openmm-langevin-dynamics-starter

Name: openmm-langevin-dynamics-starter
Author: ma-compbio-lab

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How to install openmm-langevin-dynamics-starter?

ma-compbio-lab/skillfoundry/openmm-langevin-dynamics-starter

$npx -y skills add ma-compbio-lab/SkillFoundry --skill openmm-langevin-dynamics-starter

Installs into the current project.

Summary

Use this skill to run a deterministic toy Langevin dynamics simulation in OpenMM and inspect a compact trajectory summary.

Files · 1

SKILL.md

1	# OpenMM Langevin Dynamics Starter
2
3	Use this skill to run a deterministic toy Langevin dynamics simulation in OpenMM and inspect a compact trajectory summary.
4
5	## What This Skill Does
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7	- builds a two-particle harmonic system
8	- runs short Langevin dynamics on the OpenMM Reference platform
9	- records bond-length and potential-energy snapshots over time
10
11	## When To Use It
12
13	- when you need a runnable starter for `molecular-dynamics-setup`
14	- when you want a local OpenMM smoke path before scaling to larger systems
15	- when you need deterministic MD-like outputs in repository tests
16
17	## Run
18
19	```bash
20	./slurm/envs/chem-tools/bin/python skills/computational-chemistry-and-molecular-simulation/openmm-langevin-dynamics-starter/scripts/run_openmm_langevin_dynamics.py --out scratch/openmm/langevin_dynamics_summary.json
21	```
22
23	## Notes
24
25	- This is a tiny synthetic system, not a physically meaningful production simulation.
26	- The Reference platform plus a fixed velocity seed keeps the summary reproducible.

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