OpenMM: Difference between revisions
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(Created page with "=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...") |
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=Introduction= | =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. | 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 | |||
|name=submit_openmm.cuda.sh | |||
|lang="sh" | |||
|contents= | |||
#!/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 | |||
}} | |||
Revision as of 17:53, 29 January 2022
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