Physics

Force fields included in PyMACS

The force field defines the classical physics model used by the simulation. PyMACS centers CHARMM-family workflows and ships both standard and LJ-PME-compatible CHARMM folders.

Why both CHARMM folders are shipped

  • Some systems are best prepared with the standard CHARMM36-family folder.
  • Some runs need the CHARMM36/LJ-PME-compatible route.
  • PyMACS can automatically try both paths when setup requires fallback behavior.
  • Shipping both makes curated examples and user systems more portable.

What the force field controls

Term Meaning
Bonds, angles, dihedrals How bonded atoms resist stretching, bending, and rotation.
Charges How atoms interact electrostatically.
Lennard-Jones terms How atoms attract or repel at short and medium range.
Topology files The atom, residue, molecule, and parameter definitions GROMACS needs.

How to think about alternatives

AMBER, OPLS, GROMOS, and Martini are important MD ecosystems. PyMACS highlights them educationally, but the automated workflow is built around CHARMM-family topology handling and CGenFF-style small-molecule support.