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OpenMM: Difference between revisions
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== Job submission == <!--T:7--> | == Job submission == <!--T:7--> | ||
Below is a job script for a simulation using one GPU. | Below is a job script for a simulation using one GPU. | ||
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{{File | {{File | ||
|name=submit_openmm.cuda.sh | |name=submit_openmm.cuda.sh | ||
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# Usage: sbatch $0 | # Usage: sbatch $0 | ||
module purge | module purge | ||
module load StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 | module load StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 | ||
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source $HOME/env-parmed/bin/activate | source $HOME/env-parmed/bin/activate | ||
python openmm_input.py | python openmm_input.py | ||
}} | }} | ||
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<!--T:10--> | <!--T:10--> | ||
Here openmm_input.py is a python script loading amber files, creating the OpenMM simulation system, setting up the integration, and running dynamics. Example openmm_input.py is available [https://mdbench.ace-net.ca/mdbench/idbenchmark/?q=129 here]. | Here openmm_input.py is a python script loading amber files, creating the OpenMM simulation system, setting up the integration, and running dynamics. Example openmm_input.py is available [https://mdbench.ace-net.ca/mdbench/idbenchmark/?q=129 here]. | ||