Gromacs Wrappers

Functions

Run GROMACS commands with subprocess

gromacs.simulate(mdp, top, gro, out, verbose=False, em_energy=False, mpi=False, nprocesses=4, dd=None, restraints=False)

A wrapper for running GROMACS molecular dynamics simulations

Parameters:
  • mdp – name of GROMACS Molecular Dynamics Paramters (mdp) file
  • top – name of GROMACS topology (.top)
  • gro – name of GROMACS coordinate file (.gro)
  • out – name of output simulation files
  • verbose – if True, prints simulation output to the screen
  • em_energy – if this is an energy minimzation and this argument is True, return the final total energy
  • mpi – if True, run simulation in parallel using MPI
  • nprocesses – number of MPI process for an MPI simulation
  • dd – domain decomposition grid for parallelization. If this is not specified, GROMACS decides (which usually

works) :param restraints: True if position restraints are applied

gromacs.insert_molecules(gro, solute, n, out, scale=0.4, mpi=False, nprocesses=4)

Insert n solutes into a .gro file

Parameters:
  • gro – name of coordinate file where solutes will be placed
  • solute – name of solute to add to gro
  • n – number of solutes to add to gro
  • out – name of output configuration
  • scale – Scale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The

default value of 0.57 yields density close to 1000 g/l for proteins in water