OpenMM on Biowulf

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:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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 ~]$

Batch job
Most jobs should be run as batch jobs.

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