Internal molecular dynamics workflow utilities for MD Workbench.
Project description
MD Workbench
Internal molecular dynamics workflow utilities for the Zhong lab. The PyPI package is mdw-zhong, and the Python import package is md_workbench.
Use environment.yml or scripts/install_mdw_env.sh to prepare the conda runtime, then run mdw gui, mdw run --config default_config.json, mdw plot --config default_config.json, or mdw report --config default_config.json.
For short-peptide or cyclic-peptide ligands supplied as PDB, use docking.ligand_input_mode = "pdb" with docking.docking_mode = "skip".
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