Configuration file

run_md, run_prolif, and run_gbsa accept a --config option that supplies default arguments from a YAML file. Command-line arguments override YAML values.

Example config.yml for run_md:

protein: protein.pdb
ligand: ligand.mol
steps: 3 4
md_time: 2
box_type: cubic
box_padding_nm: 1
salt_concentration: 0.15
ion_pname: NA
ion_nname: CL
water_model: tip3p
seed: 1024

Run using the configuration:

run_md --config config.yml --ncpu 32

Notes:

• Use CLI flags to override specific settings.

• Combine with --steps to skip preparation or rerun analysis when continuing an existing run (see Running Molecular Dynamics).