OpenMM: Difference between revisions
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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 = | |||
= Running Simulation with AMBER Topology and Restart Files = | |||
== Preparing Python Virtual Environment == | |||
== Job submission == | |||
Below is a job script for a simulation using one A100 GPU. | Below is a job script for a simulation using one A100 GPU. | ||
{{File | {{File | ||
Revision as of 17:59, 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.
Running Simulation with AMBER Topology and Restart Files
Preparing Python Virtual Environment
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