A high-performance toolkit for molecular simulation. Use it as an application, a library, or a flexible programming environment. It includes extensive language bindings for Python, C, C++, and even Fortran.

References:

• Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon, Yutong Zhao, Kyle A. Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande. OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics. PLoS Comput. Biol. 13:e1005659, 2017.

• OpenMM Main Site

• Module Name: openmm (see the modules page for more information)
• Environment variables set:
  • OPENMM_EXAMPLES
• Example files in $TEMPLATE_EXAMPLES
• Reference data in /fdb/TEMPLATE/

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load openmm
[user@cn3144 ~]$ cp $OPENMM_EXAMPLES/input.pdb .
[user@cn3144 ~]$ cat << EOF > go.py
from openmm.app import *
from openmm import *
from openmm.unit import *
from sys import stdout
pdb = PDBFile('input.pdb')
forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
simulation = Simulation(pdb.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.minimizeEnergy()
simulation.reporters.append(PDBReporter('output.pdb', 1000))
simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True))
simulation.step(10000)
EOF
[user@cn3144 ~]$ python go.py

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. openmm.sh). For example:

#!/bin/bash
set -e
module load openmm
cp $OPENMM_EXAMPLES/benchmark.py .
cp $OPENMM_EXAMPLES/apoa1.pdb .
OPENMM_CPU_THREADS=$SLURM_NTASKS python benchmark.py --platform=CPU --test=apoa1pme --pme-cutoff=0.8

Submit this job using the Slurm sbatch command.

sbatch --n 8 -N 1 openmm.sh