OpenMM: Difference between revisions
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This example is for the openmm/7.7.0 module. | This example is for the openmm/7.7.0 module. | ||
1. Create and actvate Python virtual environment | |||
{{Commands|prompt=[name@server ~] | {{Commands|prompt=[name@server ~] | ||
| ml python | | ml python | ||
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| source env-parmed/bin/activate | | source env-parmed/bin/activate | ||
}} | }} | ||
2. Install ParmEd and netCDF4 Python modules | |||
{{Commands|prompt=(env-parmed)[name@server ~] | {{Commands|prompt=(env-parmed)[name@server ~] | ||
| pip install parmed==3.4.3 netCDF4 | | pip install parmed==3.4.3 netCDF4 | ||
Revision as of 18:24, 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
This example is for the openmm/7.7.0 module.
1. Create and actvate Python virtual environment
[name@server ~] ml python
[name@server ~] virtualenv env-parmed
[name@server ~] source env-parmed/bin/activate
2. Install ParmEd and netCDF4 Python modules
(env-parmed)[name@server ~]
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