biomolecular-md-workflow

Plan, run, review, and report defensible biomolecular docking and molecular dynamics workflows. Use for protein-ligand docking, docking-pose review, docking-to-MD validation, protein-only MD, membrane-protein MD, multimer modeling, mutation/redocking/MD comparisons, ligand or lipid parameterization decisions, trajectory analysis, free-energy escalation, and cases where MD should be avoided or caveated because the biological assembly, membrane state, protonation, ligand parameters, or starting pose is not reliable.