OpenMM
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Introduction
OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that makes it unique among MD simulation packages.
Job submission
Below is a job script for a simulation using one A100 GPU.
File : submit_openmm.cuda.sh
#!/bin/bash
#SBATCH -c1 --gpus=1
#SBATCH --mem-per-cpu=4000 --time=1:0:0
# Usage: sbatch $0
module purge
ml StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3
ml python/3.8.10 openmm/7.7.0 netcdf/4.7.4 hdf5/1.10.6 mpi4py/3.0.3
source env-parmed/bin/activate
python openmm_input.py