Simple checkpointed Python scripting framework for Gromacs
There are some libraries around there wrapping gromacs commands (e.g.
GromacsWrapper). This one isn't a
library, it's a framework. gmxscript was designed to help programmers and
non-programmers to do reproducible science with Gromacs.
Enter sudo pip3 install gmxscript at your command line, but first you may need
to install Python 3.4 or higher. You also must have installed an working copy of
Gromacs 5 or higher. gmxscript tries to detect the Gromacs installation
automatically, but if it fails you need to source GMXRC as usual. Supposing
that you have the following sample in a file called protocol.py, run the
script with python3 protocol.py. Please take a look at a more comprehensive
example.
from gmxscript import *
# Enters in the checkpointed lysozyme/ directory, any command you run inside
# it is checkpointed. If you rerun this script, previously launched commands
# aren't started again
with system('1AKI'):
# Generate topology. The PDB file is downloaded automatically if not
# found in parent directories
pdb2gmx(
ff = 'gromos54a7',
water = 'spce',
f = PDB['1AKI'],
o = 'prot.gro',
p = 'topol.top'
)
# Apply periodic boundary condition
editconf(
f = 'prot.gro',
o = 'pbc.gro',
bt = 'dodecahedron',
d = 1.4
)
# Minimize energy using the steep descent algorithm. The .mdp file is
# looked up in parent directories and has these parameters added or
# modified
grompp(
f = MDP['em.mdp', {
'integrator': 'steep',
'emtol' : 10.0,
'nsteps' : 500,
}],
c = 'ions.gro',
o = 'sd.tpr',
p = 'topol.top'
)
# If there is a checkpoint file (.cpt) and the simulation wasn't
# finished (i.e. there isn't a .gro file), then the simulation is
# restarted. But it works only if you provides the -deffnm option here.
mdrun(deffnm = 'sd')