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Openmm forcefield assignment starter

Skill ma-compbio-lab/SkillFoundry/skills/computational-chemistry-and-molecular-simulation/openmm-forcefield-assignment-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill openmm-forcefield-assignment-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.1 KB, as published. Nobody here has run it

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

Keep looking

Skills are one crate of 328,083. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.