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gromacs-protein-analysis

gromacs-protein-analysis is a skill for Claude Code, Codex from CharlesHahn/DuIvySkills. It costs 284 tokens per session (4,033 once invoked), scanned A, original, GPL-3.0.

A workflow guide for analysing protein molecular-dynamics simulations, which model how atoms move over time. It describes procedures for correcting periodic-boundary artefacts, measuring motion and flexibility, and studying structural changes and interactions.

In plain words
What is it for?
Use it for PBC correction, RMSD, RMSF, radius of gyration, solvent-accessible surface area, dynamic correlations, contact matrices, principal-component analysis, and free-energy analysis.
Why use it?
It gives an agent an analysis process when it knows the question but not the steps or interpretation. This reduces mistakes when preparing simulation data and choosing analyses.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

not rated 22repo 2mo ago A scan 284 tokens GPL-3.0

Good fit Use it for PBC correction, RMSD, RMSF, radius of gyration, solvent-accessible surface area, dynamic correlations, contact matrices, principal-component analysis, and free-energy analysis.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/charleshahn/duivyskills/gromacs-protein-analysis
View source ↗ CharlesHahn/DuIvySkills
Install

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.

Any agent
npx skills add CharlesHahn/DuIvySkills --skill gromacs-protein-analysis
Clone the repo
git clone --depth 1 https://github.com/CharlesHahn/DuIvySkills

Made for: Claude Code, Codex.

Wrote 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.

agentmods badge for gromacs-protein-analysis

README.md
[![agentmods](https://agentmods.dev/badge/skills/charleshahn/duivyskills/gromacs-protein-analysis/github.svg)](https://agentmods.dev/skills/charleshahn/duivyskills/gromacs-protein-analysis)
Your own site
<a href="https://agentmods.dev/skills/charleshahn/duivyskills/gromacs-protein-analysis"><img src="https://agentmods.dev/badge/skills/charleshahn/duivyskills/gromacs-protein-analysis/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for gromacs-protein-analysis

Your own site · 80×15
<a href="https://agentmods.dev/skills/charleshahn/duivyskills/gromacs-protein-analysis"><img src="https://agentmods.dev/badge/skills/charleshahn/duivyskills/gromacs-protein-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 284 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,033 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00284 $0.04033
Opus 5.5 $0.00114 $0.01613
Sonnet 5.5 $0.00057 $0.00807
Haiku 4.5 $0.00028 $0.00403

Measured 2mo ago against content hash 20156864a520, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

gromacs-protein-analysis 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 2mo 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.

gromacs-protein-analysis/SKILL.md · 322 lines

The source is not reproduced here

Licensed GPL-3.0

The repository is licensed GPL-3.0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.

Read it on GitHub

Files

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.

Changes

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.

  1. 2mo ago First seen · 322 lines · 284 tokens per session scan A 20156864a520

Subscribe to this mod's changes

gromacs-protein-analysis is a skill published in the GitHub repository CharlesHahn/DuIvySkills (22 stars, last pushed 2mo ago), licensed GPL-3.0. It adds 284 tokens to every session and 4,033 once invoked, about $0.0011 per session on Opus 5.5. 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.

Scientific
Related

gromacs-protein-analysis compared with skills from other repositories

gromacs-protein-analysis next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
gromacs-protein-analysisCharlesHahn/DuIvySkillsSkill222mo agoGPL-3.0A284Claude Code, Codex
instrument-data-to-allotropeanthropics/knowledge-work-pluginsSkill35k2d agoApache-2.0A123Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA83Claude Code
matlabK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA44Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA71Claude Code, Codex
research-engineerdavila7/claude-code-templatesSkill33kyesterdayMITA43Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmedSkill5.8kyesterdayApache-2.0A205Claude Code