TAMD is an enhanced sampling method to explore free energy landscape. On the other hand, the string method has the ability to find minimum free energy paths connecting landmarks on the free energy surface.
The aim of this project is to implement TAMD/SM in PLUMED+GROMACS. The method also supports the implementation of solute tempering methods such as REST2, and gREST.
Please cite the following article if using this code:
PLUMED INSTALLATION:
- Create a new directory "mfep" to PLUMED home directory/src/
- Download and copy the MFEP.cpp and sm.h to mfep directory
- To enable MFEP, configure PLUMED with --enable-modules=mfep
- compile Plumed as usual
GROMACS INSTALLATION
- Copy the patch_resm_gmx_2019_6.patch to GROMACS home directory
- After patching with PLUMED, patch the file by executing: patch -p0 < patch_resm_gmx_2019_6.patch
- Compile GROMACS as usual.
With succesfull installation, the programs are now ready to launch string method calculation. The following input is used for SM calculation in 2D dihedral CV space
#Plumed input file:
MFEP ...
NIMAGES=8 # Number of Images
LABEL=mfep # label for code section
ARG=torsion1,torsion2 # Collective varibles
FICT=0.0,0.0 # Provide inital value for CV, with 0 it will pick the CV values directly from simulation.
KAPPA=100,100 # Force constant
GAMMABAR=100 # Friction parameter; with gammabar=0, mean force calculations can be achieved
INTERVAL=200 # Steps for force accumulation
INTERPOLATION=LINEAR # Interpolation scheme, use TAMD for TAMD calculations
FREQ=1 # Frequency for dumping the data
TEMP=0.0 # Temperature for finite tempeature string/TAMD
FICT_MAX=3.1415,3.1415 # Upper CV boundaries
FICT_MIN=-3.1415,-3.1415 # Lower CV boundaries
ATINDCV=1,2,3,4,2,3,4,5 # Local index assigned to atoms/groups/centers in CV
MCENTER=1,1,1,1,1,1,1,1 # Mass for each center
EVOLVE_ENDS=11 # Evolve both ends=11, first end=10, last end=01, Fix the end=00
... MFEP