Judgment

Best practices, provenance, and citation

PyMACS automates the workflow, but users still need scientific judgment. This page collects the practices that make runs easier to trust and easier to explain.

Best practices

  • Use a fresh run folder for every system or replicate.
  • Start with a short test run before committing to long production MD.
  • Keep raw inputs, parameter files, logs, and generated outputs together.
  • Record the ligand code, cofactor codes, force-field path, box type, and run length.
  • Review CGenFF penalty scores before treating ligand simulations as publication-grade.
  • Inspect RMSD and radius of gyration before interpreting contacts.
  • Treat contact maps as persistence evidence, not binding free energy.

Provenance note

A reproducible MD workflow should preserve the input structure, topology decisions, MDP settings, software environments, generated logs, and analysis outputs. PyMACS helps by keeping the numbered stages explicit.

Citation

Joseph M. Schulz, Robert C. Reynolds, Stephan C. Schurer. PyMACS: A python-based automation suite for GROMACS molecular dynamics setup, simulation, and analysis. European Journal of Medicinal Chemistry, Volume 316, Article 119038. DOI: 10.1016/j.ejmech.2026.119038.