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OpenMM

OpenMM is a open-source high-performance toolkit for molecular simulation. You can use it as an application, a library, or a flexible programming environment.

Keywords: biology, physics, chemistry, molecular dynamics

Available modules

There are several OpenMM modules on Midway3 that you can check via module avail opemm:

---------------------------- /software/modulefiles -----------------------------
openmm/7.5.1(default)  openmm/8.1.0
Note

OpenMM is under active development. You are encouraged to build the latest stable version from source code in your own space using the provided compilers.

Note

You can also install OpenMM into your conda environment. See http://docs.openmm.org/7.0.0/userguide/application.html for more information 

module load python/anaconda-2022.05
conda create -n your-env python=3.8
source activate your-env
conda install -c conda-forge openmm cudatoolkit=11.5

The OpenMM documentation contain useful information for improving performance of your specific calculations:

https://openmm.org/documentation

Example job script

An example batch script to run GROMACS for Midway3 is given as below 

!/bin/bash
#SBATCH --job-name=gmx-bench
#SBATCH --account=pi-[cnetid]
#SBATCH --time=01:00:00
#SBATCH --partition=gpu
#SBATCH --gres=gpu:1
#SBATCH --constraint=v100
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1

module load openmm

cd $SLURM_SUBMIT_DIR

ntasks_per_node=$SLURM_NTASKS_PER_NODE
numnodes=$SLURM_JOB_NUM_NODES
n=$(( ntasks_per_node * numnodes ))

t=1000

python run_openmm.py
where run_openmm.py is a python script that sets up the system.

Example python scripts can be found at https://github.com/openmm/openmm/blob/master/examples/. Below is an example script that reads in a protein PDB structure, selects a force field, defines a system, specifies a time integrator, performs energy minimization, sets up the output log and snapshots and finally runs the MD simulation. You can use this script as run_openmm.py in the job script above.

from openmm.app import *
from openmm import *
from openmm.unit import *
from sys import stdout

pdb = PDBFile('input.pdb')
forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*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)