openmm-forcefield-assignment-starter

Name: openmm-forcefield-assignment-starter
Author: ma-compbio-lab

36stars5forks

How to install openmm-forcefield-assignment-starter?

ma-compbio-lab/skillfoundry/openmm-forcefield-assignment-starter

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

Installs into the current project.

Summary

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

Files · 1

SKILL.md

1	# OpenMM Force-Field Assignment Starter
2
3	Use this skill to assign a simple water force field to a tiny PDB topology with OpenMM and summarize the resulting system.
4
5	## What it does
6
7	- Loads a small example PDB topology.
8	- Applies OpenMM `tip3p.xml` with deterministic `createSystem` settings.
9	- Reports particle, residue, constraint, and force-class counts in JSON.
10
11	## When to use it
12
13	- You need a verified local starter for `force-field assignment`.
14	- You want a small, deterministic system-construction check before longer OpenMM workflows.
15
16	## Example
17
18	```bash
19	./slurm/envs/chem-tools/bin/python skills/computational-chemistry-and-molecular-simulation/openmm-forcefield-assignment-starter/scripts/run_openmm_forcefield_assignment.py \
20	--input skills/computational-chemistry-and-molecular-simulation/openmm-forcefield-assignment-starter/examples/two_waters.pdb \
21	--out scratch/openmm-forcefield/summary.json
22	```
23
24	## Verification
25
26	- Skill-local tests: `python3 -m unittest discover -s skills/computational-chemistry-and-molecular-simulation/openmm-forcefield-assignment-starter/tests -p 'test_*.py'`
27	- Repository smoke target: `make smoke-openmm-forcefield`

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