Fixed all the water models (SPC, SPC/E, TIP3P, TIP5P). They should al…

…l be working again with OPLSAA (2023 version). I alwo created examples for each of these water models and tested them. (They are all working, but there is a problem with the NVT protocol in the TIP5P example. Since NPT is working for this example, fixing NVT is a lower priority. I'll fix this later when I have time.)

examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt

@@ -1,7 +1,6 @@
 import "ethylene.lt"  # <- defines the "Ethylene" molecule type.
 import "benzene.lt"  # <- defines the "Benzene" molecule type.
 
-
 # Periodic boundary conditions:
 write_once("Data Boundary") {
    0.0  48.00  xlo xhi

examples/all_atom/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/system.lt

@@ -1,5 +1,5 @@
-import "spce_oplsaa.lt" # <- defines the "SPCE" (water) molecule type.
 import "methane.lt"     # <- defines the "Methane" molecule type (uses OPLSAA)
+import "spce_oplsaa.lt" # <- defines the "SPCE" (water) molecule type.
 
 # Periodic boundary conditions:
 write_once("Data Boundary") {

examples/all_atom/force_field_OPLSAA/waterSPCE+methane/run.in.npt

@@ -35,7 +35,7 @@ write_data   "system_after_min.data"
 
 
 timestep     1.0
-dump         1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz
+dump         1 all custom 2000 traj_npt.lammpstrj id mol type x y z ix iy iz
 
 
 # Turn on the barostat and thermostat

examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README.txt

@@ -0,0 +1,29 @@
+The purpose of this example is to test the density of water
+constructed using the OPLSAA force-field.  (I think this is SPC water, not SPCE)
+
+I just wanted some kind of sanity check to make sure we are converting
+the OPLSAA parameters into moltemplate/LAMMPS format correctly.
+
+The "TEST_density_estimate.txt" contains the results of that test.
+
+-------- Instructions: ---------
+
+More detailed instructions on how to build LAMMPS input files and
+run a short simulation are provided in other README files.
+
+step 1)
+README_setup.sh
+
+step 2)
+README_run.sh
+
+
+### Customizing atomic charges
+
+In this example, atomic charge for OPLSAA atoms is determined by @atom type
+(...according to a lookup table located at the beginning of the
+"oplsaa.lt" file).
+(Note: Any atomic charges listed in the "Data Atoms" section will be ignored.)
+**These charges can be overridden.**
+See the "README.md" file located in the parent directory
+for instructions explaining how to customize atomic charge.

examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_remove_irrelevant_info.sh

@@ -0,0 +1,11 @@
+
+# Note: By default, the system.data and system.in.settings files contain
+# extra information for atoms defined in OPLSAA which you are not using
+# in this simulation.
+# This is harmless, but if you to delete this information from your
+# system.in.settings and system.in.data files, run this script:
+
+cleanup_moltemplate.sh
+
+# (Note: Removing unecessary atom types will make it easier to visualize the
+#        simulation in VMD.)

examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh

@@ -0,0 +1,20 @@
+# --- Running LAMMPS ---
+# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
+# input scripts which link to the input scripts and data files
+# you hopefully have created earlier with moltemplate.sh:
+#   system.in.init, system.in.settings, system.data
+# If not, carry out the instructions in "README_setup.sh".
+#
+#  -- Instructions: --
+# If "lmp_mpi" is the name of the command you use to invoke lammps,
+# then you would run lammps on these files this way:
+
+
+lmp_mpi -i run.in.npt  # minimization and simulation at constant pressure
+lmp_mpi -i run.in.nvt  # simulation at constant volume
+
+
+# If you have compiled the MPI version of lammps, you can run lammps in parallel
+#mpirun -np 4 lmp_mpi -i run.in.npt
+#mpirun -np 4 lmp_mpi -i run.in.nvt
+# (assuming you have 4 processors available)

examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh

@@ -0,0 +1,50 @@
+
+# Create LAMMPS input files this way:
+cd moltemplate_files
+
+  # run moltemplate
+
+  # This was the original (simple) way to run moltemplate:
+  # moltemplate.sh  system.lt  <-- COMMENTING OUT
+  # Instead, this is the recommended way to run moltemplate with OPLSAA:
+
+  moltemplate.sh  system.lt  -report-duplicates bytype __
+
+  # (The optional "-report-duplicates bytype __" arguments check to make
+  #  sure that there was no ambiguity in the dihedrals that were generated.
+  #  This is an issue with OPLSAA.  If there was, then moltemplate will create
+  #  a file named "warning_duplicate_dihedrals.txt".)
+  #
+  # (Note: You can also check for missing angle,dihedral params this way:)
+  # moltemplate.sh -checkff system.lt 
+
+
+  # Moltemplate generates various files with names ending in *.in* and *.data.
+  # Move them to the directory where you plan to run LAMMPS (in this case "../")
+  mv -f system.data system.in* ../
+
+  # Optional:
+  # The "./output_ttree/" directory is full of temporary files generated by
+  # moltemplate.  They can be useful for debugging, but are usually thrown away.
+  rm -rf output_ttree/
+
+  # Optional:
+  rm -f run.in.EXAMPLE  # not needed.  We have several run.in... files already.
+
+  # Optional:
+  # If any warnings were generated, move them to the parent folder
+  # (so they get noticed).
+  mv -f warning*.txt ../ 2> /dev/null
+
+cd ../
+
+
+
+
+# Optional:
+# Note: The system.data and system.in.settings files contain extra information
+# for atoms defined in OPLSAA which you are not using in this simulation.
+# This is harmless, but if you to delete this information from your
+# system.in.settings and system.in.data files, run this script:
+#
+# cleanup_moltemplate.sh

examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_visualize.txt

@@ -0,0 +1,87 @@
+
+ ------- To view a lammps trajectory in VMD --------
+
+
+1) Build a PSF file for use in viewing with VMD.
+
+This step works with VMD 1.9 and topotools 1.2.
+(Older versions, like VMD 1.8.6, don't support this.)
+
+
+a) Start VMD
+b) Menu  Extensions->Tk Console
+c) Enter:
+
+(I assume that the the DATA file is called "system.data")
+
+   topo readlammpsdata system.data full
+   animate write psf system.psf
+
+2)
+
+Later, to Load a trajectory in VMD:
+
+  Start VMD
+  Select menu: File->New Molecule
+ -Browse to select the PSF file you created above, and load it.
+  (Don't close the window yet.)
+ -Browse to select the trajectory file.
+  If necessary, for "file type" select: "LAMMPS Trajectory"
+  Load it.
+
+   ----  A note on trajectory format: -----
+If the trajectory is a DUMP file, then make sure the it contains the
+information you need for pbctools (see below.  I've been using this
+command in my LAMMPS scripts to create the trajectories:
+
+  dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
+
+It's a good idea to use an atom_style which supports molecule-ID numbers
+so that you can assign a molecule-ID number to each atom.  (I think this
+is needed to wrap atom coordinates without breaking molecules in half.)
+
+Of course, you don't have to save your trajectories in DUMP format,
+(other formats like DCD work fine)  I just mention dump files
+because these are the files I'm familiar with.
+
+3) -----  Wrap the coordinates to the unit cell
+          (without cutting the molecules in half)
+
+a) Start VMD
+b) Load the trajectory in VMD (see above)
+c) Menu  Extensions->Tk Console
+d) Try entering these commands:
+
+    pbc wrap -compound res -all
+    pbc box
+
+    ----- Optional ----
+    Sometimes the solvent or membrane obscures the view of the solute.
+    It can help to shift the location of the periodic boundary box
+    To shift the box in the y direction (for example) do this:
+
+    pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
+    pbc box -shiftcenterrel {0.0 0.15 0.0}
+
+    Distances are measured in units of box-length fractions, not Angstroms.
+
+    Alternately if you have a solute whose atoms are all of type 1,
+    then you can also try this to center the box around it:
+
+    pbc wrap -sel type=1 -all -centersel type=2 -center com
+
+4)
+    You should check if your periodic boundary conditions are too small.
+    To do that:
+       select Graphics->Representations menu option
+       click on the "Periodic" tab, and
+       click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
+
+5) Optional: If you like, change the atom types in the PSF file so
+   that VMD recognizes the atom types, use something like:
+
+sed -e 's/   1    1      /   C    C      /g' < system.psf > temp1.psf
+sed -e 's/   2    2      /   H    H      /g' < temp1.psf  > temp2.psf
+sed -e 's/   3    3      /   P    P      /g' < temp2.psf  > system.psf
+
+(If you do this, it might effect step 2 above.)

examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/TEST_density_estimate.txt

@@ -0,0 +1,20 @@
+This system contains 1728 water molecules
+(This is SPC water I think.)
+
+Then I ran a short simulation for 170000 timesteps at 300Kelvin and 1 atm.
+(that's when it crashed.  I'll worry about why later...)
+
+Anyway, the average volume was 52149.8 (in Angstroms^3)
+(for the last 80000 timesteps, after it had equilibrated)
+
+Given that the mass of water is 18.0154 grams per mole, I'm getting
+this value for the density:
+
+density = (1728*18.0154/6.02214129e23) / (52149.8*1e-30*1e6)
+        = 0.991 (in grams per mL)
+
+I'm only looking for gross errors in the OPLSAA force-field.
+So I'm satisfied with a 1% error.
+But I realize this is not a particularly rigorous test.
+
+Andrew 2014-5-21

examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/system.lt

@@ -0,0 +1,19 @@
+import "spc_oplsaa.lt" # <- defines the "SPC" (water) molecule type
+
+# NOTE: The "spc_oplsaa.lt" file is located in the moltemplate/force_fields/
+#       folder (distributed with moltemplate).
+
+# Periodic boundary conditions:
+write_once("Data Boundary") {
+   0.0  41.40  xlo xhi
+   0.0  41.40  ylo yhi
+   0.0  41.40  zlo zhi
+}
+
+# The next command generates a (rather dense) cubic lattice with
+# spacing 3.45 Angstroms. (The pressure must be equilibrated later.)
+
+waters = new SPC [12].move(0.00, 0.00, 3.45) 
+                 [12].move(0.00, 3.45, 0.00) 
+                 [12].move(3.45, 0.00, 0.00)
+

examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.npt

@@ -0,0 +1,45 @@
+# PREREQUISITES:
+#
+#     You must use moltemplate.sh to create 3 files:
+#        system.data  system.in.init  system.in.settings
+#     (Follow the instructions in README_setup.sh, 
+#      or run the file as a script using ./README_setup.sh)
+#
+# ------------------------------- Initialization Section --------------------
+
+include      "system.in.init"        # specify the style of force field used
+
+# ------------------------------- Atom Definition Section -------------------
+
+read_data    "system.data"
+
+# ------------------------------- Settings Section --------------------------
+
+include      "system.in.settings"    # load the force field parameters
+include      "system.in.charges"     # load the charge of each atom
+
+# ------------------------------- Run Section -------------------------------
+
+
+# -- minimization protocol --
+
+thermo       50
+minimize 1.0e-4 1.0e-6 100000 400000
+
+unfix fShakeSPC    # Disable SHAKE during minimization and pressure equilibr
+
+# Optional: write the coordinates after minimization
+write_data   "system_after_min.data"
+
+
+# -- simulation protocol --
+
+
+timestep     1.0
+dump         1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz
+fix          fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
+thermo       100
+
+run          100000
+
+write_data   "system_after_npt.data"