Commands and scripts for MD using GROMACS
Status: Not complete. Currently porting a more complex module to a stripped-back simplified version.
Creates shell scripts for running full the MD process from start to finish with some simple analysis too. Only uses Python standard library, but GROMACS (gmx) will need to be installed locally if one wishes to run anything locally (this can be a pain in Windows).
For HPC integration with BlueCrystal (UOB only), ssh-keygen and ssh-copy-id will need to be on the system path - if using Windows + Cygwin, these are in the C:/cygwin/bin directory. This is not fully implemented yet - the local script produced has be run manually.
Before running, create a directroy to work in on the local side and place the pdb(s) and MDPs here. Edit the MDP files to your liking, e.g. increase nsteps in md.mdp for longer simulations.
Simple Example:
import gmx
gmx.USER = 'yourname' # UOB BlueCrystal account username
# BCP3 used currently. Set gmx.BCP3 = '@path.to.bcp4' for BCP4 submission (not currently configured).
g = gmx.Gmx(
'mol.pdb',
cwd='path/to/work/directory',
remote=True, # for remote runs only
mpi=True, # set to True for remote runs, even if only using one node
key_gen=False, # creates RSA key pair for ssh if True
hrs=24, # hours to request in qsub
num_nodes=1, # number of nodes to run on
gpu=1) # request a gpu - increases speed
g.run_basic(
all_remote=True, # runs all commands remotely
trjconv=dict(center_group=1, out_group=1), # trjconv options
rmsd=dict(fit_group1=4, fit_group2=4)) # rms options
If running in remote or dry mode, only the run scripts are created and nothing is executed. If not dry or remote then it will attempt to run locally.