A method for using GROMACS molecular-dynamics trajectories to estimate how strongly two molecules bind. GROMACS is software that simulates molecular motion, and gmxMMPBSA is a tool for estimating binding free energy from those simulations.

Use it to study protein–protein or protein–ligand binding in any GROMACS system.

It provides a repeatable analysis process instead of requiring you to work out the binding-energy calculation from raw simulation data alone.

gmx-mmpbsa — Skill for Claude Code and Codex by CharlesHahn

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 gmx-mmpbsa

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/charleshahn/duivyskills/gmx-mmpbsa/github.svg)](https://agentmods.dev/skills/charleshahn/duivyskills/gmx-mmpbsa)

Your own site

<a href="https://agentmods.dev/skills/charleshahn/duivyskills/gmx-mmpbsa"><img src="https://agentmods.dev/badge/skills/charleshahn/duivyskills/gmx-mmpbsa/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/charleshahn/duivyskills/gmx-mmpbsa"><img src="https://agentmods.dev/badge/skills/charleshahn/duivyskills/gmx-mmpbsa.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 194 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 3,440 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.

Model	Per session	Once invoked
Fable 5.1	$0.00194	$0.03440
Opus 5.5	$0.00078	$0.01376
Sonnet 5.5	$0.00039	$0.00688
Haiku 4.5	$0.00019	$0.00344

Measured 2mo ago against content hash dbd00f6c015e, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

gmx-mmpbsa 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.

gmx-mmpbsa/SKILL.md · 231 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

6 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.

2mo ago First seen · 231 lines · 194 tokens per session scan A dbd00f6c015e

Subscribe to this mod's changes

gmx-mmpbsa is a skill published in the GitHub repository CharlesHahn/DuIvySkills (22 stars, last pushed 2mo ago), licensed GPL-3.0. It adds 194 tokens to every session and 3,440 once invoked, about $0.0008 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

gmx-mmpbsa next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
gmx-mmpbsaCharlesHahn/DuIvySkills	Skill	22	2mo ago	GPL-3.0	A	194	Claude Code, Codex
instrument-data-to-allotropeanthropics/knowledge-work-plugins	Skill	35k	2d ago	Apache-2.0	A	123	Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	83	Claude Code
matlabK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	44	Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	71	Claude Code, Codex
research-engineerdavila7/claude-code-templates	Skill	33k	yesterday	MIT	A	43	Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmed	Skill	5.8k	yesterday	Apache-2.0	A	205	Claude Code