Force fields and engine inputs

The library

CAPS ships its force fields as JSON files in data/forcefields: OPLS-AA (2005, 2020, 2024), PCFF and COMPASS (class II), CVFF, GAFF and GAFF2, AMBER, CHARMM, DREIDING, TraPPE, UFF, inorganic and clay sets, Martini and others. Commands accept a library name or a path.

caps ff info opls2005        # types, typing rules, styles and references
caps ff info pcff

1. Assign types

Typing rules are SMARTS patterns: each atom gets the type of the most specific rule it matches. caps ff type writes one type per atom and reports atoms left untyped or matched ambiguously.

caps ff type ps_md.data --ff opls2005 -o types.txt

0 untyped, 0 ambiguous
wrote types.txt

--explain prints, for every atom, the rule that won and the ones it beat; use it when a type looks wrong.

2. Parameters and engine files

caps ff apply looks up every bond, angle, dihedral and improper and the pair coefficients, assigns charges (with --charges auto, the force field's own scheme: fixed charges per type or bond increments), and writes the files for each engine:

caps ff apply ps_md.data --ff opls2005 --types types.txt -o ps_opls.data \
  --lammps-input ps_opls.in --lammps-run npt --steps 5000 --gromacs ps_opls

wrote ps_opls.in (the force field's own styles)
gromacs: CAPS's damped shifted force becomes PME in GROMACS (no DSF there)
gromacs: the cell is 23.8 Å across, less than 2 r_c (24 Å): GROMACS needs a larger cell (a supercell) or a shorter cut-off
wrote ps_opls.top, ps_opls.gro and ps_opls.mdp

The notes matter: this tutorial's cell is smaller than twice the cut-off, which GROMACS refuses. A production cell (thousands of atoms) passes. Run the results with:

lmp -in ps_opls.in
gmx grompp -f ps_opls.mdp -c ps_opls.gro -p ps_opls.top -o run.tpr && gmx mdrun -deffnm run

Class II force fields

PCFF and COMPASS carry cross terms (bond–bond, bond–angle, angle–angle, middle-bond and end-bond torsion couplings) and 9-6 Lennard-Jones pairs. The same two commands handle them; the LAMMPS input uses class2 styles:

caps ff type ps_md.data --ff pcff -o types_pcff.txt
caps ff apply ps_md.data --ff pcff --types types_pcff.txt -o ps_pcff.data --lammps-input ps_pcff.in

Options worth knowing

Next

• Tutorial 04 assigns a force field from Python and keeps it through a cure.
• Theory: Force fields for the functional forms and mixing rules.