OpenMM Force-Field Assignment Starter

Use this skill to assign a simple water force field to a tiny PDB topology with OpenMM and summarize the resulting system.

What it does

• Loads a small example PDB topology.
• Applies OpenMM tip3p.xml with deterministic createSystem settings.
• Reports particle, residue, constraint, and force-class counts in JSON.

When to use it

• You need a verified local starter for force-field assignment.
• You want a small, deterministic system-construction check before longer OpenMM workflows.

Example

./slurm/envs/chem-tools/bin/python skills/computational-chemistry-and-molecular-simulation/openmm-forcefield-assignment-starter/scripts/run_openmm_forcefield_assignment.py \
  --input skills/computational-chemistry-and-molecular-simulation/openmm-forcefield-assignment-starter/examples/two_waters.pdb \
  --out scratch/openmm-forcefield/summary.json

Verification

• Skill-local tests: python3 -m unittest discover -s skills/computational-chemistry-and-molecular-simulation/openmm-forcefield-assignment-starter/tests -p 'test_*.py'
• Repository smoke target: make smoke-openmm-forcefield