Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/ma-compbio-lab/skillfoundry/openmm-system-minimizationnpx skills add ma-compbio-lab/SkillFoundry --skill openmm-system-minimizationgit clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundryWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/openmm-system-minimization)<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/openmm-system-minimization"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/openmm-system-minimization.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00038 | $0.00394 |
| Opus 5 | $0.00019 | $0.00197 |
| Sonnet 5 | $0.00008 | $0.00079 |
| Haiku 4.5 | $0.00004 | $0.00039 |
Grade A, and why
openmm-system-minimization scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
Purpose
Provide a minimal, runnable OpenMM starter that creates a small bonded system, minimizes its energy, and reports before/after energies and coordinates.
When to use
- You need a verified local OpenMM entry point.
- You want a tiny deterministic minimization example before scaling to larger simulations.
When not to use
- You need biomolecular force-field preparation or explicit-solvent production runs.
- You need ensemble sampling or long-timescale trajectories.
Inputs
- Optional JSON summary path
Outputs
- JSON summary with OpenMM version, platform, initial/final potential energy, and final coordinates
Requirements
slurm/envs/chem-toolswith OpenMM available
Procedure
- Run
slurm/envs/chem-tools/bin/python skills/computational-chemistry-and-molecular-simulation/openmm-system-minimization/scripts/run_openmm_minimization.py. - Compare
initial_potential_energy_kj_molandfinal_potential_energy_kj_mol. - Reuse the script as a seed for more realistic system-building workflows.
Validation
- The command exits successfully.
- Final potential energy is lower than the initial potential energy.
- Final coordinates are emitted for all particles.
Failure modes and fixes
- Missing OpenMM environment: run the script with
slurm/envs/chem-tools/bin/python. - Numerical issues: reset the toy system to the bundled defaults.
Safety and limits
- Educational starter only.
- This is not a physically meaningful production system.
Provenance
- OpenMM user guide: https://docs.openmm.org/latest/userguide/
Related skills
rdkit-molecular-descriptors
What ships with it
9 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 6d ago First seen · 50 lines · 38 tokens per session scan A 3c7ba171186d
openmm-system-minimization is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (38 stars, last pushed 4mo ago), licensed Apache-2.0. It adds 38 tokens to every session and 394 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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