\n", + "Step= 136, Dmax= 6.4e-02 nm, Epot= -5.77981e+04 Fmax= 4.54376e+02, atom= 285\n", + "Step= 138, Dmax= 3.8e-02 nm, Epot= -5.78377e+04 Fmax= 1.40492e+02, atom= 5043\n", + "Step= 139, Dmax= 4.6e-02 nm, Epot= -5.78694e+04 Fmax= 7.93461e+02, atom= 4635\n", + "Step= 140, Dmax= 5.5e-02 nm, Epot= -5.79361e+04 Fmax= 6.63909e+02, atom= 285\n", + "Step= 141, Dmax= 6.6e-02 nm, Epot= -5.79552e+04 Fmax= 5.89226e+02, atom= 285\n", + "Step= 142, Dmax= 7.9e-02 nm, Epot= -5.79725e+04 Fmax= 9.40391e+02, atom= 285\n", + "Step= 143, Dmax= 9.5e-02 nm, Epot= -5.79907e+04 Fmax= 7.07770e+02, atom= 285\n", + "Step= 145, Dmax= 5.7e-02 nm, Epot= -5.80467e+04 Fmax= 2.48711e+02, atom= 5043\n", + "Step= 147, Dmax= 3.4e-02 nm, Epot= -5.80828e+04 Fmax= 1.80194e+02, atom= 4634\n", + "Step= 149, Dmax= 2.1e-02 nm, Epot= -5.81124e+04 Fmax= 1.76968e+02, atom= 4634\n", + "Step= 150, Dmax= 2.5e-02 nm, Epot= -5.81382e+04 Fmax= 2.74294e+02, atom= 2558\n", + "Step= 151, Dmax= 3.0e-02 nm, Epot= -5.81669e+04 Fmax= 2.65196e+02, atom= 2558\n", + "Step= 152, Dmax= 3.5e-02 nm, Epot= -5.81878e+04 Fmax= 3.79214e+02, atom= 2558\n", + "Step= 153, Dmax= 4.3e-02 nm, Epot= -5.82143e+04 Fmax= 3.92706e+02, atom= 2558\n", + "Step= 154, Dmax= 5.1e-02 nm, Epot= -5.82281e+04 Fmax= 5.24798e+02, atom= 2558\n", + "Step= 155, Dmax= 6.1e-02 nm, Epot= -5.82503e+04 Fmax= 5.79046e+02, atom= 2558\n", + "Step= 156, Dmax= 7.4e-02 nm, Epot= -5.82509e+04 Fmax= 7.28714e+02, atom= 2558\n", + "Step= 157, Dmax= 8.8e-02 nm, Epot= -5.82588e+04 Fmax= 8.45931e+02, atom= 2558\n", + "Step= 159, Dmax= 5.3e-02 nm, Epot= -5.83439e+04 Fmax= 2.05454e+02, atom= 2858\n", + "Step= 160, Dmax= 6.4e-02 nm, Epot= -5.83443e+04 Fmax= 1.29098e+03, atom= 285\n", + "Step= 161, Dmax= 7.6e-02 nm, Epot= -5.84063e+04 Fmax= 3.91486e+02, atom= 4635\n", + "Step= 163, Dmax= 4.6e-02 nm, Epot= -5.84326e+04 Fmax= 2.44490e+02, atom= 285\n", + "Step= 165, Dmax= 2.7e-02 nm, Epot= -5.84581e+04 Fmax= 2.18521e+02, atom= 2855\n", + "Step= 166, Dmax= 3.3e-02 nm, Epot= -5.84788e+04 Fmax= 2.95386e+02, atom= 285\n", + "Step= 167, Dmax= 4.0e-02 nm, Epot= -5.84927e+04 Fmax= 3.83630e+02, atom= 2558\n", + "Step= 168, Dmax= 4.7e-02 nm, Epot= -5.85106e+04 Fmax= 4.59339e+02, atom= 2558\n", + "Step= 169, Dmax= 5.7e-02 nm, Epot= -5.85206e+04 Fmax= 5.41944e+02, atom= 2558\n", + "Step= 170, Dmax= 6.8e-02 nm, Epot= -5.85312e+04 Fmax= 6.62982e+02, atom= 2558\n", + "Step= 172, Dmax= 4.1e-02 nm, Epot= -5.85911e+04 Fmax= 1.11736e+02, atom= 2858\n", + "Step= 173, Dmax= 4.9e-02 nm, Epot= -5.86252e+04 Fmax= 8.80132e+02, atom= 285\n", + "Step= 174, Dmax= 5.9e-02 nm, Epot= -5.86674e+04 Fmax= 2.93543e+02, atom= 285\n", + "Step= 176, Dmax= 3.5e-02 nm, Epot= -5.86879e+04 Fmax= 2.57437e+02, atom= 285\n", + "Step= 177, Dmax= 4.3e-02 nm, Epot= -5.86965e+04 Fmax= 4.14149e+02, atom= 285\n", + "Step= 178, Dmax= 5.1e-02 nm, Epot= -5.87122e+04 Fmax= 4.88773e+02, atom= 285\n", + "Step= 179, Dmax= 6.1e-02 nm, Epot= -5.87183e+04 Fmax= 5.02784e+02, atom= 285\n", + "Step= 181, Dmax= 3.7e-02 nm, Epot= -5.87685e+04 Fmax= 1.24716e+02, atom= 2558\n", + "Step= 182, Dmax= 4.4e-02 nm, Epot= -5.87783e+04 Fmax= 6.32760e+02, atom= 2558\n", + "Step= 183, Dmax= 5.3e-02 nm, Epot= -5.88269e+04 Fmax= 2.78799e+02, atom= 2558\n", + "Step= 185, Dmax= 3.2e-02 nm, Epot= -5.88438e+04 Fmax= 2.67023e+02, atom= 2558\n", + "Step= 186, Dmax= 3.8e-02 nm, Epot= -5.88562e+04 Fmax= 3.92228e+02, atom= 2558\n", + "Step= 187, Dmax= 4.6e-02 nm, Epot= -5.88719e+04 Fmax= 3.94399e+02, atom= 2558\n", + "Step= 188, Dmax= 5.5e-02 nm, Epot= -5.88777e+04 Fmax= 5.51790e+02, atom= 2558\n", + "Step= 189, Dmax= 6.6e-02 nm, Epot= -5.88898e+04 Fmax= 5.74763e+02, atom= 2558\n", + "Step= 191, Dmax= 3.9e-02 nm, Epot= -5.89313e+04 Fmax= 9.24066e+01, atom= 2558\n", + "Step= 192, Dmax= 4.7e-02 nm, Epot= -5.89464e+04 Fmax= 7.09055e+02, atom= 2558\n", + "Step= 193, Dmax= 5.7e-02 nm, Epot= -5.89983e+04 Fmax= 2.72586e+02, atom= 2558\n", + "Step= 195, Dmax= 3.4e-02 nm, Epot= -5.90113e+04 Fmax= 3.12088e+02, atom= 2558\n", + "Step= 196, Dmax= 4.1e-02 nm, Epot= -5.90177e+04 Fmax= 3.89366e+02, atom= 2558\n", + "Step= 197, Dmax= 4.9e-02 nm, Epot= -5.90259e+04 Fmax= 4.71057e+02, atom= 2750\n", + "Step= 199, Dmax= 2.9e-02 nm, Epot= -5.90633e+04 Fmax= 1.07989e+02, atom= 2750\n", + "Step= 200, Dmax= 3.5e-02 nm, Epot= -5.90842e+04 Fmax= 6.97884e+02, atom= 2750\n", + "Step= 201, Dmax= 4.2e-02 nm, Epot= -5.91077e+04 Fmax= 1.90523e+02, atom= 2750\n", + "Step= 203, Dmax= 2.5e-02 nm, Epot= -5.91226e+04 Fmax= 2.20171e+02, atom= 2750\n", + "Step= 204, Dmax= 3.1e-02 nm, Epot= -5.91348e+04 Fmax= 2.94176e+02, atom= 2750\n", + "Step= 205, Dmax= 3.7e-02 nm, Epot= -5.91476e+04 Fmax= 3.56281e+02, atom= 2750\n", + "Step= 206, Dmax= 4.4e-02 nm, Epot= -5.91563e+04 Fmax= 3.82359e+02, atom= 2750\n", + "Step= 207, Dmax= 5.3e-02 nm, Epot= -5.91628e+04 Fmax= 5.88973e+02, atom= 2750\n", + "Step= 208, Dmax= 6.3e-02 nm, Epot= -5.91732e+04 Fmax= 4.85093e+02, atom= 2750\n", + "Step= 210, Dmax= 3.8e-02 nm, Epot= -5.92039e+04 Fmax= 1.35743e+02, atom= 1037\n", + "Step= 211, Dmax= 4.6e-02 nm, Epot= -5.92141e+04 Fmax= 5.65706e+02, atom= 1037\n", + "Step= 212, Dmax= 5.5e-02 nm, Epot= -5.92410e+04 Fmax= 4.54354e+02, atom= 1037\n", + "Step= 214, Dmax= 3.3e-02 nm, Epot= -5.92579e+04 Fmax= 1.66848e+02, atom= 2750\n", + "Step= 215, Dmax= 3.9e-02 nm, Epot= -5.92647e+04 Fmax= 6.44873e+02, atom= 2750\n", + "Step= 216, Dmax= 4.7e-02 nm, Epot= -5.92871e+04 Fmax= 2.43525e+02, atom= 2750\n", + "Step= 218, Dmax= 2.8e-02 nm, Epot= -5.93006e+04 Fmax= 1.95952e+02, atom= 2750\n", + "Step= 219, Dmax= 3.4e-02 nm, Epot= -5.93089e+04 Fmax= 3.67029e+02, atom= 2750\n", + "Step= 220, Dmax= 4.1e-02 nm, Epot= -5.93240e+04 Fmax= 3.34144e+02, atom= 2750\n", + "Step= 221, Dmax= 4.9e-02 nm, Epot= -5.93247e+04 Fmax= 4.66065e+02, atom= 1037\n", + "Step= 222, Dmax= 5.9e-02 nm, Epot= -5.93346e+04 Fmax= 5.60595e+02, atom= 1037\n", + "Step= 224, Dmax= 3.5e-02 nm, Epot= -5.93648e+04 Fmax= 1.09633e+02, atom= 2750\n", + "Step= 225, Dmax= 4.2e-02 nm, Epot= -5.93780e+04 Fmax= 8.31451e+02, atom= 2750\n", + "Step= 226, Dmax= 5.1e-02 nm, Epot= -5.94053e+04 Fmax= 2.09115e+02, atom= 2750\n", + "Step= 228, Dmax= 3.1e-02 nm, Epot= -5.94176e+04 Fmax= 2.62302e+02, atom= 2750\n", + "Step= 229, Dmax= 3.7e-02 nm, Epot= -5.94262e+04 Fmax= 3.36118e+02, atom= 2750\n", + "Step= 230, Dmax= 4.4e-02 nm, Epot= -5.94357e+04 Fmax= 4.10895e+02, atom= 2750\n", + "Step= 231, Dmax= 5.3e-02 nm, Epot= -5.94403e+04 Fmax= 4.45711e+02, atom= 2750\n", + "Step= 233, Dmax= 3.2e-02 nm, Epot= -5.94655e+04 Fmax= 7.20466e+01, atom= 1037\n", + "Step= 234, Dmax= 3.8e-02 nm, Epot= -5.94950e+04 Fmax= 4.87951e+02, atom= 1037\n", + "Step= 235, Dmax= 4.6e-02 nm, Epot= -5.95155e+04 Fmax= 3.33452e+02, atom= 1037\n", + "Step= 237, Dmax= 2.7e-02 nm, Epot= -5.95271e+04 Fmax= 1.38156e+02, atom= 2750\n", + "Step= 238, Dmax= 3.3e-02 nm, Epot= -5.95330e+04 Fmax= 5.13054e+02, atom= 2750\n", + "Step= 239, Dmax= 3.9e-02 nm, Epot= -5.95524e+04 Fmax= 2.04268e+02, atom= 2750\n", + "Step= 241, Dmax= 2.4e-02 nm, Epot= -5.95633e+04 Fmax= 1.66953e+02, atom= 2750\n", + "Step= 242, Dmax= 2.8e-02 nm, Epot= -5.95715e+04 Fmax= 2.97517e+02, atom= 2750\n", + "Step= 243, Dmax= 3.4e-02 nm, Epot= -5.95832e+04 Fmax= 2.83477e+02, atom= 1037\n", + "Step= 244, Dmax= 4.1e-02 nm, Epot= -5.95869e+04 Fmax= 3.94152e+02, atom= 1037\n", + "Step= 245, Dmax= 4.9e-02 nm, Epot= -5.95965e+04 Fmax= 4.43375e+02, atom= 1037\n", + "Step= 247, Dmax= 2.9e-02 nm, Epot= -5.96171e+04 Fmax= 8.59002e+01, atom= 2750\n", + "Step= 248, Dmax= 3.5e-02 nm, Epot= -5.96313e+04 Fmax= 6.37273e+02, atom= 2750\n", + "Step= 249, Dmax= 4.2e-02 nm, Epot= -5.96541e+04 Fmax= 1.76496e+02, atom= 2750\n", + "Step= 251, Dmax= 2.5e-02 nm, Epot= -5.96643e+04 Fmax= 2.22371e+02, atom= 2750\n", + "Step= 252, Dmax= 3.0e-02 nm, Epot= -5.96723e+04 Fmax= 2.74291e+02, atom= 2750\n", + "Step= 253, Dmax= 3.7e-02 nm, Epot= -5.96804e+04 Fmax= 3.39338e+02, atom= 2750\n", + "Step= 254, Dmax= 4.4e-02 nm, Epot= -5.96857e+04 Fmax= 3.71865e+02, atom= 2750\n", + "Step= 255, Dmax= 5.3e-02 nm, Epot= -5.96876e+04 Fmax= 5.34522e+02, atom= 2750\n", + "Step= 256, Dmax= 6.3e-02 nm, Epot= -5.96929e+04 Fmax= 4.90829e+02, atom= 2750\n", + "Step= 258, Dmax= 3.8e-02 nm, Epot= -5.97230e+04 Fmax= 1.29100e+02, atom= 1037\n", + "Step= 259, Dmax= 4.5e-02 nm, Epot= -5.97247e+04 Fmax= 5.78329e+02, atom= 1037\n", + "Step= 260, Dmax= 5.5e-02 nm, Epot= -5.97496e+04 Fmax= 3.53992e+02, atom= 1037\n", + "Step= 262, Dmax= 3.3e-02 nm, Epot= -5.97610e+04 Fmax= 1.91255e+02, atom= 1037\n", + "Step= 264, Dmax= 2.0e-02 nm, Epot= -5.97701e+04 Fmax= 1.35681e+02, atom= 1037\n", + "Step= 265, Dmax= 2.4e-02 nm, Epot= -5.97786e+04 Fmax= 2.54210e+02, atom= 1037\n", + "Step= 266, Dmax= 2.8e-02 nm, Epot= -5.97881e+04 Fmax= 2.22014e+02, atom= 1037\n", + "Step= 267, Dmax= 3.4e-02 nm, Epot= -5.97931e+04 Fmax= 3.36883e+02, atom= 1037\n", + "Step= 268, Dmax= 4.1e-02 nm, Epot= -5.98018e+04 Fmax= 3.49815e+02, atom= 1037\n", + "Step= 269, Dmax= 4.9e-02 nm, Epot= -5.98032e+04 Fmax= 4.53508e+02, atom= 1037\n", + "Step= 270, Dmax= 5.9e-02 nm, Epot= -5.98085e+04 Fmax= 5.35072e+02, atom= 1037\n", + "Step= 272, Dmax= 3.5e-02 nm, Epot= -5.98330e+04 Fmax= 8.22722e+01, atom= 2750\n", + "Step= 273, Dmax= 4.2e-02 nm, Epot= -5.98371e+04 Fmax= 8.31920e+02, atom= 2750\n", + "Step= 274, Dmax= 5.1e-02 nm, Epot= -5.98695e+04 Fmax= 1.78990e+02, atom= 2750\n", + "Step= 276, Dmax= 3.0e-02 nm, Epot= -5.98776e+04 Fmax= 2.87462e+02, atom= 2750\n", + "Step= 277, Dmax= 3.6e-02 nm, Epot= -5.98843e+04 Fmax= 3.00568e+02, atom= 2750\n", + "Step= 278, Dmax= 4.4e-02 nm, Epot= -5.98884e+04 Fmax= 4.18449e+02, atom= 2750\n", + "Step= 279, Dmax= 5.3e-02 nm, Epot= -5.98928e+04 Fmax= 4.22419e+02, atom= 2750\n", + "Step= 281, Dmax= 3.2e-02 nm, Epot= -5.99127e+04 Fmax= 8.00841e+01, atom= 1037\n", + "Step= 282, Dmax= 3.8e-02 nm, Epot= -5.99217e+04 Fmax= 5.07395e+02, atom= 1037\n", + "Step= 283, Dmax= 4.5e-02 nm, Epot= -5.99439e+04 Fmax= 2.62831e+02, atom= 1037\n", + "Step= 285, Dmax= 2.7e-02 nm, Epot= -5.99519e+04 Fmax= 1.83905e+02, atom= 1037\n", + "Step= 286, Dmax= 3.3e-02 nm, Epot= -5.99549e+04 Fmax= 3.78590e+02, atom= 1037\n", + "Step= 287, Dmax= 3.9e-02 nm, Epot= -5.99652e+04 Fmax= 2.74147e+02, atom= 1037\n", + "Step= 289, Dmax= 2.4e-02 nm, Epot= -5.99761e+04 Fmax= 1.13455e+02, atom= 1037\n", + "Step= 290, Dmax= 2.8e-02 nm, Epot= -5.99826e+04 Fmax= 3.45366e+02, atom= 1037\n", + "Step= 291, Dmax= 3.4e-02 nm, Epot= -5.99945e+04 Fmax= 2.19360e+02, atom= 1037\n", + "Step= 293, Dmax= 2.0e-02 nm, Epot= -6.00023e+04 Fmax= 1.17656e+02, atom= 1037\n", + "Step= 294, Dmax= 2.4e-02 nm, Epot= -6.00091e+04 Fmax= 3.00515e+02, atom= 1037\n", + "Step= 295, Dmax= 2.9e-02 nm, Epot= -6.00184e+04 Fmax= 1.87183e+02, atom= 1037\n", + "Step= 296, Dmax= 3.5e-02 nm, Epot= -6.00195e+04 Fmax= 4.17089e+02, atom= 1037\n", + "Step= 297, Dmax= 4.2e-02 nm, Epot= -6.00310e+04 Fmax= 2.84840e+02, atom= 1037\n", + "Step= 299, Dmax= 2.5e-02 nm, Epot= -6.00418e+04 Fmax= 1.31955e+02, atom= 1037\n", + "Step= 300, Dmax= 3.0e-02 nm, Epot= -6.00463e+04 Fmax= 3.60137e+02, atom= 1037\n", + "Step= 301, Dmax= 3.6e-02 nm, Epot= -6.00579e+04 Fmax= 2.45266e+02, atom= 1037\n", + "Step= 303, Dmax= 2.2e-02 nm, Epot= -6.00661e+04 Fmax= 1.16807e+02, atom= 1037\n", + "Step= 304, Dmax= 2.6e-02 nm, Epot= -6.00720e+04 Fmax= 3.33042e+02, atom= 1037\n", + "Step= 305, Dmax= 3.1e-02 nm, Epot= -6.00822e+04 Fmax= 1.91207e+02, atom= 1037\n", + "Step= 307, Dmax= 1.9e-02 nm, Epot= -6.00896e+04 Fmax= 1.22868e+02, atom= 1037\n", + "Step= 308, Dmax= 2.3e-02 nm, Epot= -6.00962e+04 Fmax= 2.45731e+02, atom= 1037\n", + "Step= 309, Dmax= 2.7e-02 nm, Epot= -6.01039e+04 Fmax= 2.08716e+02, atom= 1037\n", + "Step= 310, Dmax= 3.3e-02 nm, Epot= -6.01076e+04 Fmax= 3.23587e+02, atom= 1037\n", + "Step= 311, Dmax= 3.9e-02 nm, Epot= -6.01146e+04 Fmax= 3.30965e+02, atom= 1037\n", + "Step= 312, Dmax= 4.7e-02 nm, Epot= -6.01152e+04 Fmax= 4.35908e+02, atom= 1037\n", + "Step= 313, Dmax= 5.6e-02 nm, Epot= -6.01193e+04 Fmax= 5.06340e+02, atom= 1037\n", + "Step= 315, Dmax= 3.4e-02 nm, Epot= -6.01402e+04 Fmax= 6.74224e+01, atom= 2750\n", + "Step= 317, Dmax= 2.0e-02 nm, Epot= -6.01506e+04 Fmax= 2.75903e+02, atom= 1037\n", + "Step= 318, Dmax= 2.4e-02 nm, Epot= -6.01599e+04 Fmax= 1.34990e+02, atom= 1037\n", + "Step= 319, Dmax= 2.9e-02 nm, Epot= -6.01621e+04 Fmax= 3.70568e+02, atom= 1037\n", + "Step= 320, Dmax= 3.5e-02 nm, Epot= -6.01737e+04 Fmax= 2.16357e+02, atom= 1037\n", + "Step= 322, Dmax= 2.1e-02 nm, Epot= -6.01817e+04 Fmax= 1.31919e+02, atom= 1037\n", + "Step= 323, Dmax= 2.5e-02 nm, Epot= -6.01867e+04 Fmax= 2.79645e+02, atom= 1037\n", + "Step= 324, Dmax= 3.0e-02 nm, Epot= -6.01951e+04 Fmax= 2.25485e+02, atom= 1037\n", + "Step= 325, Dmax= 3.6e-02 nm, Epot= -6.01964e+04 Fmax= 3.67171e+02, atom= 1037\n", + "Step= 326, Dmax= 4.4e-02 nm, Epot= -6.02041e+04 Fmax= 3.60232e+02, atom= 1037\n", + "Step= 328, Dmax= 2.6e-02 nm, Epot= -6.02166e+04 Fmax= 7.92455e+01, atom= 1037\n", + "Step= 329, Dmax= 3.1e-02 nm, Epot= -6.02207e+04 Fmax= 4.79290e+02, atom= 1037\n", + "Step= 330, Dmax= 3.8e-02 nm, Epot= -6.02388e+04 Fmax= 1.65514e+02, atom= 1037\n", + "Step= 332, Dmax= 2.3e-02 nm, Epot= -6.02444e+04 Fmax= 2.13497e+02, atom= 1037\n", + "Step= 333, Dmax= 2.7e-02 nm, Epot= -6.02497e+04 Fmax= 2.34472e+02, atom= 1037\n", + "Step= 334, Dmax= 3.3e-02 nm, Epot= -6.02538e+04 Fmax= 3.14438e+02, atom= 1037\n", + "Step= 335, Dmax= 3.9e-02 nm, Epot= -6.02584e+04 Fmax= 3.29824e+02, atom= 1037\n", + "Step= 336, Dmax= 4.7e-02 nm, Epot= -6.02588e+04 Fmax= 4.61035e+02, atom= 1037\n", + "Step= 337, Dmax= 5.6e-02 nm, Epot= -6.02622e+04 Fmax= 4.64117e+02, atom= 1037\n", + "Step= 339, Dmax= 3.4e-02 nm, Epot= -6.02836e+04 Fmax= 8.26266e+01, atom= 1037\n", + "Step= 340, Dmax= 4.1e-02 nm, Epot= -6.02865e+04 Fmax= 5.54988e+02, atom= 1037\n", + "Step= 341, Dmax= 4.9e-02 nm, Epot= -6.03081e+04 Fmax= 2.47292e+02, atom= 1037\n", + "Step= 343, Dmax= 2.9e-02 nm, Epot= -6.03138e+04 Fmax= 2.30271e+02, atom= 1037\n", + "Step= 344, Dmax= 3.5e-02 nm, Epot= -6.03161e+04 Fmax= 3.58030e+02, atom= 1037\n", + "Step= 345, Dmax= 4.2e-02 nm, Epot= -6.03217e+04 Fmax= 3.34048e+02, atom= 1037\n", + "Step= 347, Dmax= 2.5e-02 nm, Epot= -6.03334e+04 Fmax= 7.76801e+01, atom= 1037\n", + "Step= 348, Dmax= 3.0e-02 nm, Epot= -6.03398e+04 Fmax= 4.07179e+02, atom= 1037\n", + "Step= 349, Dmax= 3.6e-02 nm, Epot= -6.03535e+04 Fmax= 1.90604e+02, atom= 1037\n", + "Step= 351, Dmax= 2.2e-02 nm, Epot= -6.03590e+04 Fmax= 1.67562e+02, atom= 1037\n", + "Step= 352, Dmax= 2.6e-02 nm, Epot= -6.03628e+04 Fmax= 2.72241e+02, atom= 1037\n", + "Step= 353, Dmax= 3.1e-02 nm, Epot= -6.03686e+04 Fmax= 2.45528e+02, atom= 1037\n", + "Step= 354, Dmax= 3.8e-02 nm, Epot= -6.03690e+04 Fmax= 3.89593e+02, atom= 1037\n", + "Step= 355, Dmax= 4.5e-02 nm, Epot= -6.03747e+04 Fmax= 3.56036e+02, atom= 1037\n", + "Step= 357, Dmax= 2.7e-02 nm, Epot= -6.03881e+04 Fmax= 8.61068e+01, atom= 1037\n", + "Step= 358, Dmax= 3.3e-02 nm, Epot= -6.03886e+04 Fmax= 4.35313e+02, atom= 1037\n", + "Step= 359, Dmax= 3.9e-02 nm, Epot= -6.04053e+04 Fmax= 2.07639e+02, atom= 1037\n", + "Step= 361, Dmax= 2.3e-02 nm, Epot= -6.04109e+04 Fmax= 1.78364e+02, atom= 1037\n", + "Step= 362, Dmax= 2.8e-02 nm, Epot= -6.04121e+04 Fmax= 2.95268e+02, atom= 1037\n", + "Step= 363, Dmax= 3.4e-02 nm, Epot= -6.04179e+04 Fmax= 2.62369e+02, atom= 1037\n", + "Step= 365, Dmax= 2.0e-02 nm, Epot= -6.04286e+04 Fmax= 7.02098e+01, atom= 1037\n", + "Step= 367, Dmax= 1.2e-02 nm, Epot= -6.04340e+04 Fmax= 1.27299e+02, atom= 1037\n", + "Step= 368, Dmax= 1.5e-02 nm, Epot= -6.04391e+04 Fmax= 1.16376e+02, atom= 1037\n", + "Step= 369, Dmax= 1.7e-02 nm, Epot= -6.04420e+04 Fmax= 1.70247e+02, atom= 1037\n", + "Step= 370, Dmax= 2.1e-02 nm, Epot= -6.04457e+04 Fmax= 1.82795e+02, atom= 1949\n", + "Step= 372, Dmax= 1.3e-02 nm, Epot= -6.04557e+04 Fmax= 3.24653e+01, atom= 1223\n", + "Step= 373, Dmax= 1.5e-02 nm, Epot= -6.04636e+04 Fmax= 2.56892e+02, atom= 1223\n", + "Step= 374, Dmax= 1.8e-02 nm, Epot= -6.04776e+04 Fmax= 7.03043e+01, atom= 1223\n", + "Step= 376, Dmax= 1.1e-02 nm, Epot= -6.04828e+04 Fmax= 1.18501e+02, atom= 1223\n", + "Step= 377, Dmax= 1.3e-02 nm, Epot= -6.04876e+04 Fmax= 1.07331e+02, atom= 1223\n", + "Step= 378, Dmax= 1.6e-02 nm, Epot= -6.04915e+04 Fmax= 1.70629e+02, atom= 1223\n", + "Step= 379, Dmax= 1.9e-02 nm, Epot= -6.04965e+04 Fmax= 1.56634e+02, atom= 1223\n", + "Step= 380, Dmax= 2.3e-02 nm, Epot= -6.04986e+04 Fmax= 2.41043e+02, atom= 1223\n", + "Step= 381, Dmax= 2.7e-02 nm, Epot= -6.05037e+04 Fmax= 2.29850e+02, atom= 1223\n", + "Step= 383, Dmax= 1.6e-02 nm, Epot= -6.05126e+04 Fmax= 5.26314e+01, atom= 1223\n", + "Step= 384, Dmax= 1.9e-02 nm, Epot= -6.05193e+04 Fmax= 2.92343e+02, atom= 1223\n", + "Step= 385, Dmax= 2.3e-02 nm, Epot= -6.05295e+04 Fmax= 1.30780e+02, atom= 1223\n", + "Step= 387, Dmax= 1.4e-02 nm, Epot= -6.05342e+04 Fmax= 1.05053e+02, atom= 1223\n", + "Step= 388, Dmax= 1.7e-02 nm, Epot= -6.05381e+04 Fmax= 1.89563e+02, atom= 1223\n", + "Step= 389, Dmax= 2.0e-02 nm, Epot= -6.05433e+04 Fmax= 1.57603e+02, atom= 1223\n", + "Step= 390, Dmax= 2.4e-02 nm, Epot= -6.05448e+04 Fmax= 2.65033e+02, atom= 1223\n", + "Step= 391, Dmax= 2.9e-02 nm, Epot= -6.05503e+04 Fmax= 2.37203e+02, atom= 1223\n", + "Step= 393, Dmax= 1.7e-02 nm, Epot= -6.05586e+04 Fmax= 6.57889e+01, atom= 1223\n", + "Step= 394, Dmax= 2.1e-02 nm, Epot= -6.05627e+04 Fmax= 3.05352e+02, atom= 1223\n", + "Step= 395, Dmax= 2.5e-02 nm, Epot= -6.05727e+04 Fmax= 1.44005e+02, atom= 1223\n", + "Step= 397, Dmax= 1.5e-02 nm, Epot= -6.05773e+04 Fmax= 1.08536e+02, atom= 1223\n", + "Step= 398, Dmax= 1.8e-02 nm, Epot= -6.05807e+04 Fmax= 2.07503e+02, atom= 1223\n", + "Step= 399, Dmax= 2.2e-02 nm, Epot= -6.05861e+04 Fmax= 1.64592e+02, atom= 1223\n", + "Step= 400, Dmax= 2.6e-02 nm, Epot= -6.05864e+04 Fmax= 2.88908e+02, atom= 1223\n", + "Step= 401, Dmax= 3.1e-02 nm, Epot= -6.05924e+04 Fmax= 2.49418e+02, atom= 1223\n", + "Step= 403, Dmax= 1.9e-02 nm, Epot= -6.06012e+04 Fmax= 7.42693e+01, atom= 1223\n", + "Step= 404, Dmax= 2.3e-02 nm, Epot= -6.06030e+04 Fmax= 3.24604e+02, atom= 1223\n", + "Step= 405, Dmax= 2.7e-02 nm, Epot= -6.06140e+04 Fmax= 1.57066e+02, atom= 1223\n", + "Step= 407, Dmax= 1.6e-02 nm, Epot= -6.06188e+04 Fmax= 1.13301e+02, atom= 1223\n", + "Step= 408, Dmax= 1.9e-02 nm, Epot= -6.06213e+04 Fmax= 2.26259e+02, atom= 1223\n", + "Step= 409, Dmax= 2.3e-02 nm, Epot= -6.06271e+04 Fmax= 1.72987e+02, atom= 1223\n", + "Step= 411, Dmax= 1.4e-02 nm, Epot= -6.06328e+04 Fmax= 6.94849e+01, atom= 1223\n", + "Step= 412, Dmax= 1.7e-02 nm, Epot= -6.06371e+04 Fmax= 2.19846e+02, atom= 1223\n", + "Step= 413, Dmax= 2.0e-02 nm, Epot= -6.06437e+04 Fmax= 1.33677e+02, atom= 1223\n", + "Step= 414, Dmax= 2.4e-02 nm, Epot= -6.06437e+04 Fmax= 2.86011e+02, atom= 1223\n", + "Step= 415, Dmax= 2.9e-02 nm, Epot= -6.06508e+04 Fmax= 2.16489e+02, atom= 1223\n", + "Step= 417, Dmax= 1.7e-02 nm, Epot= -6.06582e+04 Fmax= 7.43573e+01, atom= 1223\n", + "Step= 418, Dmax= 2.1e-02 nm, Epot= -6.06584e+04 Fmax= 3.06738e+02, atom= 1223\n", + "Step= 419, Dmax= 2.5e-02 nm, Epot= -6.06699e+04 Fmax= 1.31746e+02, atom= 1223\n", + "Step= 421, Dmax= 1.5e-02 nm, Epot= -6.06743e+04 Fmax= 1.24125e+02, atom= 1223\n", + "Step= 422, Dmax= 1.8e-02 nm, Epot= -6.06772e+04 Fmax= 1.85336e+02, atom= 1223\n", + "Step= 423, Dmax= 2.2e-02 nm, Epot= -6.06812e+04 Fmax= 1.91020e+02, atom= 1223\n", + "Step= 424, Dmax= 2.6e-02 nm, Epot= -6.06825e+04 Fmax= 2.56809e+02, atom= 1223\n", + "Step= 425, Dmax= 3.1e-02 nm, Epot= -6.06852e+04 Fmax= 2.81063e+02, atom= 1223\n", + "Step= 427, Dmax= 1.9e-02 nm, Epot= -6.06969e+04 Fmax= 5.07303e+01, atom= 2326\n", + "Step= 428, Dmax= 2.2e-02 nm, Epot= -6.07028e+04 Fmax= 3.54027e+02, atom= 2326\n", + "Step= 429, Dmax= 2.7e-02 nm, Epot= -6.07137e+04 Fmax= 1.30348e+02, atom= 1223\n", + "Step= 431, Dmax= 1.6e-02 nm, Epot= -6.07179e+04 Fmax= 1.33923e+02, atom= 1223\n", + "Step= 432, Dmax= 1.9e-02 nm, Epot= -6.07204e+04 Fmax= 1.96251e+02, atom= 1223\n", + "Step= 433, Dmax= 2.3e-02 nm, Epot= -6.07244e+04 Fmax= 2.06369e+02, atom= 1223\n", + "Step= 434, Dmax= 2.8e-02 nm, Epot= -6.07254e+04 Fmax= 2.73626e+02, atom= 1223\n", + "Step= 435, Dmax= 3.4e-02 nm, Epot= -6.07282e+04 Fmax= 3.02467e+02, atom= 1223\n", + "Step= 437, Dmax= 2.0e-02 nm, Epot= -6.07402e+04 Fmax= 6.05849e+01, atom= 2326\n", + "Step= 438, Dmax= 2.4e-02 nm, Epot= -6.07457e+04 Fmax= 3.65725e+02, atom= 2326\n", + "Step= 439, Dmax= 2.9e-02 nm, Epot= -6.07549e+04 Fmax= 1.42202e+02, atom= 2326\n", + "Step= 441, Dmax= 1.7e-02 nm, Epot= -6.07592e+04 Fmax= 1.38473e+02, atom= 1223\n", + "Step= 442, Dmax= 2.1e-02 nm, Epot= -6.07611e+04 Fmax= 2.15298e+02, atom= 1223\n", + "Step= 443, Dmax= 2.5e-02 nm, Epot= -6.07657e+04 Fmax= 2.15387e+02, atom= 1223\n", + "Step= 445, Dmax= 1.5e-02 nm, Epot= -6.07728e+04 Fmax= 5.21423e+01, atom= 2326\n", + "Step= 446, Dmax= 1.8e-02 nm, Epot= -6.07796e+04 Fmax= 2.56476e+02, atom= 2326\n", + "Step= 447, Dmax= 2.2e-02 nm, Epot= -6.07864e+04 Fmax= 1.17198e+02, atom= 1223\n", + "Step= 449, Dmax= 1.3e-02 nm, Epot= -6.07907e+04 Fmax= 9.99643e+01, atom= 1223\n", + "Step= 450, Dmax= 1.6e-02 nm, Epot= -6.07940e+04 Fmax= 1.64265e+02, atom= 1223\n", + "Step= 451, Dmax= 1.9e-02 nm, Epot= -6.07984e+04 Fmax= 1.60225e+02, atom= 1223\n", + "Step= 452, Dmax= 2.2e-02 nm, Epot= -6.08005e+04 Fmax= 2.22581e+02, atom= 1223\n", + "Step= 453, Dmax= 2.7e-02 nm, Epot= -6.08042e+04 Fmax= 2.41085e+02, atom= 1223\n", + "Step= 454, Dmax= 3.2e-02 nm, Epot= -6.08045e+04 Fmax= 3.11641e+02, atom= 1223\n", + "Step= 455, Dmax= 3.9e-02 nm, Epot= -6.08066e+04 Fmax= 3.48347e+02, atom= 1223\n", + "Step= 457, Dmax= 2.3e-02 nm, Epot= -6.08208e+04 Fmax= 6.99340e+01, atom= 2326\n", + "Step= 458, Dmax= 2.8e-02 nm, Epot= -6.08238e+04 Fmax= 4.30790e+02, atom= 2326\n", + "Step= 459, Dmax= 3.4e-02 nm, Epot= -6.08347e+04 Fmax= 1.58143e+02, atom= 2326\n", + "Step= 461, Dmax= 2.0e-02 nm, Epot= -6.08390e+04 Fmax= 1.59487e+02, atom= 2327\n", + "Step= 462, Dmax= 2.4e-02 nm, Epot= -6.08398e+04 Fmax= 2.41392e+02, atom= 1223\n", + "Step= 463, Dmax= 2.9e-02 nm, Epot= -6.08440e+04 Fmax= 2.52208e+02, atom= 1223\n", + "Step= 465, Dmax= 1.7e-02 nm, Epot= -6.08533e+04 Fmax= 6.02601e+01, atom= 2326\n", + "Step= 466, Dmax= 2.1e-02 nm, Epot= -6.08591e+04 Fmax= 2.91071e+02, atom= 2326\n", + "Step= 467, Dmax= 2.5e-02 nm, Epot= -6.08663e+04 Fmax= 1.35117e+02, atom= 2326\n", + "Step= 469, Dmax= 1.5e-02 nm, Epot= -6.08708e+04 Fmax= 1.09440e+02, atom= 2327\n", + "Step= 470, Dmax= 1.8e-02 nm, Epot= -6.08733e+04 Fmax= 1.90966e+02, atom= 1223\n", + "Step= 471, Dmax= 2.2e-02 nm, Epot= -6.08780e+04 Fmax= 1.81492e+02, atom= 1223\n", + "Step= 472, Dmax= 2.6e-02 nm, Epot= -6.08789e+04 Fmax= 2.58389e+02, atom= 1223\n", + "Step= 473, Dmax= 3.1e-02 nm, Epot= -6.08827e+04 Fmax= 2.73250e+02, atom= 1223\n", + "Step= 475, Dmax= 1.9e-02 nm, Epot= -6.08927e+04 Fmax= 5.96241e+01, atom= 2326\n", + "Step= 476, Dmax= 2.2e-02 nm, Epot= -6.08978e+04 Fmax= 3.29611e+02, atom= 2326\n", + "Step= 477, Dmax= 2.7e-02 nm, Epot= -6.09063e+04 Fmax= 1.34986e+02, atom= 2326\n", + "Step= 479, Dmax= 1.6e-02 nm, Epot= -6.09107e+04 Fmax= 1.24750e+02, atom= 2327\n", + "Step= 480, Dmax= 1.9e-02 nm, Epot= -6.09128e+04 Fmax= 1.97233e+02, atom= 1223\n", + "Step= 481, Dmax= 2.3e-02 nm, Epot= -6.09170e+04 Fmax= 2.01198e+02, atom= 1223\n", + "Step= 482, Dmax= 2.8e-02 nm, Epot= -6.09176e+04 Fmax= 2.70444e+02, atom= 1223\n", + "Step= 483, Dmax= 3.3e-02 nm, Epot= -6.09205e+04 Fmax= 2.98919e+02, atom= 1223\n", + "Step= 485, Dmax= 2.0e-02 nm, Epot= -6.09324e+04 Fmax= 6.28237e+01, atom= 2326\n", + "Step= 486, Dmax= 2.4e-02 nm, Epot= -6.09374e+04 Fmax= 3.51108e+02, atom= 2326\n", + "Step= 487, Dmax= 2.9e-02 nm, Epot= -6.09460e+04 Fmax= 1.44706e+02, atom= 2326\n", + "Step= 489, Dmax= 1.7e-02 nm, Epot= -6.09503e+04 Fmax= 1.35641e+02, atom= 2327\n", + "Step= 490, Dmax= 2.1e-02 nm, Epot= -6.09523e+04 Fmax= 2.04670e+02, atom= 2327\n", + "Step= 491, Dmax= 2.5e-02 nm, Epot= -6.09560e+04 Fmax= 2.16173e+02, atom= 1223\n", + "Step= 493, Dmax= 1.5e-02 nm, Epot= -6.09637e+04 Fmax= 5.23354e+01, atom= 2326\n", + "Step= 494, Dmax= 1.8e-02 nm, Epot= -6.09703e+04 Fmax= 2.48278e+02, atom= 2326\n", + "Step= 495, Dmax= 2.2e-02 nm, Epot= -6.09767e+04 Fmax= 1.17648e+02, atom= 2326\n", + "Step= 497, Dmax= 1.3e-02 nm, Epot= -6.09810e+04 Fmax= 9.57970e+01, atom= 2327\n", + "Step= 498, Dmax= 1.6e-02 nm, Epot= -6.09842e+04 Fmax= 1.56906e+02, atom= 1223\n", + "Step= 499, Dmax= 1.9e-02 nm, Epot= -6.09882e+04 Fmax= 1.64292e+02, atom= 1223\n", + "Step= 500, Dmax= 2.2e-02 nm, Epot= -6.09903e+04 Fmax= 2.12035e+02, atom= 1223\n", + "Step= 501, Dmax= 2.7e-02 nm, Epot= -6.09931e+04 Fmax= 2.46997e+02, atom= 1223\n", + "Step= 502, Dmax= 3.2e-02 nm, Epot= -6.09936e+04 Fmax= 2.96341e+02, atom= 1223\n", + "Step= 503, Dmax= 3.9e-02 nm, Epot= -6.09937e+04 Fmax= 3.56965e+02, atom= 1223\n", + "Step= 505, Dmax= 2.3e-02 nm, Epot= -6.10108e+04 Fmax= 6.71921e+01, atom= 2326\n", + "Step= 506, Dmax= 2.8e-02 nm, Epot= -6.10157e+04 Fmax= 4.04859e+02, atom= 2326\n", + "Step= 507, Dmax= 3.3e-02 nm, Epot= -6.10247e+04 Fmax= 1.62177e+02, atom= 2326\n", + "Step= 509, Dmax= 2.0e-02 nm, Epot= -6.10290e+04 Fmax= 1.63104e+02, atom= 2327\n", + "Step= 510, Dmax= 2.4e-02 nm, Epot= -6.10306e+04 Fmax= 2.28723e+02, atom= 2327\n", + "Step= 511, Dmax= 2.9e-02 nm, Epot= -6.10336e+04 Fmax= 2.46947e+02, atom= 2327\n", + "Step= 513, Dmax= 1.7e-02 nm, Epot= -6.10428e+04 Fmax= 6.12178e+01, atom= 2326\n", + "Step= 514, Dmax= 2.1e-02 nm, Epot= -6.10473e+04 Fmax= 2.91723e+02, atom= 2326\n", + "Step= 515, Dmax= 2.5e-02 nm, Epot= -6.10550e+04 Fmax= 1.31883e+02, atom= 2326\n", + "Step= 517, Dmax= 1.5e-02 nm, Epot= -6.10593e+04 Fmax= 1.15556e+02, atom= 2327\n", + "Step= 518, Dmax= 1.8e-02 nm, Epot= -6.10619e+04 Fmax= 1.74574e+02, atom= 2327\n", + "Step= 519, Dmax= 2.2e-02 nm, Epot= -6.10655e+04 Fmax= 1.83451e+02, atom= 2327\n", + "Step= 520, Dmax= 2.6e-02 nm, Epot= -6.10659e+04 Fmax= 2.47827e+02, atom= 2327\n", + "Step= 521, Dmax= 3.1e-02 nm, Epot= -6.10684e+04 Fmax= 2.73296e+02, atom= 1223\n", + "Step= 523, Dmax= 1.9e-02 nm, Epot= -6.10802e+04 Fmax= 6.18504e+01, atom= 2326\n", + "Step= 524, Dmax= 2.2e-02 nm, Epot= -6.10843e+04 Fmax= 3.14941e+02, atom= 2326\n", + "Step= 525, Dmax= 2.7e-02 nm, Epot= -6.10925e+04 Fmax= 1.38163e+02, atom= 2326\n", + "Step= 527, Dmax= 1.6e-02 nm, Epot= -6.10968e+04 Fmax= 1.27977e+02, atom= 2327\n", + "Step= 528, Dmax= 1.9e-02 nm, Epot= -6.10990e+04 Fmax= 1.84856e+02, atom= 2327\n", + "Step= 529, Dmax= 2.3e-02 nm, Epot= -6.11021e+04 Fmax= 1.99339e+02, atom= 2327\n", + "Step= 531, Dmax= 1.4e-02 nm, Epot= -6.11093e+04 Fmax= 4.64262e+01, atom= 2326\n", + "Step= 532, Dmax= 1.7e-02 nm, Epot= -6.11156e+04 Fmax= 2.30252e+02, atom= 2326\n", + "Step= 533, Dmax= 2.0e-02 nm, Epot= -6.11221e+04 Fmax= 1.07528e+02, atom= 2326\n", + "Step= 535, Dmax= 1.2e-02 nm, Epot= -6.11259e+04 Fmax= 9.38625e+01, atom= 2327\n", + "Step= 536, Dmax= 1.4e-02 nm, Epot= -6.11291e+04 Fmax= 1.40430e+02, atom= 2327\n", + "Step= 537, Dmax= 1.7e-02 nm, Epot= -6.11325e+04 Fmax= 1.48252e+02, atom= 2327\n", + "Step= 538, Dmax= 2.1e-02 nm, Epot= -6.11340e+04 Fmax= 1.97714e+02, atom= 2327\n", + "Step= 539, Dmax= 2.5e-02 nm, Epot= -6.11365e+04 Fmax= 2.16855e+02, atom= 1223\n", + "Step= 541, Dmax= 1.5e-02 nm, Epot= -6.11456e+04 Fmax= 4.98271e+01, atom= 2326\n", + "Step= 542, Dmax= 1.8e-02 nm, Epot= -6.11506e+04 Fmax= 2.48533e+02, atom= 2326\n", + "Step= 543, Dmax= 2.2e-02 nm, Epot= -6.11577e+04 Fmax= 1.13798e+02, atom= 2326\n", + "Step= 545, Dmax= 1.3e-02 nm, Epot= -6.11615e+04 Fmax= 1.02535e+02, atom= 2327\n", + "Step= 546, Dmax= 1.5e-02 nm, Epot= -6.11641e+04 Fmax= 1.49348e+02, atom= 2327\n", + "Step= 547, Dmax= 1.9e-02 nm, Epot= -6.11672e+04 Fmax= 1.60635e+02, atom= 2327\n", + "Step= 548, Dmax= 2.2e-02 nm, Epot= -6.11681e+04 Fmax= 2.10958e+02, atom= 2327\n", + "Step= 549, Dmax= 2.7e-02 nm, Epot= -6.11699e+04 Fmax= 2.31711e+02, atom= 2327\n", + "Step= 551, Dmax= 1.6e-02 nm, Epot= -6.11808e+04 Fmax= 5.42368e+01, atom= 2326\n", + "Step= 552, Dmax= 1.9e-02 nm, Epot= -6.11837e+04 Fmax= 2.69126e+02, atom= 2326\n", + "Step= 553, Dmax= 2.3e-02 nm, Epot= -6.11920e+04 Fmax= 1.20699e+02, atom= 2326\n", + "Step= 555, Dmax= 1.4e-02 nm, Epot= -6.11958e+04 Fmax= 1.12091e+02, atom= 2327\n", + "Step= 556, Dmax= 1.7e-02 nm, Epot= -6.11980e+04 Fmax= 1.57795e+02, atom= 2327\n", + "Step= 557, Dmax= 2.0e-02 nm, Epot= -6.12007e+04 Fmax= 1.74921e+02, atom= 2327\n", + "Step= 558, Dmax= 2.4e-02 nm, Epot= -6.12009e+04 Fmax= 2.23417e+02, atom= 2327\n", + "Step= 559, Dmax= 2.9e-02 nm, Epot= -6.12016e+04 Fmax= 2.51672e+02, atom= 2327\n", + "Step= 561, Dmax= 1.7e-02 nm, Epot= -6.12149e+04 Fmax= 5.52209e+01, atom= 2326\n", + "Step= 562, Dmax= 2.1e-02 nm, Epot= -6.12168e+04 Fmax= 2.93120e+02, atom= 2326\n", + "Step= 563, Dmax= 2.5e-02 nm, Epot= -6.12263e+04 Fmax= 1.26087e+02, atom= 2326\n", + "Step= 565, Dmax= 1.5e-02 nm, Epot= -6.12300e+04 Fmax= 1.24136e+02, atom= 2327\n", + "Step= 566, Dmax= 1.8e-02 nm, Epot= -6.12320e+04 Fmax= 1.65719e+02, atom= 2327\n", + "Step= 567, Dmax= 2.1e-02 nm, Epot= -6.12341e+04 Fmax= 1.91486e+02, atom= 2327\n", + "Step= 568, Dmax= 2.6e-02 nm, Epot= -6.12342e+04 Fmax= 2.35788e+02, atom= 2327\n", + "Step= 570, Dmax= 1.5e-02 nm, Epot= -6.12457e+04 Fmax= 3.28485e+01, atom= 1949\n", + "Step= 571, Dmax= 1.9e-02 nm, Epot= -6.12528e+04 Fmax= 3.12952e+02, atom= 1949\n", + "Step= 572, Dmax= 2.2e-02 nm, Epot= -6.12635e+04 Fmax= 8.37420e+01, atom= 1949\n", + "Step= 574, Dmax= 1.3e-02 nm, Epot= -6.12669e+04 Fmax= 1.46378e+02, atom= 1949\n", + "Step= 575, Dmax= 1.6e-02 nm, Epot= -6.12704e+04 Fmax= 1.24146e+02, atom= 1949\n", + "Step= 576, Dmax= 1.9e-02 nm, Epot= -6.12724e+04 Fmax= 2.11671e+02, atom= 1949\n", + "Step= 577, Dmax= 2.3e-02 nm, Epot= -6.12763e+04 Fmax= 1.78723e+02, atom= 1949\n", + "Step= 579, Dmax= 1.4e-02 nm, Epot= -6.12815e+04 Fmax= 5.08404e+01, atom= 1949\n", + "Step= 580, Dmax= 1.7e-02 nm, Epot= -6.12853e+04 Fmax= 2.25402e+02, atom= 1949\n", + "Step= 581, Dmax= 2.0e-02 nm, Epot= -6.12922e+04 Fmax= 1.14717e+02, atom= 1949\n", + "Step= 583, Dmax= 1.2e-02 nm, Epot= -6.12957e+04 Fmax= 8.96617e+01, atom= 1949\n", + "Step= 584, Dmax= 1.4e-02 nm, Epot= -6.12986e+04 Fmax= 1.61616e+02, atom= 1949\n", + "Step= 585, Dmax= 1.7e-02 nm, Epot= -6.13024e+04 Fmax= 1.31872e+02, atom= 1949\n", + "Step= 586, Dmax= 2.1e-02 nm, Epot= -6.13036e+04 Fmax= 2.31553e+02, atom= 1949\n", + "Step= 587, Dmax= 2.5e-02 nm, Epot= -6.13080e+04 Fmax= 1.89964e+02, atom= 1949\n", + "Step= 589, Dmax= 1.5e-02 nm, Epot= -6.13136e+04 Fmax= 5.63080e+01, atom= 1949\n", + "Step= 590, Dmax= 1.8e-02 nm, Epot= -6.13161e+04 Fmax= 2.41869e+02, atom= 1949\n", + "Step= 591, Dmax= 2.1e-02 nm, Epot= -6.13239e+04 Fmax= 1.23513e+02, atom= 1949\n", + "Step= 593, Dmax= 1.3e-02 nm, Epot= -6.13275e+04 Fmax= 9.63505e+01, atom= 1949\n", + "Step= 594, Dmax= 1.5e-02 nm, Epot= -6.13300e+04 Fmax= 1.73277e+02, atom= 1949\n", + "Step= 595, Dmax= 1.9e-02 nm, Epot= -6.13339e+04 Fmax= 1.42028e+02, atom= 1949\n", + "Step= 596, Dmax= 2.2e-02 nm, Epot= -6.13347e+04 Fmax= 2.48073e+02, atom= 1949\n", + "Step= 597, Dmax= 2.7e-02 nm, Epot= -6.13392e+04 Fmax= 2.04293e+02, atom= 1949\n", + "Step= 599, Dmax= 1.6e-02 nm, Epot= -6.13453e+04 Fmax= 5.91080e+01, atom= 1949\n", + "Step= 600, Dmax= 1.9e-02 nm, Epot= -6.13467e+04 Fmax= 2.61541e+02, atom= 1949\n", + "Step= 601, Dmax= 2.3e-02 nm, Epot= -6.13554e+04 Fmax= 1.30293e+02, atom= 1949\n", + "Step= 603, Dmax= 1.4e-02 nm, Epot= -6.13590e+04 Fmax= 1.05596e+02, atom= 1949\n", + "Step= 604, Dmax= 1.7e-02 nm, Epot= -6.13612e+04 Fmax= 1.83230e+02, atom= 1949\n", + "Step= 605, Dmax= 2.0e-02 nm, Epot= -6.13651e+04 Fmax= 1.54879e+02, atom= 1949\n", + "Step= 606, Dmax= 2.4e-02 nm, Epot= -6.13653e+04 Fmax= 2.63165e+02, atom= 1949\n", + "Step= 607, Dmax= 2.9e-02 nm, Epot= -6.13698e+04 Fmax= 2.21558e+02, atom= 1949\n", + "Step= 609, Dmax= 1.7e-02 nm, Epot= -6.13767e+04 Fmax= 6.02873e+01, atom= 1949\n", + "Step= 611, Dmax= 1.0e-02 nm, Epot= -6.13804e+04 Fmax= 1.15753e+02, atom= 1949\n", + "Step= 612, Dmax= 1.2e-02 nm, Epot= -6.13838e+04 Fmax= 9.54349e+01, atom= 1949\n", + "Step= 613, Dmax= 1.5e-02 nm, Epot= -6.13864e+04 Fmax= 1.54037e+02, atom= 1949\n", + "Step= 614, Dmax= 1.8e-02 nm, Epot= -6.13899e+04 Fmax= 1.50894e+02, atom= 1949\n", + "Step= 615, Dmax= 2.1e-02 nm, Epot= -6.13913e+04 Fmax= 2.07060e+02, atom= 1949\n", + "Step= 616, Dmax= 2.6e-02 nm, Epot= -6.13939e+04 Fmax= 2.35138e+02, atom= 1949\n", + "Step= 617, Dmax= 3.1e-02 nm, Epot= -6.13943e+04 Fmax= 2.78445e+02, atom= 1949\n", + "Step= 619, Dmax= 1.8e-02 nm, Epot= -6.14049e+04 Fmax= 2.74896e+01, atom= 3323\n", + "Step= 620, Dmax= 2.2e-02 nm, Epot= -6.14121e+04 Fmax= 3.33049e+02, atom= 3323\n", + "Step= 621, Dmax= 2.7e-02 nm, Epot= -6.14272e+04 Fmax= 1.25677e+02, atom= 1949\n", + "Step= 623, Dmax= 1.6e-02 nm, Epot= -6.14299e+04 Fmax= 1.41946e+02, atom= 1949\n", + "Step= 624, Dmax= 1.9e-02 nm, Epot= -6.14319e+04 Fmax= 1.91541e+02, atom= 1949\n", + "Step= 625, Dmax= 2.3e-02 nm, Epot= -6.14346e+04 Fmax= 1.97188e+02, atom= 1949\n", + "Step= 627, Dmax= 1.4e-02 nm, Epot= -6.14412e+04 Fmax= 3.12574e+01, atom= 3323\n", + "Step= 628, Dmax= 1.7e-02 nm, Epot= -6.14471e+04 Fmax= 2.47294e+02, atom= 1949\n", + "Step= 629, Dmax= 2.0e-02 nm, Epot= -6.14568e+04 Fmax= 9.19825e+01, atom= 1949\n", + "Step= 631, Dmax= 1.2e-02 nm, Epot= -6.14598e+04 Fmax= 1.09206e+02, atom= 1949\n", + "Step= 632, Dmax= 1.4e-02 nm, Epot= -6.14627e+04 Fmax= 1.36560e+02, atom= 1949\n", + "Step= 633, Dmax= 1.7e-02 nm, Epot= -6.14654e+04 Fmax= 1.53138e+02, atom= 1949\n", + "Step= 634, Dmax= 2.1e-02 nm, Epot= -6.14674e+04 Fmax= 2.01566e+02, atom= 1949\n", + "Step= 635, Dmax= 2.5e-02 nm, Epot= -6.14699e+04 Fmax= 2.13372e+02, atom= 1949\n", + "Step= 637, Dmax= 1.5e-02 nm, Epot= -6.14770e+04 Fmax= 3.05146e+01, atom= 3323\n", + "Step= 638, Dmax= 1.8e-02 nm, Epot= -6.14823e+04 Fmax= 2.71011e+02, atom= 1949\n", + "Step= 639, Dmax= 2.1e-02 nm, Epot= -6.14939e+04 Fmax= 9.39666e+01, atom= 1949\n", + "Step= 641, Dmax= 1.3e-02 nm, Epot= -6.14968e+04 Fmax= 1.21082e+02, atom= 1949\n", + "Step= 642, Dmax= 1.5e-02 nm, Epot= -6.14997e+04 Fmax= 1.42449e+02, atom= 1949\n", + "Step= 643, Dmax= 1.8e-02 nm, Epot= -6.15021e+04 Fmax= 1.67905e+02, atom= 1949\n", + "Step= 644, Dmax= 2.2e-02 nm, Epot= -6.15040e+04 Fmax= 2.12542e+02, atom= 1949\n", + "Step= 645, Dmax= 2.7e-02 nm, Epot= -6.15060e+04 Fmax= 2.31949e+02, atom= 1949\n", + "Step= 647, Dmax= 1.6e-02 nm, Epot= -6.15144e+04 Fmax= 3.02890e+01, atom= 3323\n", + "Step= 648, Dmax= 1.9e-02 nm, Epot= -6.15187e+04 Fmax= 2.87664e+02, atom= 1949\n", + "Step= 649, Dmax= 2.3e-02 nm, Epot= -6.15322e+04 Fmax= 1.07222e+02, atom= 1949\n", + "Step= 651, Dmax= 1.4e-02 nm, Epot= -6.15352e+04 Fmax= 1.23671e+02, atom= 1949\n", + "Step= 652, Dmax= 1.7e-02 nm, Epot= -6.15376e+04 Fmax= 1.60224e+02, atom= 1949\n", + "Step= 653, Dmax= 2.0e-02 nm, Epot= -6.15403e+04 Fmax= 1.73212e+02, atom= 1949\n", + "Step= 654, Dmax= 2.4e-02 nm, Epot= -6.15413e+04 Fmax= 2.36454e+02, atom= 1949\n", + "Step= 655, Dmax= 2.9e-02 nm, Epot= -6.15439e+04 Fmax= 2.40930e+02, atom= 1949\n", + "Step= 657, Dmax= 1.7e-02 nm, Epot= -6.15530e+04 Fmax= 3.99922e+01, atom= 3323\n", + "Step= 659, Dmax= 1.0e-02 nm, Epot= -6.15576e+04 Fmax= 1.33768e+02, atom= 1949\n", + "Step= 660, Dmax= 1.2e-02 nm, Epot= -6.15620e+04 Fmax= 7.56548e+01, atom= 1949\n", + "Step= 661, Dmax= 1.5e-02 nm, Epot= -6.15640e+04 Fmax= 1.71268e+02, atom= 1949\n", + "Step= 662, Dmax= 1.8e-02 nm, Epot= -6.15687e+04 Fmax= 1.29578e+02, atom= 1949\n", + "Step= 664, Dmax= 1.1e-02 nm, Epot= -6.15731e+04 Fmax= 5.24324e+01, atom= 1949\n", + "Step= 665, Dmax= 1.3e-02 nm, Epot= -6.15767e+04 Fmax= 1.67527e+02, atom= 1949\n", + "Step= 666, Dmax= 1.5e-02 nm, Epot= -6.15815e+04 Fmax= 9.30733e+01, atom= 1949\n", + "Step= 667, Dmax= 1.8e-02 nm, Epot= -6.15824e+04 Fmax= 2.25481e+02, atom= 1949\n", + "Step= 668, Dmax= 2.2e-02 nm, Epot= -6.15882e+04 Fmax= 1.47792e+02, atom= 1949\n", + "Step= 670, Dmax= 1.3e-02 nm, Epot= -6.15926e+04 Fmax= 7.13658e+01, atom= 1949\n", + "Step= 671, Dmax= 1.6e-02 nm, Epot= -6.15947e+04 Fmax= 1.92535e+02, atom= 1949\n", + "Step= 672, Dmax= 1.9e-02 nm, Epot= -6.16001e+04 Fmax= 1.28400e+02, atom= 1949\n", + "Step= 674, Dmax= 1.1e-02 nm, Epot= -6.16041e+04 Fmax= 6.58039e+01, atom= 1949\n", + "Step= 675, Dmax= 1.4e-02 nm, Epot= -6.16072e+04 Fmax= 1.69507e+02, atom= 1949\n", + "Step= 676, Dmax= 1.7e-02 nm, Epot= -6.16117e+04 Fmax= 1.09017e+02, atom= 1949\n", + "Step= 677, Dmax= 2.0e-02 nm, Epot= -6.16123e+04 Fmax= 2.32233e+02, atom= 1949\n", + "Step= 678, Dmax= 2.4e-02 nm, Epot= -6.16177e+04 Fmax= 1.67062e+02, atom= 1949\n", + "Step= 680, Dmax= 1.4e-02 nm, Epot= -6.16228e+04 Fmax= 6.73887e+01, atom= 1949\n", + "Step= 681, Dmax= 1.7e-02 nm, Epot= -6.16243e+04 Fmax= 2.15799e+02, atom= 1949\n", + "Step= 682, Dmax= 2.1e-02 nm, Epot= -6.16309e+04 Fmax= 1.28582e+02, atom= 1949\n", + "Step= 684, Dmax= 1.2e-02 nm, Epot= -6.16349e+04 Fmax= 7.97385e+01, atom= 1949\n", + "Step= 685, Dmax= 1.5e-02 nm, Epot= -6.16372e+04 Fmax= 1.72885e+02, atom= 1949\n", + "Step= 686, Dmax= 1.8e-02 nm, Epot= -6.16416e+04 Fmax= 1.25784e+02, atom= 1949\n", + "Step= 687, Dmax= 2.1e-02 nm, Epot= -6.16417e+04 Fmax= 2.40575e+02, atom= 1949\n", + "Step= 688, Dmax= 2.6e-02 nm, Epot= -6.16469e+04 Fmax= 1.87556e+02, atom= 1949\n", + "Step= 690, Dmax= 1.5e-02 nm, Epot= -6.16529e+04 Fmax= 6.60799e+01, atom= 3323\n", + "Step= 691, Dmax= 1.8e-02 nm, Epot= -6.16537e+04 Fmax= 2.40106e+02, atom= 3323\n", + "Step= 692, Dmax= 2.2e-02 nm, Epot= -6.16616e+04 Fmax= 1.29555e+02, atom= 3323\n", + "Step= 694, Dmax= 1.3e-02 nm, Epot= -6.16654e+04 Fmax= 9.36283e+01, atom= 3323\n", + "Step= 695, Dmax= 1.6e-02 nm, Epot= -6.16674e+04 Fmax= 1.74793e+02, atom= 3323\n", + "Step= 696, Dmax= 1.9e-02 nm, Epot= -6.16715e+04 Fmax= 1.46095e+02, atom= 3323\n", + "Step= 698, Dmax= 1.1e-02 nm, Epot= -6.16762e+04 Fmax= 4.50594e+01, atom= 3323\n", + "Step= 699, Dmax= 1.4e-02 nm, Epot= -6.16805e+04 Fmax= 1.84908e+02, atom= 3323\n", + "Step= 700, Dmax= 1.6e-02 nm, Epot= -6.16862e+04 Fmax= 9.14170e+01, atom= 3323\n", + "Step= 702, Dmax= 9.9e-03 nm, Epot= -6.16895e+04 Fmax= 7.54193e+01, atom= 3323\n", + "Step= 703, Dmax= 1.2e-02 nm, Epot= -6.16926e+04 Fmax= 1.24684e+02, atom= 3323\n", + "Step= 704, Dmax= 1.4e-02 nm, Epot= -6.16961e+04 Fmax= 1.14940e+02, atom= 3323\n", + "Step= 705, Dmax= 1.7e-02 nm, Epot= -6.16980e+04 Fmax= 1.74170e+02, atom= 3323\n", + "Step= 706, Dmax= 2.1e-02 nm, Epot= -6.17014e+04 Fmax= 1.70701e+02, atom= 3323\n", + "Step= 707, Dmax= 2.5e-02 nm, Epot= -6.17016e+04 Fmax= 2.46551e+02, atom= 3323\n", + "Step= 708, Dmax= 3.0e-02 nm, Epot= -6.17043e+04 Fmax= 2.49177e+02, atom= 3323\n", + "Step= 710, Dmax= 1.8e-02 nm, Epot= -6.17140e+04 Fmax= 4.56564e+01, atom= 3323\n", + "Step= 711, Dmax= 2.1e-02 nm, Epot= -6.17147e+04 Fmax= 3.10156e+02, atom= 3323\n", + "Step= 712, Dmax= 2.6e-02 nm, Epot= -6.17275e+04 Fmax= 1.18057e+02, atom= 3323\n", + "Step= 714, Dmax= 1.5e-02 nm, Epot= -6.17303e+04 Fmax= 1.40059e+02, atom= 3323\n", + "Step= 715, Dmax= 1.8e-02 nm, Epot= -6.17327e+04 Fmax= 1.69299e+02, atom= 3323\n", + "Step= 716, Dmax= 2.2e-02 nm, Epot= -6.17346e+04 Fmax= 2.00894e+02, atom= 3323\n", + "Step= 717, Dmax= 2.6e-02 nm, Epot= -6.17358e+04 Fmax= 2.46036e+02, atom= 3323\n", + "Step= 718, Dmax= 3.2e-02 nm, Epot= -6.17362e+04 Fmax= 2.85767e+02, atom= 3323\n", + "Step= 720, Dmax= 1.9e-02 nm, Epot= -6.17488e+04 Fmax= 3.10433e+01, atom= 3323\n", + "Step= 721, Dmax= 2.3e-02 nm, Epot= -6.17512e+04 Fmax= 3.54161e+02, atom= 3323\n", + "Step= 722, Dmax= 2.7e-02 nm, Epot= -6.17691e+04 Fmax= 1.10459e+02, atom= 3323\n", + "Step= 724, Dmax= 1.6e-02 nm, Epot= -6.17708e+04 Fmax= 1.67762e+02, atom= 3323\n", + "Step= 725, Dmax= 2.0e-02 nm, Epot= -6.17742e+04 Fmax= 1.65501e+02, atom= 3323\n", + "Step= 727, Dmax= 1.2e-02 nm, Epot= -6.17800e+04 Fmax= 3.57628e+01, atom= 3323\n", + "Step= 728, Dmax= 1.4e-02 nm, Epot= -6.17848e+04 Fmax= 2.05701e+02, atom= 3323\n", + "Step= 729, Dmax= 1.7e-02 nm, Epot= -6.17919e+04 Fmax= 8.54245e+01, atom= 3323\n", + "Step= 731, Dmax= 1.0e-02 nm, Epot= -6.17950e+04 Fmax= 8.67985e+01, atom= 3323\n", + "Step= 732, Dmax= 1.2e-02 nm, Epot= -6.17978e+04 Fmax= 1.21109e+02, atom= 3323\n", + "Step= 733, Dmax= 1.5e-02 nm, Epot= -6.18008e+04 Fmax= 1.27346e+02, atom= 3323\n", + "Step= 734, Dmax= 1.8e-02 nm, Epot= -6.18025e+04 Fmax= 1.70965e+02, atom= 3323\n", + "Step= 735, Dmax= 2.1e-02 nm, Epot= -6.18049e+04 Fmax= 1.87542e+02, atom= 3323\n", + "Step= 736, Dmax= 2.5e-02 nm, Epot= -6.18051e+04 Fmax= 2.40863e+02, atom= 3323\n", + "Step= 737, Dmax= 3.1e-02 nm, Epot= -6.18060e+04 Fmax= 2.76327e+02, atom= 3323\n", + "Step= 739, Dmax= 1.8e-02 nm, Epot= -6.18181e+04 Fmax= 3.75260e+01, atom= 3323\n", + "Step= 741, Dmax= 1.1e-02 nm, Epot= -6.18229e+04 Fmax= 1.43857e+02, atom= 3323\n", + "Step= 742, Dmax= 1.3e-02 nm, Epot= -6.18272e+04 Fmax= 8.13268e+01, atom= 3323\n", + "Step= 743, Dmax= 1.6e-02 nm, Epot= -6.18282e+04 Fmax= 1.86414e+02, atom= 3323\n", + "Step= 744, Dmax= 1.9e-02 nm, Epot= -6.18330e+04 Fmax= 1.36189e+02, atom= 3323\n", + "Step= 746, Dmax= 1.1e-02 nm, Epot= -6.18373e+04 Fmax= 5.46422e+01, atom= 3323\n", + "Step= 747, Dmax= 1.4e-02 nm, Epot= -6.18394e+04 Fmax= 1.77559e+02, atom= 3323\n", + "Step= 748, Dmax= 1.6e-02 nm, Epot= -6.18449e+04 Fmax= 9.81546e+01, atom= 3323\n", + "Step= 750, Dmax= 9.9e-03 nm, Epot= -6.18481e+04 Fmax= 6.92657e+01, atom= 3323\n", + "Step= 751, Dmax= 1.2e-02 nm, Epot= -6.18505e+04 Fmax= 1.29277e+02, atom= 3323\n", + "Step= 752, Dmax= 1.4e-02 nm, Epot= -6.18538e+04 Fmax= 1.11387e+02, atom= 3323\n", + "Step= 753, Dmax= 1.7e-02 nm, Epot= -6.18547e+04 Fmax= 1.76156e+02, atom= 3323\n", + "Step= 754, Dmax= 2.0e-02 nm, Epot= -6.18577e+04 Fmax= 1.69428e+02, atom= 3323\n", + "Step= 756, Dmax= 1.2e-02 nm, Epot= -6.18638e+04 Fmax= 3.54448e+01, atom= 3323\n", + "Step= 757, Dmax= 1.5e-02 nm, Epot= -6.18662e+04 Fmax= 2.16367e+02, atom= 3323\n", + "Step= 758, Dmax= 1.8e-02 nm, Epot= -6.18749e+04 Fmax= 8.04779e+01, atom= 3323\n", + "Step= 760, Dmax= 1.1e-02 nm, Epot= -6.18775e+04 Fmax= 9.98588e+01, atom= 3323\n", + "Step= 761, Dmax= 1.3e-02 nm, Epot= -6.18799e+04 Fmax= 1.13861e+02, atom= 3323\n", + "Step= 762, Dmax= 1.5e-02 nm, Epot= -6.18816e+04 Fmax= 1.44921e+02, atom= 3323\n", + "Step= 763, Dmax= 1.8e-02 nm, Epot= -6.18834e+04 Fmax= 1.63846e+02, atom= 3323\n", + "Step= 764, Dmax= 2.2e-02 nm, Epot= -6.18835e+04 Fmax= 2.07417e+02, atom= 3323\n", + "Step= 765, Dmax= 2.6e-02 nm, Epot= -6.18839e+04 Fmax= 2.38270e+02, atom= 3323\n", + "Step= 767, Dmax= 1.6e-02 nm, Epot= -6.18959e+04 Fmax= 3.25907e+01, atom= 3323\n", + "Step= 769, Dmax= 9.5e-03 nm, Epot= -6.18999e+04 Fmax= 1.23018e+02, atom= 3323\n", + "Step= 770, Dmax= 1.1e-02 nm, Epot= -6.19041e+04 Fmax= 7.19840e+01, atom= 3323\n", + "Step= 771, Dmax= 1.4e-02 nm, Epot= -6.19044e+04 Fmax= 1.58267e+02, atom= 3323\n", + "Step= 772, Dmax= 1.6e-02 nm, Epot= -6.19089e+04 Fmax= 1.21307e+02, atom= 3323\n", + "Step= 774, Dmax= 9.8e-03 nm, Epot= -6.19134e+04 Fmax= 4.35690e+01, atom= 3323\n", + "Step= 775, Dmax= 1.2e-02 nm, Epot= -6.19146e+04 Fmax= 1.59358e+02, atom= 3323\n", + "Step= 776, Dmax= 1.4e-02 nm, Epot= -6.19206e+04 Fmax= 7.88613e+01, atom= 3323\n", + "Step= 778, Dmax= 8.5e-03 nm, Epot= -6.19235e+04 Fmax= 6.66403e+01, atom= 3323\n", + "Step= 779, Dmax= 1.0e-02 nm, Epot= -6.19255e+04 Fmax= 1.04174e+02, atom= 3323\n", + "Step= 780, Dmax= 1.2e-02 nm, Epot= -6.19282e+04 Fmax= 1.04693e+02, atom= 3323\n", + "Step= 781, Dmax= 1.5e-02 nm, Epot= -6.19292e+04 Fmax= 1.42981e+02, atom= 3323\n", + "Step= 782, Dmax= 1.8e-02 nm, Epot= -6.19310e+04 Fmax= 1.57064e+02, atom= 1040\n", + "Step= 784, Dmax= 1.1e-02 nm, Epot= -6.19380e+04 Fmax= 2.27104e+01, atom= 1040\n", + "Step= 785, Dmax= 1.3e-02 nm, Epot= -6.19430e+04 Fmax= 1.90449e+02, atom= 1040\n", + "Step= 786, Dmax= 1.5e-02 nm, Epot= -6.19515e+04 Fmax= 6.69500e+01, atom= 1040\n", + "Step= 788, Dmax= 9.1e-03 nm, Epot= -6.19538e+04 Fmax= 8.98881e+01, atom= 1040\n", + "Step= 789, Dmax= 1.1e-02 nm, Epot= -6.19563e+04 Fmax= 9.69127e+01, atom= 1040\n", + "Step= 790, Dmax= 1.3e-02 nm, Epot= -6.19578e+04 Fmax= 1.27878e+02, atom= 1040\n", + "Step= 791, Dmax= 1.6e-02 nm, Epot= -6.19599e+04 Fmax= 1.41222e+02, atom= 1040\n", + "Step= 792, Dmax= 1.9e-02 nm, Epot= -6.19601e+04 Fmax= 1.82178e+02, atom= 1040\n", + "Step= 793, Dmax= 2.3e-02 nm, Epot= -6.19612e+04 Fmax= 2.05354e+02, atom= 1040\n", + "Step= 795, Dmax= 1.4e-02 nm, Epot= -6.19711e+04 Fmax= 2.85714e+01, atom= 1040\n", + "Step= 796, Dmax= 1.6e-02 nm, Epot= -6.19713e+04 Fmax= 2.54575e+02, atom= 1040\n", + "Step= 797, Dmax= 2.0e-02 nm, Epot= -6.19841e+04 Fmax= 8.58721e+01, atom= 1040\n", + "Step= 799, Dmax= 1.2e-02 nm, Epot= -6.19861e+04 Fmax= 1.15620e+02, atom= 1040\n", + "Step= 800, Dmax= 1.4e-02 nm, Epot= -6.19883e+04 Fmax= 1.26179e+02, atom= 1040\n", + "Step= 801, Dmax= 1.7e-02 nm, Epot= -6.19892e+04 Fmax= 1.63102e+02, atom= 1040\n", + "Step= 802, Dmax= 2.0e-02 nm, Epot= -6.19906e+04 Fmax= 1.84593e+02, atom= 1040\n", + "Step= 804, Dmax= 1.2e-02 nm, Epot= -6.19983e+04 Fmax= 2.27677e+01, atom= 1040\n", + "Step= 805, Dmax= 1.5e-02 nm, Epot= -6.20034e+04 Fmax= 2.24568e+02, atom= 1040\n", + "Step= 806, Dmax= 1.8e-02 nm, Epot= -6.20131e+04 Fmax= 7.26377e+01, atom= 1040\n", + "Step= 808, Dmax= 1.1e-02 nm, Epot= -6.20151e+04 Fmax= 1.09182e+02, atom= 1040\n", + "Step= 809, Dmax= 1.3e-02 nm, Epot= -6.20177e+04 Fmax= 1.06686e+02, atom= 1040\n", + "Step= 810, Dmax= 1.5e-02 nm, Epot= -6.20186e+04 Fmax= 1.52878e+02, atom= 1040\n", + "Step= 811, Dmax= 1.8e-02 nm, Epot= -6.20209e+04 Fmax= 1.57619e+02, atom= 1040\n", + "Step= 813, Dmax= 1.1e-02 nm, Epot= -6.20268e+04 Fmax= 2.99193e+01, atom= 1040\n", + "Step= 814, Dmax= 1.3e-02 nm, Epot= -6.20296e+04 Fmax= 1.94079e+02, atom= 1040\n", + "Step= 815, Dmax= 1.6e-02 nm, Epot= -6.20371e+04 Fmax= 7.75292e+01, atom= 1040\n", + "Step= 817, Dmax= 9.5e-03 nm, Epot= -6.20396e+04 Fmax= 8.38311e+01, atom= 1040\n", + "Step= 818, Dmax= 1.1e-02 nm, Epot= -6.20416e+04 Fmax= 1.10206e+02, atom= 1040\n", + "Step= 819, Dmax= 1.4e-02 nm, Epot= -6.20438e+04 Fmax= 1.21578e+02, atom= 1040\n", + "Step= 820, Dmax= 1.6e-02 nm, Epot= -6.20449e+04 Fmax= 1.57570e+02, atom= 1040\n", + "Step= 821, Dmax= 2.0e-02 nm, Epot= -6.20464e+04 Fmax= 1.76421e+02, atom= 1040\n", + "Step= 823, Dmax= 1.2e-02 nm, Epot= -6.20535e+04 Fmax= 3.59349e+01, atom= 1782\n", + "Step= 824, Dmax= 1.4e-02 nm, Epot= -6.20582e+04 Fmax= 1.45222e+02, atom= 1040\n", + "Step= 825, Dmax= 1.7e-02 nm, Epot= -6.20607e+04 Fmax= 1.46283e+02, atom= 1040\n", + "Step= 827, Dmax= 1.0e-02 nm, Epot= -6.20664e+04 Fmax= 4.02890e+01, atom= 1782\n", + "Step= 828, Dmax= 1.2e-02 nm, Epot= -6.20708e+04 Fmax= 1.11162e+02, atom= 1040\n", + "Step= 829, Dmax= 1.5e-02 nm, Epot= -6.20723e+04 Fmax= 1.37422e+02, atom= 1040\n", + "Step= 830, Dmax= 1.8e-02 nm, Epot= -6.20734e+04 Fmax= 1.63267e+02, atom= 1040\n", + "Step= 831, Dmax= 2.1e-02 nm, Epot= -6.20738e+04 Fmax= 1.96144e+02, atom= 1040\n", + "Step= 833, Dmax= 1.3e-02 nm, Epot= -6.20834e+04 Fmax= 4.40350e+01, atom= 1782\n", + "Step= 834, Dmax= 1.5e-02 nm, Epot= -6.20886e+04 Fmax= 1.03352e+02, atom= 1040\n", + "Step= 836, Dmax= 9.1e-03 nm, Epot= -6.20925e+04 Fmax= 5.41424e+01, atom= 1040\n", + "Step= 837, Dmax= 1.1e-02 nm, Epot= -6.20932e+04 Fmax= 1.32904e+02, atom= 4937\n", + "Step= 838, Dmax= 1.3e-02 nm, Epot= -6.20977e+04 Fmax= 9.61326e+01, atom= 4937\n", + "Step= 840, Dmax= 7.9e-03 nm, Epot= -6.21014e+04 Fmax= 4.11376e+01, atom= 4937\n", + "Step= 841, Dmax= 9.4e-03 nm, Epot= -6.21036e+04 Fmax= 1.17201e+02, atom= 4937\n", + "Step= 842, Dmax= 1.1e-02 nm, Epot= -6.21076e+04 Fmax= 7.87920e+01, atom= 4937\n", + "Step= 844, Dmax= 6.8e-03 nm, Epot= -6.21105e+04 Fmax= 3.82117e+01, atom= 4937\n", + "Step= 845, Dmax= 8.2e-03 nm, Epot= -6.21129e+04 Fmax= 1.06706e+02, atom= 4937\n", + "Step= 846, Dmax= 9.8e-03 nm, Epot= -6.21165e+04 Fmax= 6.35798e+01, atom= 4937\n", + "Step= 847, Dmax= 1.2e-02 nm, Epot= -6.21170e+04 Fmax= 1.42991e+02, atom= 4937\n", + "Step= 848, Dmax= 1.4e-02 nm, Epot= -6.21211e+04 Fmax= 1.03213e+02, atom= 4937\n", + "Step= 850, Dmax= 8.5e-03 nm, Epot= -6.21246e+04 Fmax= 4.43484e+01, atom= 4937\n", + "Step= 851, Dmax= 1.0e-02 nm, Epot= -6.21266e+04 Fmax= 1.25828e+02, atom= 4937\n", + "Step= 852, Dmax= 1.2e-02 nm, Epot= -6.21303e+04 Fmax= 8.48035e+01, atom= 4937\n", + "Step= 854, Dmax= 7.3e-03 nm, Epot= -6.21333e+04 Fmax= 4.11273e+01, atom= 4937\n", + "Step= 855, Dmax= 8.8e-03 nm, Epot= -6.21354e+04 Fmax= 1.14631e+02, atom= 4937\n", + "Step= 856, Dmax= 1.1e-02 nm, Epot= -6.21390e+04 Fmax= 6.88454e+01, atom= 4937\n", + "Step= 857, Dmax= 1.3e-02 nm, Epot= -6.21392e+04 Fmax= 1.53268e+02, atom= 4937\n", + "Step= 858, Dmax= 1.5e-02 nm, Epot= -6.21433e+04 Fmax= 1.12028e+02, atom= 4937\n", + "Step= 860, Dmax= 9.1e-03 nm, Epot= -6.21469e+04 Fmax= 4.66405e+01, atom= 4937\n", + "Step= 861, Dmax= 1.1e-02 nm, Epot= -6.21487e+04 Fmax= 1.36129e+02, atom= 4937\n", + "Step= 862, Dmax= 1.3e-02 nm, Epot= -6.21526e+04 Fmax= 9.02350e+01, atom= 4937\n", + "Step= 864, Dmax= 7.9e-03 nm, Epot= -6.21554e+04 Fmax= 4.53374e+01, atom= 4937\n", + "Step= 865, Dmax= 9.4e-03 nm, Epot= -6.21574e+04 Fmax= 1.21818e+02, atom= 4937\n", + "Step= 866, Dmax= 1.1e-02 nm, Epot= -6.21610e+04 Fmax= 7.56580e+01, atom= 4937\n", + "Step= 868, Dmax= 6.8e-03 nm, Epot= -6.21636e+04 Fmax= 4.35774e+01, atom= 4937\n", + "Step= 869, Dmax= 8.1e-03 nm, Epot= -6.21661e+04 Fmax= 9.42887e+01, atom= 4937\n", + "Step= 870, Dmax= 9.8e-03 nm, Epot= -6.21688e+04 Fmax= 7.59747e+01, atom= 4937\n", + "Step= 871, Dmax= 1.2e-02 nm, Epot= -6.21700e+04 Fmax= 1.25936e+02, atom= 4937\n", + "Step= 872, Dmax= 1.4e-02 nm, Epot= -6.21728e+04 Fmax= 1.18387e+02, atom= 4937\n", + "Step= 874, Dmax= 8.4e-03 nm, Epot= -6.21767e+04 Fmax= 2.82705e+01, atom= 4937\n", + "Step= 875, Dmax= 1.0e-02 nm, Epot= -6.21796e+04 Fmax= 1.55920e+02, atom= 4937\n", + "Step= 876, Dmax= 1.2e-02 nm, Epot= -6.21851e+04 Fmax= 5.99825e+01, atom= 4937\n", + "Step= 878, Dmax= 7.3e-03 nm, Epot= -6.21875e+04 Fmax= 6.96112e+01, atom= 4937\n", + "Step= 879, Dmax= 8.8e-03 nm, Epot= -6.21897e+04 Fmax= 8.14074e+01, atom= 4937\n", + "Step= 880, Dmax= 1.1e-02 nm, Epot= -6.21917e+04 Fmax= 1.02919e+02, atom= 4937\n", + "Step= 881, Dmax= 1.3e-02 nm, Epot= -6.21937e+04 Fmax= 1.16141e+02, atom= 4937\n", + "Step= 882, Dmax= 1.5e-02 nm, Epot= -6.21949e+04 Fmax= 1.48130e+02, atom= 4937\n", + "Step= 883, Dmax= 1.8e-02 nm, Epot= -6.21960e+04 Fmax= 1.68631e+02, atom= 4937\n", + "Step= 884, Dmax= 2.2e-02 nm, Epot= -6.21961e+04 Fmax= 2.10300e+02, atom= 4937\n", + "Step= 886, Dmax= 1.3e-02 nm, Epot= -6.22052e+04 Fmax= 2.65702e+01, atom= 4938\n", + "Step= 887, Dmax= 1.6e-02 nm, Epot= -6.22084e+04 Fmax= 2.46009e+02, atom= 4938\n", + "Step= 888, Dmax= 1.9e-02 nm, Epot= -6.22175e+04 Fmax= 9.12969e+01, atom= 4937\n", + "Step= 890, Dmax= 1.1e-02 nm, Epot= -6.22197e+04 Fmax= 1.10043e+02, atom= 4937\n", + "Step= 891, Dmax= 1.4e-02 nm, Epot= -6.22214e+04 Fmax= 1.25301e+02, atom= 4937\n", + "Step= 892, Dmax= 1.6e-02 nm, Epot= -6.22226e+04 Fmax= 1.60125e+02, atom= 4937\n", + "Step= 893, Dmax= 2.0e-02 nm, Epot= -6.22236e+04 Fmax= 1.81383e+02, atom= 4937\n", + "Step= 895, Dmax= 1.2e-02 nm, Epot= -6.22309e+04 Fmax= 2.21315e+01, atom= 4937\n", + "Step= 896, Dmax= 1.4e-02 nm, Epot= -6.22382e+04 Fmax= 1.89503e+02, atom= 4937\n", + "Step= 897, Dmax= 1.7e-02 nm, Epot= -6.22443e+04 Fmax= 9.73893e+01, atom= 4937\n", + "Step= 899, Dmax= 1.0e-02 nm, Epot= -6.22471e+04 Fmax= 8.18655e+01, atom= 4937\n", + "Step= 900, Dmax= 1.2e-02 nm, Epot= -6.22482e+04 Fmax= 1.29203e+02, atom= 4937\n", + "Step= 901, Dmax= 1.5e-02 nm, Epot= -6.22506e+04 Fmax= 1.25820e+02, atom= 4937\n", + "Step= 903, Dmax= 8.7e-03 nm, Epot= -6.22551e+04 Fmax= 2.63156e+01, atom= 4937\n", + "Step= 904, Dmax= 1.0e-02 nm, Epot= -6.22592e+04 Fmax= 1.47918e+02, atom= 938\n", + "Step= 905, Dmax= 1.3e-02 nm, Epot= -6.22643e+04 Fmax= 7.25947e+01, atom= 938\n", + "Step= 907, Dmax= 7.6e-03 nm, Epot= -6.22668e+04 Fmax= 6.09570e+01, atom= 938\n", + "Step= 908, Dmax= 9.1e-03 nm, Epot= -6.22689e+04 Fmax= 9.46149e+01, atom= 938\n", + "Step= 909, Dmax= 1.1e-02 nm, Epot= -6.22712e+04 Fmax= 9.64365e+01, atom= 938\n", + "Step= 910, Dmax= 1.3e-02 nm, Epot= -6.22726e+04 Fmax= 1.30240e+02, atom= 938\n", + "Step= 911, Dmax= 1.6e-02 nm, Epot= -6.22743e+04 Fmax= 1.43357e+02, atom= 938\n", + "Step= 912, Dmax= 1.9e-02 nm, Epot= -6.22745e+04 Fmax= 1.85040e+02, atom= 938\n", + "Step= 913, Dmax= 2.3e-02 nm, Epot= -6.22748e+04 Fmax= 2.06568e+02, atom= 938\n", + "Step= 915, Dmax= 1.4e-02 nm, Epot= -6.22848e+04 Fmax= 2.89039e+01, atom= 939\n", + "Step= 916, Dmax= 1.6e-02 nm, Epot= -6.22867e+04 Fmax= 2.56133e+02, atom= 938\n", + "Step= 917, Dmax= 1.9e-02 nm, Epot= -6.22971e+04 Fmax= 9.03164e+01, atom= 938\n", + "Step= 919, Dmax= 1.2e-02 nm, Epot= -6.22990e+04 Fmax= 1.16369e+02, atom= 938\n", + "Step= 920, Dmax= 1.4e-02 nm, Epot= -6.23012e+04 Fmax= 1.25718e+02, atom= 938\n", + "Step= 921, Dmax= 1.7e-02 nm, Epot= -6.23022e+04 Fmax= 1.67778e+02, atom= 938\n", + "Step= 922, Dmax= 2.0e-02 nm, Epot= -6.23039e+04 Fmax= 1.83211e+02, atom= 938\n", + "Step= 924, Dmax= 1.2e-02 nm, Epot= -6.23098e+04 Fmax= 2.97891e+01, atom= 938\n", + "Step= 925, Dmax= 1.5e-02 nm, Epot= -6.23118e+04 Fmax= 2.12365e+02, atom= 938\n", + "Step= 926, Dmax= 1.7e-02 nm, Epot= -6.23196e+04 Fmax= 9.45052e+01, atom= 938\n", + "Step= 928, Dmax= 1.0e-02 nm, Epot= -6.23222e+04 Fmax= 8.84470e+01, atom= 9387\n", + "Step= 929, Dmax= 1.3e-02 nm, Epot= -6.23230e+04 Fmax= 1.31686e+02, atom= 938\n", + "Step= 930, Dmax= 1.5e-02 nm, Epot= -6.23255e+04 Fmax= 1.31326e+02, atom= 938\n", + "Step= 932, Dmax= 9.1e-03 nm, Epot= -6.23301e+04 Fmax= 2.91377e+01, atom= 2427\n", + "Step= 933, Dmax= 1.1e-02 nm, Epot= -6.23324e+04 Fmax= 1.65391e+02, atom= 2427\n", + "Step= 934, Dmax= 1.3e-02 nm, Epot= -6.23384e+04 Fmax= 6.71878e+01, atom= 2427\n", + "Step= 936, Dmax= 7.8e-03 nm, Epot= -6.23406e+04 Fmax= 6.66937e+01, atom= 4937\n", + "Step= 937, Dmax= 9.4e-03 nm, Epot= -6.23422e+04 Fmax= 9.63323e+01, atom= 4937\n", + "Step= 938, Dmax= 1.1e-02 nm, Epot= -6.23444e+04 Fmax= 1.01690e+02, atom= 4937\n", + "Step= 939, Dmax= 1.4e-02 nm, Epot= -6.23452e+04 Fmax= 1.34622e+02, atom= 4937\n", + "Step= 940, Dmax= 1.6e-02 nm, Epot= -6.23470e+04 Fmax= 1.49160e+02, atom= 4937\n", + "Step= 942, Dmax= 9.7e-03 nm, Epot= -6.23527e+04 Fmax= 2.66976e+01, atom= 2427\n", + "Step= 943, Dmax= 1.2e-02 nm, Epot= -6.23557e+04 Fmax= 1.79183e+02, atom= 2427\n", + "Step= 944, Dmax= 1.4e-02 nm, Epot= -6.23619e+04 Fmax= 7.03322e+01, atom= 4937\n", + "Step= 946, Dmax= 8.4e-03 nm, Epot= -6.23641e+04 Fmax= 7.98115e+01, atom= 4937\n", + "Step= 947, Dmax= 1.0e-02 nm, Epot= -6.23660e+04 Fmax= 9.62597e+01, atom= 4937\n", + "Step= 948, Dmax= 1.2e-02 nm, Epot= -6.23678e+04 Fmax= 1.17195e+02, atom= 4937\n", + "Step= 949, Dmax= 1.5e-02 nm, Epot= -6.23691e+04 Fmax= 1.38279e+02, atom= 4937\n", + "Step= 950, Dmax= 1.7e-02 nm, Epot= -6.23703e+04 Fmax= 1.67205e+02, atom= 4937\n", + "Step= 951, Dmax= 2.1e-02 nm, Epot= -6.23704e+04 Fmax= 2.01543e+02, atom= 4937\n", + "Step= 952, Dmax= 2.5e-02 nm, Epot= -6.23709e+04 Fmax= 2.35760e+02, atom= 4937\n", + "Step= 954, Dmax= 1.5e-02 nm, Epot= -6.23809e+04 Fmax= 4.28066e+01, atom= 4938\n", + "Step= 956, Dmax= 9.0e-03 nm, Epot= -6.23838e+04 Fmax= 1.01697e+02, atom= 4232\n", + "Step= 957, Dmax= 1.1e-02 nm, Epot= -6.23862e+04 Fmax= 8.75414e+01, atom= 4937\n", + "Step= 958, Dmax= 1.3e-02 nm, Epot= -6.23872e+04 Fmax= 1.43666e+02, atom= 4937\n", + "Step= 959, Dmax= 1.6e-02 nm, Epot= -6.23897e+04 Fmax= 1.32980e+02, atom= 4937\n", + "Step= 961, Dmax= 9.4e-03 nm, Epot= -6.23936e+04 Fmax= 3.15960e+01, atom= 4937\n", + "Step= 962, Dmax= 1.1e-02 nm, Epot= -6.23977e+04 Fmax= 1.50721e+02, atom= 4937\n", + "Step= 963, Dmax= 1.3e-02 nm, Epot= -6.24016e+04 Fmax= 8.27897e+01, atom= 4937\n", + "Step= 965, Dmax= 8.1e-03 nm, Epot= -6.24039e+04 Fmax= 5.95661e+01, atom= 4937\n", + "Step= 966, Dmax= 9.7e-03 nm, Epot= -6.24059e+04 Fmax= 1.11909e+02, atom= 4937\n", + "Step= 967, Dmax= 1.2e-02 nm, Epot= -6.24085e+04 Fmax= 9.38756e+01, atom= 4937\n", + "Step= 968, Dmax= 1.4e-02 nm, Epot= -6.24096e+04 Fmax= 1.52476e+02, atom= 4937\n", + "Step= 969, Dmax= 1.7e-02 nm, Epot= -6.24120e+04 Fmax= 1.45137e+02, atom= 4937\n", + "Step= 970, Dmax= 2.0e-02 nm, Epot= -6.24121e+04 Fmax= 2.07900e+02, atom= 4937\n", + "Step= 971, Dmax= 2.4e-02 nm, Epot= -6.24135e+04 Fmax= 2.21125e+02, atom= 4937\n", + "Step= 973, Dmax= 1.5e-02 nm, Epot= -6.24210e+04 Fmax= 3.03283e+01, atom= 4937\n", + "Step= 974, Dmax= 1.7e-02 nm, Epot= -6.24262e+04 Fmax= 2.34137e+02, atom= 4937\n", + "Step= 975, Dmax= 2.1e-02 nm, Epot= -6.24323e+04 Fmax= 1.23070e+02, atom= 4937\n", + "Step= 977, Dmax= 1.3e-02 nm, Epot= -6.24349e+04 Fmax= 1.03752e+02, atom= 4937\n", + "Step= 978, Dmax= 1.5e-02 nm, Epot= -6.24363e+04 Fmax= 1.55823e+02, atom= 4937\n", + "Step= 979, Dmax= 1.8e-02 nm, Epot= -6.24382e+04 Fmax= 1.64005e+02, atom= 4937\n", + "Step= 980, Dmax= 2.2e-02 nm, Epot= -6.24387e+04 Fmax= 2.12617e+02, atom= 4937\n", + "Step= 981, Dmax= 2.6e-02 nm, Epot= -6.24391e+04 Fmax= 2.46961e+02, atom= 4937\n", + "Step= 982, Dmax= 3.1e-02 nm, Epot= -6.24392e+04 Fmax= 2.92519e+02, atom= 4937\n", + "Step= 984, Dmax= 1.9e-02 nm, Epot= -6.24498e+04 Fmax= 5.74096e+01, atom= 4938\n", + "Step= 986, Dmax= 1.1e-02 nm, Epot= -6.24524e+04 Fmax= 1.25219e+02, atom= 4232\n", + "Step= 987, Dmax= 1.3e-02 nm, Epot= -6.24548e+04 Fmax= 1.09413e+02, atom= 4232\n", + "Step= 988, Dmax= 1.6e-02 nm, Epot= -6.24557e+04 Fmax= 1.79087e+02, atom= 4232\n", + "Step= 989, Dmax= 1.9e-02 nm, Epot= -6.24583e+04 Fmax= 1.57637e+02, atom= 4232\n", + "Step= 991, Dmax= 1.2e-02 nm, Epot= -6.24624e+04 Fmax= 4.41992e+01, atom= 4937\n", + "Step= 992, Dmax= 1.4e-02 nm, Epot= -6.24650e+04 Fmax= 1.84347e+02, atom= 4937\n", + "Step= 993, Dmax= 1.7e-02 nm, Epot= -6.24693e+04 Fmax= 1.04549e+02, atom= 4937\n", + "Step= 995, Dmax= 1.0e-02 nm, Epot= -6.24717e+04 Fmax= 7.27234e+01, atom= 4937\n", + "Step= 996, Dmax= 1.2e-02 nm, Epot= -6.24734e+04 Fmax= 1.39498e+02, atom= 4937\n", + "Step= 997, Dmax= 1.4e-02 nm, Epot= -6.24759e+04 Fmax= 1.17886e+02, atom= 4937\n", + "Step= 998, Dmax= 1.7e-02 nm, Epot= -6.24766e+04 Fmax= 1.89061e+02, atom= 4232\n", + "Step= 999, Dmax= 2.1e-02 nm, Epot= -6.24787e+04 Fmax= 1.80077e+02, atom= 4937\n", + "Step= 1000, Dmax= 2.5e-02 nm, Epot= -6.24779e+04 Fmax= 2.64158e+02, atom= 4232\n", "Energy minimization reached the maximum number of steps before the forces\n", "reached the requested precision Fmax < 10.\n", "\n", "writing lowest energy coordinates.\n", "\n", + "Back Off! I just backed up em.pdb to ./#em.pdb.1#\n", + "\n", "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n", - "Potential Energy = -6.2504758e+04\n", - "Maximum force = 2.5688226e+02 on atom 4100\n", - "Norm of force = 5.8315262e+00\n", + "Potential Energy = -6.2478738e+04\n", + "Maximum force = 1.8007661e+02 on atom 4937\n", + "Norm of force = 5.3058659e+00\n", "\n", - "GROMACS reminds you: \"Furious activity is no substitute for understanding.\" (H.H. Williams)\n", + "GROMACS reminds you: \"The greatest shortcoming of the human race is our inability to understand the exponential function.\" (Albert Bartlett)\n", "\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb'\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6157,9 +6518,13 @@ "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top\n", "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", - "GROMACS reminds you: \"Way to Go Dude\" (Beavis and Butthead)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Everybody Lie Down On the Floor and Keep Calm\" (KLF)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -6175,7 +6540,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 936892543\n", + "Setting the LD random seed to 2008514542\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -6207,7 +6572,7 @@ " '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top']}" ] }, - "execution_count": 19, + "execution_count": 44, "metadata": {}, "output_type": "execute_result" } @@ -6234,20 +6599,14 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 45, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v\n", " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", "\n", "Executable: /usr/local/gromacs/bin/gmx\n", @@ -6257,7 +6616,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 10 to 50, rlist from 1.1 to 1.233\n", + "Changing nstlist from 10 to 50, rlist from 1.1 to 1.228\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -6268,18 +6627,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "100000 steps, 1000.0 ps.\n", + "100000 steps, 1000.0 ps (continuing from step 100000, 1000.0 ps).\n", "\n", - "Step 0 Warning: pressure scaling more than 1%, mu: 0.972666 0.972666 0.972666\n", - "step 99900, remaining wall clock time: 0 s \n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 100000, remaining wall clock time: 0 s \n", + "NOTE: 31 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 316.146 79.037 400.0\n", + " Time: 0.128 0.032 398.5\n", " (ns/day) (hour/ns)\n", - "Performance: 1093.175 0.022\n", + "Performance: 26.842 0.894\n", "\n", - "GROMACS reminds you: \"Why Do *You* Use Constraints ?\" (H.J.C. Berendsen)\n", + "GROMACS reminds you: \"Everybody Lie Down On the Floor and Keep Calm\" (KLF)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n" ] @@ -6290,7 +6652,7 @@ "0" ] }, - "execution_count": 20, + "execution_count": 45, "metadata": {}, "output_type": "execute_result" } @@ -6308,7 +6670,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 46, "metadata": {}, "outputs": [ { @@ -6318,7 +6680,6 @@ "mdpow.equil : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro').\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] input mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 't']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6334,10 +6695,14 @@ "Command line:\n", " gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -t /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt\n", "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "Last frame -1 time 1000.000 \n", "\n", - "GROMACS reminds you: \"Why Do *You* Use Constraints ?\" (H.J.C. Berendsen)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"It was something to at least have a choice of nightmares\" (Joseph Conrad)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -6362,7 +6727,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1163133461\n", + "Setting the LD random seed to -33575937\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -6394,7 +6759,7 @@ "output_type": "stream", "text": [ "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 10 to 25, rlist from 1.108 to 1.222\n", + "Changing nstlist from 10 to 25, rlist from 1.108 to 1.223\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -6405,16 +6770,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "500000 steps, 10000.0 ps.\n", - "step 499900, remaining wall clock time: 0 s ll finish Mon Sep 4 21:46:53 202388600, will finish Mon Sep 4 21:46:52 2023248000, remaining wall clock time: 219 s 370400, remaining wall clock time: 113 s , remaining wall clock time: 9 s \n", + "500000 steps, 10000.0 ps (continuing from step 500000, 10000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 500000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 1881.626 470.407 400.0\n", + " Time: 0.060 0.015 397.1\n", " (ns/day) (hour/ns)\n", - "Performance: 1836.712 0.013\n", + "Performance: 114.104 0.210\n", "\n", - "GROMACS reminds you: \"These are Ideas, They are Not Lies\" (Magnapop)\n", + "GROMACS reminds you: \"Your Country Needs YOU\" (U.S. Army)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n" ] @@ -6425,7 +6792,7 @@ "0" ] }, - "execution_count": 21, + "execution_count": 46, "metadata": {}, "output_type": "execute_result" } @@ -6443,7 +6810,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 47, "metadata": {}, "outputs": [ { @@ -6451,6 +6818,9 @@ "output_type": "stream", "text": [ "mdpow.fep : INFO Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.gro').\n", + "/home/awsm/MDPOW/mdpow/fep.py:596: UserWarning: Directory 'FEP/octanol' already exists --- will overwrite existing files.\n", + " warnings.warn(wmsg)\n", + "mdpow.fep : WARNING Directory 'FEP/octanol' already exists --- will overwrite existing files.\n", "mdpow.fep : INFO Solvation free energy calculation for molecule BENZ in solvent octanol.\n", "mdpow.fep : INFO Base directory is '/home/awsm/MDPOW/doc/examples/martini'\n", "mdpow.fep : INFO Using setup directories under 'FEP/octanol': {'coulomb': 'FEP/octanol/Coulomb', 'vdw': 'FEP/octanol/VDW'}\n", @@ -6459,7 +6829,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6496,13 +6865,17 @@ " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n", "Number of degrees of freedom in T-Coupling group System is 15339.00\n", "\n", "There were 2 NOTEs\n", "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Hey Man You Know, I'm Really OK\" (Offspring)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Microsecond Here I Come\" (P.J. Van Maaren)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -6516,7 +6889,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6552,14 +6924,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1006616575\n", + "Setting the LD random seed to 1989017199\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -6592,7 +6966,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Contemplating answers that could break my bonds.\" (Peter Hammill)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Microsecond Here I Come\" (P.J. Van Maaren)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -6606,7 +6982,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6642,14 +7017,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1409249663\n", + "Setting the LD random seed to -1346895930\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -6682,7 +7059,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Contemplating answers that could break my bonds.\" (Peter Hammill)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"If everything seems under control, you're just not going fast enough.\" (Mario Andretti)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -6696,7 +7075,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6732,14 +7110,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -271363881\n", + "Setting the LD random seed to -478482449\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -6772,7 +7152,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"A computer once beat me at chess, but it was no match for me at kick boxing.\" (Emo Philips)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"If everything seems under control, you're just not going fast enough.\" (Mario Andretti)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -6786,7 +7168,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6822,14 +7203,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -939803669\n", + "Setting the LD random seed to 2145386303\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -6862,7 +7245,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"My Brothers are Protons (Protons!), My Sisters are Neurons (Neurons)\" (Gogol Bordello)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"The soul? There's nothing but chemistry here\" (Breaking Bad)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -6878,7 +7263,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -6914,14 +7298,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1611204865\n", + "Setting the LD random seed to -67141633\n", "\n", "Generated 844 of the 356590 non-bonded parameter combinations\n", "\n", @@ -6954,7 +7340,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"My Brothers are Protons (Protons!), My Sisters are Neurons (Neurons)\" (Gogol Bordello)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"The soul? There's nothing but chemistry here\" (Breaking Bad)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -6968,7 +7356,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7004,14 +7391,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 800586729\n", + "Setting the LD random seed to -1247367\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7044,7 +7433,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Nobody Never Learnt No-Nothing from No History\" (Gogol Bordello)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Bring Out the Gimp\" (Pulp Fiction)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7058,7 +7449,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7094,14 +7484,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1243615521\n", + "Setting the LD random seed to -438780993\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7134,7 +7526,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Royale With Cheese\" (Pulp Fiction)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Space May Be the Final Frontier, But It's Made in a Hollywood Basement\" (Red Hot Chili Peppers)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7148,7 +7542,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7184,14 +7577,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -784465921\n", + "Setting the LD random seed to -806387971\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7224,7 +7619,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Royale With Cheese\" (Pulp Fiction)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Space May Be the Final Frontier, But It's Made in a Hollywood Basement\" (Red Hot Chili Peppers)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7238,7 +7635,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7274,14 +7670,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -33784117\n", + "Setting the LD random seed to -608984233\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7314,7 +7712,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Science is a way of thinking much more than it is a body of knowledge.\" (Carl Sagan)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Let's Unzip And Let's Unfold\" (Red Hot Chili Peppers)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7328,7 +7728,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7364,14 +7763,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1609039455\n", + "Setting the LD random seed to -102383660\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7404,7 +7805,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Science is a way of thinking much more than it is a body of knowledge.\" (Carl Sagan)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Let's Unzip And Let's Unfold\" (Red Hot Chili Peppers)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7418,7 +7821,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7454,14 +7856,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1609899597\n", + "Setting the LD random seed to 1946023915\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7494,7 +7898,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"I think everybody should like everybody.\" (Andy Warhol)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"A Pretty Village Burning Makes a Pretty Fire\" (David Sandstrom)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7508,7 +7914,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7544,14 +7949,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1077948441\n", + "Setting the LD random seed to -1091582337\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7584,7 +7991,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"It Doesn't Have to Be Tip Top\" (Pulp Fiction)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"A Pretty Village Burning Makes a Pretty Fire\" (David Sandstrom)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7598,7 +8007,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7634,14 +8042,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -14691763\n", + "Setting the LD random seed to 989822767\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7674,7 +8084,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"It Doesn't Have to Be Tip Top\" (Pulp Fiction)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"I don't want to achieve immortality through my work... I want to achieve it through not dying!\" (Woody Allen)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7688,7 +8100,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7724,14 +8135,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 2096885113\n", + "Setting the LD random seed to -33818753\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7764,7 +8177,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"I never see what has been done; I only see what remains to be done.\" (Marie Curie)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"There are three kinds of men. The one that learns by reading. The few who learn by observation. The rest of them have to pee on the electric fence for themselves.\" (Will Rogers)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7778,7 +8193,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7814,14 +8228,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to 1864226270\n", + "Setting the LD random seed to -1074663713\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7854,7 +8270,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"I never see what has been done; I only see what remains to be done.\" (Marie Curie)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"There are three kinds of men. The one that learns by reading. The few who learn by observation. The rest of them have to pee on the electric fence for themselves.\" (Will Rogers)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7868,7 +8286,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7904,14 +8321,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -10538113\n", + "Setting the LD random seed to -1106905097\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -7944,7 +8363,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Royale With Cheese\" (Pulp Fiction)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Trying is the first step towards failure.\" (Homer Simpson)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -7958,7 +8379,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -7994,14 +8414,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -394711249\n", + "Setting the LD random seed to -1090936833\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -8034,7 +8456,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"No great discovery was ever made without a bold guess.\" (Marie Curie)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"Trying is the first step towards failure.\" (Homer Simpson)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -8048,7 +8472,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -8084,14 +8507,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -536871077\n", + "Setting the LD random seed to 1511798142\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -8124,7 +8549,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"No great discovery was ever made without a bold guess.\" (Marie Curie)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"All that glitters may not be gold, but at least it contains free electrons.\" (John Desmond Baernal)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -8138,7 +8565,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -8174,14 +8600,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1090605057\n", + "Setting the LD random seed to -33820819\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -8214,7 +8642,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"Yeah, uh uh, Neil's Head !\" (Neil)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"All that glitters may not be gold, but at least it contains free electrons.\" (John Desmond Baernal)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -8228,7 +8658,6 @@ "mdpow.fep : INFO Setting dhdl file to edr format\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] Setting up MD...\n", "gromacs.setup: INFO [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] input mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n", - "gromacs.utilities: INFO Working in '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000' (newly created)...\n", "gromacs.cbook: INFO editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n", "gromacs.cbook: WARNING Not substituted in 'md.mdp': ['pp', 'maxwarn']\n", "gromacs.setup: WARNING Unprocessed mdp option are interpreted as options for grompp:\n", @@ -8264,14 +8693,16 @@ " be unstable for equilibration. If your system crashes, try equilibrating\n", " first with Berendsen pressure coupling. If you are not equilibrating the\n", " system, you can probably ignore this warning.\n", - "\n" + "\n", + "\n", + "Back Off! I just backed up processed.top to ./#processed.top.1#\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -285245490\n", + "Setting the LD random seed to -6356998\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -8304,7 +8735,9 @@ "\n", "There was 1 WARNING\n", "\n", - "GROMACS reminds you: \"They don't have any beavers in India, so they have to simulate them\" (The Tubes)\n", + "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n", + "\n", + "GROMACS reminds you: \"You can get into a habit of thought in which you enjoy making fun of all those other people who don't see things as clearly as you do. We have to guard carefully against it.\" (Carl Sagan)\n", "\n", "gromacs.qsub: INFO Setting up queuing system script './local.sh'...\n", "gromacs.cbook: INFO editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n", @@ -8324,7 +8757,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Setting the LD random seed to -1614840594\n", + "Setting the LD random seed to 1861188408\n", "\n", "Generated 1689 of the 357435 non-bonded parameter combinations\n", "\n", @@ -8374,7 +8807,7 @@ " 'calc_lambda_neighbors': -1}" ] }, - "execution_count": 22, + "execution_count": 47, "metadata": {}, "output_type": "execute_result" } @@ -8385,12 +8818,19 @@ ] }, { - "cell_type": "code", - "execution_count": 23, + "cell_type": "markdown", "metadata": {}, - "outputs": [ - { - "name": "stderr", + "source": [ + "These lambda windows take about twice as long as the water calculations on the author's desktop machine." + ] + }, + { + "cell_type": "code", + "execution_count": 48, + "metadata": {}, + "outputs": [ + { + "name": "stderr", "output_type": "stream", "text": [ "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -8403,7 +8843,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", + "Changing nstlist from 20 to 25, rlist from 1.177 to 1.221\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8414,16 +8854,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 182.577 45.644 400.0\n", + " Time: 0.058 0.015 398.7\n", " (ns/day) (hour/ns)\n", - "Performance: 1892.938 0.013\n", + "Performance: 118.985 0.202\n", "\n", - "GROMACS reminds you: \"Why, how now, Claudio ! Whence Comes this Restraint ?\" (Lucio in Measure for measure, Act 1, Scene 4, William Shakespeare)\n", + "GROMACS reminds you: \"Chemistry: It tends to be a messy science.\" (Gunnar von Heijne, former chair of the Nobel Committee for chemistry)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -8436,7 +8878,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8447,16 +8889,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 250.913 62.728 400.0\n", + " Time: 0.058 0.015 398.6\n", " (ns/day) (hour/ns)\n", - "Performance: 1377.395 0.017\n", + "Performance: 118.740 0.202\n", "\n", - "GROMACS reminds you: \"It Was My Pleasure\" (Pulp Fiction)\n", + "GROMACS reminds you: \"We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation.\" (Joseph Gay-Lussac, 1808)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -8469,7 +8913,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8480,16 +8924,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 205.528 51.382 400.0\n", + " Time: 0.063 0.016 398.7\n", " (ns/day) (hour/ns)\n", - "Performance: 1681.555 0.014\n", + "Performance: 109.130 0.220\n", "\n", - "GROMACS reminds you: \"There are three kinds of men. The one that learns by reading. The few who learn by observation. The rest of them have to pee on the electric fence for themselves.\" (Will Rogers)\n", + "GROMACS reminds you: \"We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation.\" (Joseph Gay-Lussac, 1808)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -8502,7 +8948,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.223\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8513,16 +8959,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 212.060 53.015 400.0\n", + " Time: 0.055 0.014 394.1\n", " (ns/day) (hour/ns)\n", - "Performance: 1629.756 0.015\n", + "Performance: 124.605 0.193\n", "\n", - "GROMACS reminds you: \"A real scientist solves problems, not wails that they are unsolvable.\" (Anne McCaffrey)\n", + "GROMACS reminds you: \"...sometimes a scream is better than a thesis.\" (Ralph Waldo Emerson)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -8535,7 +8983,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8546,16 +8994,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s , remaining wall clock time: 24 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 237.020 59.255 400.0\n", + " Time: 0.068 0.017 398.7\n", " (ns/day) (hour/ns)\n", - "Performance: 1458.132 0.016\n", + "Performance: 100.751 0.238\n", "\n", - "GROMACS reminds you: \"When doing HPC, don't communica\" (Jim Demmel)\n", + "GROMACS reminds you: \"Have a Nice Day\" (R. McDonald)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -8568,7 +9018,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8579,16 +9029,21 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 16 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", " Core t (s) Wall t (s) (%)\n", - " Time: 250.708 62.677 400.0\n", + " Time: 0.069 0.017 398.8\n", " (ns/day) (hour/ns)\n", - "Performance: 1378.522 0.017\n", + "Performance: 99.759 0.241\n", "\n", - "GROMACS reminds you: \"After a few talks we usually sit down to do some work... or drinking.\" (Mike Klein)\n", + "GROMACS reminds you: \"I wanted to make a clever chemistry joke, but the best ones Argon.\" (39.948)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -8601,7 +9056,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8612,16 +9067,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 188.780 47.195 400.0\n", + " Time: 0.078 0.020 399.0\n", " (ns/day) (hour/ns)\n", - "Performance: 1830.737 0.013\n", + "Performance: 88.427 0.271\n", "\n", - "GROMACS reminds you: \"Therefore, things must be learned only to be unlearned again or, more likely, to be corrected.\" (Richard Feynman)\n", + "GROMACS reminds you: \"I wanted to make a clever chemistry joke, but the best ones Argon.\" (39.948)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -8634,7 +9091,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", + "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8645,16 +9102,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 180.190 45.048 400.0\n", + " Time: 0.061 0.015 398.6\n", " (ns/day) (hour/ns)\n", - "Performance: 1918.007 0.013\n", + "Performance: 113.755 0.211\n", "\n", - "GROMACS reminds you: \"I can't help but think the model is ungrateful for all that nice data I gave it. Jerk.\" (Kate Stafford)\n", + "GROMACS reminds you: \"Science progresses best when observations force us to alter our preconceptions.\" (Vera Rubin)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -8667,7 +9126,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8678,16 +9137,18 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 49900, remaining wall clock time: 0 s \n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", "step 50000, remaining wall clock time: 0 s \n", " Core t (s) Wall t (s) (%)\n", - " Time: 202.058 50.514 400.0\n", + " Time: 0.061 0.015 398.7\n", " (ns/day) (hour/ns)\n", - "Performance: 1710.436 0.014\n", + "Performance: 112.992 0.212\n", "\n", - "GROMACS reminds you: \"The biggest lie in science is 'data and code available upon request'\" (Michael Eisen)\n", + "GROMACS reminds you: \"There is no place like ~\" (Anonymous)\n", "\n", "gromacs.run : INFO MDrun completed ok, returncode = 0\n", "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", @@ -8700,7 +9161,7 @@ " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", "\n", "Reading file md.tpr, VERSION 2023.2 (single precision)\n", - "Changing nstlist from 20 to 25, rlist from 1.179 to 1.224\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", "\n", "1 GPU selected for this run.\n", "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", @@ -8711,139 +9172,1135 @@ "Using 4 OpenMP threads \n", "\n", "starting mdrun 'Compound BENZ in octanol in water'\n", - "50000 steps, 1000.0 ps.\n", - "step 27300, remaining wall clock time: 32 s " - ] - } - ], - "source": [ - "for dir_ in goct.fep_dirs():\n", - " r = gromacs.run.MDrunner(\n", - " dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=True\n", - " )\n", - " r.run() # runs mdrun in the python shell" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg' with bzip2\n", - "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg.bz2'\n", - "mdpow.fep : INFO [FEP/octanol] Finding dgdl xvg files, reading with stride=1 permissive=False.\n", - "mdpow.fep : INFO Analysis stride is 1.\n", - "mdpow.fep : INFO Analyzing stored data.\n", - "mdpow.fep : INFO [BENZ coulomb] Computing averages and errors for 5 lambda values.\n", - "numkit.integration: WARNING Approximating Simpson integration statistical error with the average spacing.\n", - "mdpow.fep : INFO [BENZ vdw] Computing averages and errors for 16 lambda values.\n", - "numkit.integration: WARNING Approximating Simpson integration statistical error with the average spacing.\n", - "mdpow.fep : INFO DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n", - "mdpow.fep : INFO [BENZ] Octanol solvation free energy (coulomb) -25109.1 (13.01) kJ/mol\n", - "mdpow.fep : INFO [BENZ] Octanol solvation free energy (vdw) -25105.4 (6.33) kJ/mol\n", - "mdpow.fep : INFO [BENZ] Octanol solvation free energy (Gibbs) 50214.5 (14.47) kJ/mol\n" - ] - }, - { - "data": { - "image/png": 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", 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" - ] - }, - "execution_count": 22, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "goct.convert_edr()\n", - "goct.analyze_alchemlyb()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "plot_results(goct)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "mdpow.fep : INFO [BENZ] transfer free energy water --> octanol calculation\n", - "mdpow.fep : INFO The solvent is water .\n", - "mdpow.fep : INFO Using already calculated free energy DeltaA\n", - "mdpow.fep : INFO The solvent is octanol .\n", - "mdpow.fep : INFO Using already calculated free energy DeltaA\n", - "mdpow.fep : INFO [BENZ] Values at T = 300 K\n", - "mdpow.fep : INFO [BENZ] Free energy of transfer water --> octanol: -17812.254 (15.182) kJ/mol\n", - "mdpow.fep : INFO [BENZ] log P_ow: 3101.325 (2.643)\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "log P_ow = 3101.324683550301 ± 2.643399588149987\n" - ] - } - ], - "source": [ - "delta_G, p_OW = mdpow.fep.pOW(gwat, goct)\n", - "print(f\"log P_ow = {p_OW.value} ± {p_OW.error}\")" + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 11 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.073 0.018 398.9\n", + " (ns/day) (hour/ns)\n", + "Performance: 94.679 0.253\n", + "\n", + "GROMACS reminds you: \"Academia is kind of like applied Marxism. The workers really do own the means of production.\" (Niklas Blomberg)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.084 0.021 399.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 82.075 0.292\n", + "\n", + "GROMACS reminds you: \"Academia is kind of like applied Marxism. The workers really do own the means of production.\" (Niklas Blomberg)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.054 0.013 398.5\n", + " (ns/day) (hour/ns)\n", + "Performance: 128.290 0.187\n", + "\n", + "GROMACS reminds you: \"My Brothers are Protons (Protons!), My Sisters are Neurons (Neurons)\" (Gogol Bordello)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 44 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.141 0.035 399.4\n", + " (ns/day) (hour/ns)\n", + "Performance: 48.911 0.491\n", + "\n", + "GROMACS reminds you: \"For the first time we can now mechanically simulate the cognitive process. We can make studies in artificial intelligence. Beyond that, this mechanism can be used to assist humans in learning. As we are going to have more mature students in greater numbers as time goes on, this type of teaching will probably be increasingly important.\" (Sister Mary Kenneth Keller)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.057 0.014 398.7\n", + " (ns/day) (hour/ns)\n", + "Performance: 120.860 0.199\n", + "\n", + "GROMACS reminds you: \"After a few talks we usually sit down to do some work... or drinking.\" (Mike Klein)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 12 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.088 0.022 396.5\n", + " (ns/day) (hour/ns)\n", + "Performance: 77.863 0.308\n", + "\n", + "GROMACS reminds you: \"After a few talks we usually sit down to do some work... or drinking.\" (Mike Klein)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.054 0.014 398.6\n", + " (ns/day) (hour/ns)\n", + "Performance: 127.768 0.188\n", + "\n", + "GROMACS reminds you: \"Step On the Brakes\" (2 Unlimited)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 23 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.072 0.018 398.9\n", + " (ns/day) (hour/ns)\n", + "Performance: 95.165 0.252\n", + "\n", + "GROMACS reminds you: \"Here's the Way It Might End\" (G. Michael)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.223\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.064 0.016 398.7\n", + " (ns/day) (hour/ns)\n", + "Performance: 107.736 0.223\n", + "\n", + "GROMACS reminds you: \"As we all know, blinking lights means science.\" (Joss Whedon)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.059 0.015 398.6\n", + " (ns/day) (hour/ns)\n", + "Performance: 116.516 0.206\n", + "\n", + "GROMACS reminds you: \"This is Tense !\" (Star Wars Episode I The Phantom Menace)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + "NOTE: 20 % of the run time was spent in pair search,\n", + " you might want to increase nstlist (this has no effect on accuracy)\n", + "\n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.067 0.017 398.8\n", + " (ns/day) (hour/ns)\n", + "Performance: 103.547 0.232\n", + "\n", + "GROMACS reminds you: \"This is Tense !\" (Star Wars Episode I The Phantom Menace)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n", + "gromacs.run : INFO gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + " :-) GROMACS - gmx mdrun, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000\n", + "Command line:\n", + " gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n", + "\n", + "Reading file md.tpr, VERSION 2023.2 (single precision)\n", + "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n", + "\n", + "1 GPU selected for this run.\n", + "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n", + " PP:0\n", + "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n", + "PP task will update and constrain coordinates on the CPU\n", + "Using 1 MPI thread\n", + "Using 4 OpenMP threads \n", + "\n", + "starting mdrun 'Compound BENZ in octanol in water'\n", + "50000 steps, 1000.0 ps (continuing from step 50000, 1000.0 ps).\n", + "\n", + "Writing final coordinates.\n", + "\n", + "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n", + "step 50000, remaining wall clock time: 0 s \n", + " Core t (s) Wall t (s) (%)\n", + " Time: 0.056 0.014 392.0\n", + " (ns/day) (hour/ns)\n", + "Performance: 119.907 0.200\n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "gromacs.run : INFO MDrun completed ok, returncode = 0\n" + ] + } + ], + "source": [ + "for dir_ in goct.fep_dirs():\n", + " r = gromacs.run.MDrunner(\n", + " dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=True\n", + " )\n", + " r.run() # runs mdrun in the python shell" + ] + }, + { + "cell_type": "code", + "execution_count": 49, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [FEP/octanol] Converting EDR -> XVG.bz2\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 200 time 800.000 mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg\n", + "\n", + "\n", + "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 60 time 240.000 " + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.tpr, VERSION 2023.2 (single precision)\n", + "Reading energy frame 200 time 800.000 " + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg\n", + " :-) GROMACS - gmx energy, 2023.2 (-:\n", + "\n", + "Executable: /usr/local/gromacs/bin/gmx\n", + "Data prefix: /usr/local/gromacs\n", + "Working dir: /home/awsm/MDPOW/doc/examples/martini\n", + "Command line:\n", + " gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg\n", + "\n", + "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.edr as single precision energy file\n", + "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.tpr, VERSION 2023.2 (single precision)\n", + "Last energy frame read 250 time 1000.000 \n", + "\n", + "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n", + "\n", + "mdpow.fep : INFO Analysis stride is 1.\n", + "mdpow.fep : INFO Analysis starts from frame 0.\n", + "mdpow.fep : INFO Analysis stops at frame None.\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg.bz2'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg\n", + "\n", + "\n", + "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg' with bzip2\n", + "mdpow.fep : INFO [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg.bz2'\n", + "mdpow.fep : INFO [FEP/octanol] Finding dgdl xvg files, reading with stride=1 permissive=False.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0000\n", + "\u001b[32m2023-09-04 22:41:16.809\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.812\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 15.84.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.813\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 312.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 7.9840.\n", + "mdpow.fep : INFO The data are subsampled every 8 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0250\n", + "\u001b[32m2023-09-04 22:41:16.884\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.887\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 19.32.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.888\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 250.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.9640.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0500\n", + "\u001b[32m2023-09-04 22:41:16.961\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.963\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.68.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:16.963\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 0750\n", + "\u001b[32m2023-09-04 22:41:17.036\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.038\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 26.28.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.039\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 185.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 13.4649.\n", + "mdpow.fep : INFO The data are subsampled every 14 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window coulomb 1000\n", + "\u001b[32m2023-09-04 22:41:17.113\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.118\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.10.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.119\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.9740.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0000\n", + "\u001b[32m2023-09-04 22:41:17.331\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.333\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.09.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.333\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0050\n", + "\u001b[32m2023-09-04 22:41:17.543\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.545\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 24.34.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.546\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 200.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 12.4550.\n", + "mdpow.fep : INFO The data are subsampled every 13 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0100\n", + "\u001b[32m2023-09-04 22:41:17.800\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.802\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.81.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:17.802\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.9928.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0200\n", + "\u001b[32m2023-09-04 22:41:18.078\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.081\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 30.67.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.082\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 161.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 15.4720.\n", + "mdpow.fep : INFO The data are subsampled every 16 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0300\n", + "\u001b[32m2023-09-04 22:41:18.295\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.296\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.93.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.297\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.4728.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0400\n", + "\u001b[32m2023-09-04 22:41:18.511\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.512\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.32.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.513\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.4728.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0500\n", + "\u001b[32m2023-09-04 22:41:18.731\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.732\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.77.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.733\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.9928.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0600\n", + "\u001b[32m2023-09-04 22:41:18.942\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.943\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.68.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:18.944\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.9928.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0650\n", + "\u001b[32m2023-09-04 22:41:19.168\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.169\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.03.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.170\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.9928.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0700\n", + "\u001b[32m2023-09-04 22:41:19.399\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.400\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.22.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.401\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.9928.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0750\n", + "\u001b[32m2023-09-04 22:41:19.637\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.638\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.34.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.639\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0800\n", + "\u001b[32m2023-09-04 22:41:19.853\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.854\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.97.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:19.855\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.4728.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0850\n", + "\u001b[32m2023-09-04 22:41:20.088\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.089\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.34.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.090\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0900\n", + "\u001b[32m2023-09-04 22:41:20.323\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.324\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.22.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.325\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 0950\n", + "\u001b[32m2023-09-04 22:41:20.541\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.542\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.59.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.543\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 9.4715.\n", + "mdpow.fep : INFO The data are subsampled every 10 frames.\n", + "mdpow.fep : INFO Performing statistical inefficiency analysis for window vdw 1000\n", + "\u001b[32m2023-09-04 22:41:20.771\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.772\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.95.\u001b[0m\n", + "\u001b[32m2023-09-04 22:41:20.775\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n", + "mdpow.fep : INFO The statistical inefficiency value is 8.4728.\n", + "mdpow.fep : INFO The data are subsampled every 9 frames.\n", + "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/pymbar/other_estimators.py:510: RuntimeWarning: invalid value encountered in sqrt\n", + " dDeltaF = np.sqrt(variance)\n", + "mdpow.fep : INFO DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n", + "mdpow.fep : INFO [BENZ] Octanol solvation free energy (coulomb) 0 (nan) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Octanol solvation free energy (vdw) 6.69992 (0.20) kJ/mol\n", + "mdpow.fep : INFO [BENZ] Octanol solvation free energy (Gibbs) -6.69992 (nan) kJ/mol\n" + ] + }, + { + "data": { + "text/plain": [ + "-6.69992 (nan)" + ] + }, + "execution_count": 49, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "goct.convert_edr()\n", + "goct.analyze_alchemlyb()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Results\n", + "\n", + "Finally, we can compare the calculated free energies of solvation, taking the difference to find the free energy of transfer and then converting to a partition coefficient." + ] + }, + { + "cell_type": "code", + "execution_count": 50, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "mdpow.fep : INFO [BENZ] transfer free energy water --> octanol calculation\n", + "mdpow.fep : INFO The solvent is water .\n", + "mdpow.fep : INFO Using already calculated free energy DeltaA\n", + "mdpow.fep : INFO The solvent is octanol .\n", + "mdpow.fep : INFO Using already calculated free energy DeltaA\n", + "mdpow.fep : INFO [BENZ] Values at T = 300 K\n", + "mdpow.fep : INFO [BENZ] Free energy of transfer water --> octanol: -13.445 (nan) kJ/mol\n", + "mdpow.fep : INFO [BENZ] log P_ow: 2.341 (nan)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "log P_ow = 2.340869841742325 ± nan\n" + ] + } + ], + "source": [ + "delta_G, p_OW = mdpow.fep.pOW(gwat, goct)\n", + "print(f\"log P_ow = {p_OW.value} ± {p_OW.error}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The actual value is $\\log P_{ow} \\approx 2.13$." ] } ], From d2307a05e9b61bca9c7b07c7ab3eca5fe3053205 Mon Sep 17 00:00:00 2001 From: Shujie Fan Date: Tue, 5 Sep 2023 12:24:27 +0800 Subject: [PATCH 34/38] remove logger for SI in mdpow.fep --- mdpow/fep.py | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/mdpow/fep.py b/mdpow/fep.py index 4edd0362..71c75627 100644 --- a/mdpow/fep.py +++ b/mdpow/fep.py @@ -1179,7 +1179,6 @@ def collect_alchemlyb( for l in lambdas: xvg_file = self.dgdl_xvg(self.wdir(component, l)) xvg_df = extract(xvg_file, T=self.Temperature).iloc[start:stop:stride] - full_len = len(xvg_df) if SI: logger.info( "Performing statistical inefficiency analysis for window %s %04d" @@ -1190,16 +1189,6 @@ def collect_alchemlyb( ts = ts.set_index("time") # use the statistical_inefficiency function to subsample the data xvg_df = statistical_inefficiency(xvg_df, ts, conservative=True) - logger.info( - "The statistical inefficiency value is {:.4f}.".format( - full_len / len(xvg_df) / 2 - ) - ) - logger.info( - "The data are subsampled every {:d} frames.".format( - int(np.ceil(full_len / len(xvg_df) / 2)) - ) - ) val.append(xvg_df) self.results.xvg[component] = (np.array(lambdas), pd.concat(val)) From fd0a033b90ea0a86e144861565f3a4b332e6d58f Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 6 Sep 2023 19:05:40 +0100 Subject: [PATCH 35/38] Use get_forcefield() + docstrings --- mdpow/equil.py | 32 ++++++++++++-------------------- mdpow/forcefields.py | 25 +++++++++++++++++-------- 2 files changed, 29 insertions(+), 28 deletions(-) diff --git a/mdpow/equil.py b/mdpow/equil.py index 0f0ca3ae..29213ae3 100644 --- a/mdpow/equil.py +++ b/mdpow/equil.py @@ -35,7 +35,7 @@ import shutil from pathlib import Path from string import Template -from typing import Optional +from typing import Union import MDAnalysis as mda @@ -144,7 +144,10 @@ class Simulation(Journalled): } def __init__( - self, molecule=None, ff_class: Optional[forcefields.Forcefield] = None, **kwargs + self, + molecule=None, + forcefield: Union[forcefields.Forcefield, str] = "OPLS-AA", + **kwargs, ): """Set up Simulation instance. @@ -161,11 +164,9 @@ def __init__( :meth:`~mdpow.equil.Simulation.save`. *dirname* base directory; all other directories are created under it - *ff_class* - A :class:`mdpow.forcefields.Forcefield` instance. *forcefield* - A string representation of the forcefield, when using one of the defaults: - 'OPLS-AA' or 'CHARMM' or 'AMBER'. Not needed when :arg:`ff_class` is specified. + A :class:`~forcefields.Forcefield`, or the string name of a + packaged forcefield: 'OPLS-AA', 'CHARMM' or 'AMBER'. *solvent* 'water' or 'octanol' or 'cyclohexane' or 'wetoctanol' or 'toluene' *solventmodel* @@ -186,25 +187,16 @@ def __init__( advanced keywords for short-circuiting; see :data:`mdpow.equil.Simulation.filekeys`. + .. versionchanged:: 0.9.0 + `forcefield` may now be either a :class:`~forcefields.Forcefield` or + the string name of a builtin forcefield. + """ self.__cache = {} filename = kwargs.pop("filename", None) dirname = kwargs.pop("dirname", self.dirname_default) - if ff_class is not None: - if not isinstance(ff_class, forcefields.Forcefield): - raise TypeError( - f"`ff_class` must be a `forcefields.Forcefield` instance." - ) - forcefield: forcefields.Forcefield = ff_class - else: - forcefield_name = kwargs.pop("forcefield", "OPLS-AA") - try: - forcefield = forcefields.ALL_FORCEFIELDS[forcefield_name] - except KeyError: - raise ValueError( - f"No forcefield called `{forcefield_name}` is implemented. Please amend the `mdpow.forcefields.ALL_FORCEFIELDS` dictionary if you think it should be." - ) + forcefield = forcefields.get_forcefield(forcefield) solvent = kwargs.pop("solvent", self.solvent_default) # mdp files --- should get values from default runinput.cfg # None values in the kwarg mdp dict are ignored diff --git a/mdpow/forcefields.py b/mdpow/forcefields.py index 3de2fe84..7b15c04d 100644 --- a/mdpow/forcefields.py +++ b/mdpow/forcefields.py @@ -12,9 +12,10 @@ different force fields and the corresponding solvent topologies. The OPLS-AA, CHARMM/CGENFF and the AMBER/GAFF force field are directly -supported. In the principle it is possible to switch to a -different force field by supplying alternative template -files. +supported. It is possible to use a different forcefield by implementing +a :class:`Forcefield` with the correct files and supplying suitable +``.mdp`` files. For an example of how to do this, look at the +``martini-example.ipynb`` under ``doc/examples/martini-example``. .. autodata:: DEFAULT_FORCEFIELD @@ -39,6 +40,8 @@ :noindex: .. autodata:: GROMACS_SOLVENT_MODELS :noindex: +.. autodata:: ALL_FORCEFIELDS + :noindex: Internal classes and functions ------------------------------ @@ -232,7 +235,7 @@ def get_water_model(watermodel="tip4p"): class Forcefield: """Contains information about files corresponding to a forcefield. - .. versionadded: 0.9.0 + .. versionadded:: 0.9.0 """ @@ -348,6 +351,8 @@ def __repr__(self) -> str: default_water_model="tip3p", ) +#: The builtin forcefields' names and the corresponding :class:`Forcefield` +#: instance ALL_FORCEFIELDS: Dict[str, Forcefield] = { "OPLS-AA": OPLS_AA, "CHARMM": CHARMM, @@ -363,8 +368,12 @@ def __repr__(self) -> str: } -def _get_forcefield(ff: Union[str, Forcefield]) -> Forcefield: - """Get the :class:`Forcefield` instance corresponding to a given name.""" +def get_forcefield(ff: Union[str, Forcefield]) -> Forcefield: + """Get the :class:`Forcefield` instance corresponding to a given name. + + .. versionadded:: 0.9.0 + + """ if isinstance(ff, Forcefield): return ff try: @@ -404,7 +413,7 @@ def get_solvent_identifier( Raises :exc:`ValueError` instead of returning ``None``. """ - forcefield = _get_forcefield(forcefield) + forcefield = get_forcefield(forcefield) if solvent_type == "water": identifier = ( @@ -438,7 +447,7 @@ def get_solvent_model(identifier, forcefield: Union[Forcefield, str] = OPLS_AA): Function can now also accept a :class:`Forcefield` for the ``forcefield`` argument. """ - forcefield = _get_forcefield(forcefield) + forcefield = get_forcefield(forcefield) if identifier == "water": identifier = forcefield.default_water_model From 301c08e4e53d2848a12162b5ff2c6eed0d83a8e4 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 6 Sep 2023 19:06:06 +0100 Subject: [PATCH 36/38] Test ff __repr__ and use ALL_FORCEFIELDS --- mdpow/tests/test_forcefields.py | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/mdpow/tests/test_forcefields.py b/mdpow/tests/test_forcefields.py index e2f70746..ee728cf4 100644 --- a/mdpow/tests/test_forcefields.py +++ b/mdpow/tests/test_forcefields.py @@ -33,21 +33,28 @@ def test_oplsaa_ff(): @pytest.mark.parametrize( "ff_str,ff_instance", - [ - ("OPLS-AA", forcefields.OPLS_AA), - ("CHARMM", forcefields.CHARMM), - ("AMBER", forcefields.AMBER), - ("Violet Parr", None), + list( + forcefields.ALL_FORCEFIELDS.items() + ) # List of (ff_name, ff_instance) for all builtins + + [ + ("Violet Parr", None), # Nonexistent builtin ], ) def test_get_forcefield(self, ff_str, ff_instance): """Check that we can correctly cast a `Forcefield`.""" if ff_instance is not None: - assert forcefields._get_forcefield(ff_str) == ff_instance - assert forcefields._get_forcefield(ff_instance) == ff_instance + assert forcefields.get_forcefield(ff_str) == ff_instance + assert forcefields.get_forcefield(ff_instance) == ff_instance else: with pytest.raises(ValueError): - forcefields._get_forcefield(ff_str) + forcefields.get_forcefield(ff_str) + + @pytest.mark.parametrize( + "ff_str,ff_instance", list(forcefields.ALL_FORCEFIELDS.items()) + ) + def test_ff_repr(self, ff_str: str, ff_instance: forcefields.Forcefield): + """Test that forcefields are correctly represented by their names.""" + assert repr(ff_instance) == ff_str class TestIncludedSolvents(object): From 62687651bd126e517c642d383ee4f6a15b026c37 Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Wed, 6 Sep 2023 19:34:37 +0100 Subject: [PATCH 37/38] Fix reference to ff_class --- doc/examples/martini/martini-benzene.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/examples/martini/martini-benzene.ipynb b/doc/examples/martini/martini-benzene.ipynb index 21638773..4ac48b9b 100644 --- a/doc/examples/martini/martini-benzene.ipynb +++ b/doc/examples/martini/martini-benzene.ipynb @@ -1577,7 +1577,7 @@ "\n", "sim = WaterSimulation(\n", " molecule=\"BENZ\",\n", - " ff_class=MARTINI,\n", + " forcefield=MARTINI,\n", " mdp={\n", " \"energy_minimize\": str(EM_FILE.absolute()),\n", " \"MD_relaxed\": str(EQ_FILE.absolute()),\n", @@ -6582,7 +6582,7 @@ "\n", "oct_sim = OctanolSimulation(\n", " molecule=\"BENZ\",\n", - " ff_class=MARTINI,\n", + " forcefield=MARTINI,\n", " mdp={\n", " \"energy_minimize\": str(EM_FILE.absolute()),\n", " \"MD_relaxed\": str(EQ_FILE.absolute()),\n", From 364577631ab3b7c0782338c18578549662dc6b5d Mon Sep 17 00:00:00 2001 From: Alexander Moriarty Date: Thu, 7 Sep 2023 16:41:15 +0100 Subject: [PATCH 38/38] Correct init-lambda-value --- doc/examples/martini/run.mdp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/examples/martini/run.mdp b/doc/examples/martini/run.mdp index ed84f749..88e034e6 100644 --- a/doc/examples/martini/run.mdp +++ b/doc/examples/martini/run.mdp @@ -69,7 +69,7 @@ sc-r-power = 6 ; Which intermediate state do we start with? Doesn't really matter, it leaves soon ;------- -init-lambda-state = sedstate +init-lambda-state = 0.0 ; What are the values of lambda at the intermediate states? ;-------