Submits SLURM jobs to mindlessly run OpenMM simulations for pdb files in a folder.
Nonstandard amino acids, heteroatoms, and missing atoms are treated per the pdbfixer defaults.
See runtime/config/default_nvt_config.yaml for other default run parameters.
Developed for usage on bridges2 - modify the run_slurm_bridges.sh to your needs.
Usage:
- scp over our OpenMM apptainer container sif file to your repo directory
- Run the following bash command - replace the pdb_search_dir with the pdb directory and slurm_output_dir with the location for slurm output and error logs:
find pdb_search_dir -name "*.pdb" -exec sbatch --export=PDB_FILE={} --export=SLURM_OUTPUT_DIR=/ocean/projects/che210028p/skumar7/slurm_dumps run_slurm_bridges.sh
Docker container at: https://hub.docker.com/repository/docker/xygen34/dumd/general