parmed.tools.simulations.openmm module

This module contains functionality for running simulations with OpenMM using parameters defined in an input file for sander and pmemd.

parmed.tools.simulations.openmm.energy(parm, args, output=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)

Computes a single-point energy using OpenMM and prints the result to the desired output destination (defaults to stdout)

parmed.tools.simulations.openmm.minimize(parm, igb, saltcon, cutoff, restraintmask, weight, script, platform, precision, norun, tol, maxcyc)

Minimizes a snapshot. Use the existing System if it exists

parmed.tools.simulations.openmm.positional_restraints(mask, weights, refc, scriptfile=None)

Creates a positional restraint force from CustomExternalForce using the coordinates given in the refc restart file for the atoms specified in ‘mask’

parmed.tools.simulations.openmm.simulate(parm, args)

Runs a simulation using OpenMM