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Agent skill

Gromacs

by ZimoLiao in ZimoLiao/scholaraio

A skill your agent uses when working on biomolecular molecular dynamics with GROMACS, including system setup, equilibration, production runs, trajectory analysis, or MM/PBSA-style post-processing.

MITAuto-check passedResearch & Science

Install Gromacs

skills CLI
$ npx skills add ZimoLiao/scholaraio --skill gromacs -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install ZimoLiao/scholaraio gromacs --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/gromacs .claude/skills/gromacs && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
gromacs
GitHub stars
577
Token cost
~848 tokens
SKILL.md length
288 words
Files
1
Skills in repo
43
Repo updated
First seen
Licence
MIT

At a glance

A skill your agent uses when working on biomolecular molecular dynamics with GROMACS, including system setup, equilibration, production runs, trajectory analysis, or MM/PBSA-style post-processing.

  • Works in 5 steps: 先判断问题属于哪一层：gmx 子命令、.mdp 参数、分析工具、力场/拓扑流程 → 写 .mdp 前先查… → 对用户自然语言说法，先 search 再 show → …
  • Working on biomolecular molecular dynamics with GROMACS
  • SKILL.md covers Agent 默认协议（toolref-first）, 前置条件, 何时使用 and Toolref 优先, plus 5 more sections
  • Calls conda and pip

What it does

Gromacs is an agent skill from ZimoLiao/scholaraio. Use when working on biomolecular molecular dynamics with GROMACS, including system setup, equilibration, production runs, trajectory analysis, or MM/PBSA-style post-processing.

Its SKILL.md is about 850 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Physical and earth sciences. The repository describes itself as: Scholar All-In-One: A research infrastructure for AI agents. The licence is MIT.

When your agent uses it

  • Working on biomolecular molecular dynamics with GROMACS
  • Including system setup
  • Production runs
  • Trajectory analysis

Example prompts

  • “/gromacs”

Requirements

  • Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. 先判断问题属于哪一层：gmx 子命令、.mdp 参数、分析工具、力场/拓扑流程
  2. 写 .mdp 前先查 thermostat、barostat、constraints、cutoff、输出频率这类高风险参数
  3. 对用户自然语言说法，先 search 再 show
  4. 如果 toolref 已经能回答，就不要在 skill 中重复堆参数表
  5. 如果 toolref 缺页或命中不理想，agent 应先完成任务，并明确这是 toolref 覆盖缺口，而不是用户需要自己手动适配

What it can do on your machine

Read from SKILL.md and the folder at commit 777628b. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • conda
    • pip

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Gromacs loads about 848 tokens when it runs. Until then it costs about 46 tokens; SKILL.md has 288 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~46
When it runs · the whole SKILL.md, loaded when a task matches
~848

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ZimoLiao/scholaraio at commit 777628b, republished under its MIT licence (© ZimoLiao). 288 words, ~848 tokens.

Download SKILL.mdSave it as .claude/skills/gromacs/SKILL.md (or your agent's skills folder).
name
gromacs
description
Use when working on biomolecular molecular dynamics with GROMACS, including system setup, equilibration, production runs, trajectory analysis, or MM/PBSA-style post-processing.

GROMACS 分子动力学

用 GROMACS 做分子动力学模拟：从体系搭建、平衡、产出 MD 到轨迹分析和结合自由能评估。

本 skill 故意保持轻量：

  • 它负责告诉 agent 什么时候该用 GROMACS、标准工作流是什么、哪些科学规范不能踩
  • 它不充当完整命令手册
  • 具体命令行选项、.mdp 参数、子命令语法统一去查 scholaraio toolref

Agent 默认协议（toolref-first）

对 GROMACS 问题，agent 默认按这个顺序工作：

  1. 先判断问题属于哪一层：gmx 子命令、.mdp 参数、分析工具、力场/拓扑流程
  2. 写 .mdp 前先查 thermostat、barostat、constraints、cutoff、输出频率这类高风险参数
  3. 对用户自然语言说法，先 search 再 show
  4. 如果 toolref 已经能回答，就不要在 skill 中重复堆参数表
  5. 如果 toolref 缺页或命中不理想，agent 应先完成任务，并明确这是 toolref 覆盖缺口，而不是用户需要自己手动适配

这意味着：

  • 普通用户不需要自己打磨 GROMACS 参数映射
  • agent 应优先自己把 Parrinello-Rahman、v-rescale thermostat、constraints h-bonds 等问法映射到参数页
  • skill 负责路线和规范，toolref 负责参数与接口

前置条件

bash
# 安装
conda install -c conda-forge gromacs
# 配体参数化
conda install -c conda-forge acpype ambertools
# 结合自由能
pip install gmx-MMPBSA
# 可视化（可选）
conda install -c conda-forge pymol-open-source

验证：gmx --version 应显示版本号和 GPU 支持信息。

何时使用

适合：

  • 蛋白-配体结合、蛋白构象变化、膜蛋白、溶液中生物大分子
  • 需要标准 MD 流程、轨迹分析、MM/PBSA 估算

不适合：

  • 需要量子化学精度时，转 DFT / QM/MM
  • 配体参数化来源不明、力场体系不一致时，不要直接推进

Toolref 优先

当 agent 不确定子命令、选项、.mdp 参数含义时，先查 toolref。

常用查法：

bash
scholaraio toolref search gromacs "temperature coupling"
scholaraio toolref show gromacs mdp integrator
scholaraio toolref show gromacs mdp pcoupl
scholaraio toolref show gromacs mdp tau-t
scholaraio toolref show gromacs mdp ref-t

推荐习惯：

  • 写 .mdp 前，先逐项查核心参数
  • 不靠记忆拼写 thermostat/barostat 选项
  • 对“这项参数在当前版本是否还推荐”这类问题，优先相信 toolref 而不是旧教程

如果遇到覆盖缺口：

  • 先继续使用 GROMACS 官方文档完成任务
  • 在输出中点明这里超出了当前 toolref 覆盖
  • 不要把补齐 toolref 当成普通用户的前置工作

核心流程

知识库协作模式

这是本 skill 与普通 GROMACS 教程的核心区别。在任何模拟开始前：

  1. 用 scholaraio usearch "<体系关键词>" 检索知识库中的相关论文
  2. 从论文中提取：力场选择依据、模拟参数（温度、压力、时长）、验证基准数据
  3. 在 .mdp 文件注释中标注参数来源（如 "# 300 K, per Homeyer et al. 2014 JCTC"）
  4. 模拟完成后，将结果与论文数据定量对比

建议工作流：

  1. 读论文，确定力场、温压条件、盐浓度、模拟时长和验证指标
  2. 准备蛋白/配体结构与拓扑
  3. 构建溶剂盒并加离子
  4. 能量最小化
  5. NVT / NPT 平衡
  6. 产出 MD
  7. 轨迹分析
  8. 必要时做 MM/PBSA，并和文献/实验对比

典型输出：

  • RMSD / RMSF / 氢键 / 回旋半径
  • 关键构象快照或轨迹动画
  • 结合自由能及误差条
  • 对应文献基准的对比图
常见查询点
  • .mdp 核心参数：integrator, dt, pcoupl, tcoupl, tau-t, ref-t
  • 产出阶段系综设置
  • PME / cutoff / 压缩轨迹输出参数
  • 不同版本对 thermostat/barostat 的推荐配置

这些都应优先通过 toolref 查询，而不是写死在 skill 里。

科学规范（专家级检查清单）

检查项正确做法常见错误
力场CHARMM36m 或 AMBER ff19SB用过时的 OPLS-AA
配体参数化GAFF2 + AM1-BCC (ACPYPE)自动生成的垃圾拓扑
力场一致性全 AMBER 或全 CHARMM，不混用CHARMM 蛋白 + GAFF 配体
产出恒压器Parrinello-Rahman产出阶段用 Berendsen
盒子形状十二面体（省 30% 水）立方体
离子浓度0.15 M NaCl只中和电荷不加盐
MM/PBSA 取样最后 10 ns（平衡后）用整条轨迹
误差报告ΔG ± σ只报单个值

附加规范：

  • 平衡阶段和产出阶段不要混用目标不同的耦合设置而不说明理由
  • 配体参数化来源必须可追溯
  • 报告结果时不要只给一条 RMSD 曲线，要回到生物物理问题本身

可视化

工具用途
PyMOL结合口袋特写、氢键、光线追踪静态图
VMD轨迹动画、表面渲染
matplotlibRMSD/RMSF/能量时间序列、验证对比图
nglviewJupyter 中交互式 3D

性能参考

体系大小GPU 配置预期性能
~45k 原子1×A100~150 ns/day
~45k 原子4×A100~400-600 ns/day
~100k 原子4×A100~200-300 ns/day

Agent 行为准则

  • 不要背诵 .mdp 参数，查 toolref
  • 不要把“跑完轨迹”当成完成，必须给稳定性和机制解释
  • 不要忽略力场一致性问题
  • 不要把 MM/PBSA 单值当结论，必须报告区间和误差

© ZimoLiao, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in .claude/skills/gromacs of ZimoLiao/scholaraio.

Open the folder on GitHubat commit 777628b

Compare with similar skills

Gromacs next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

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Categories

Questions about Gromacs

What does Gromacs do?

A skill your agent uses when working on biomolecular molecular dynamics with GROMACS, including system setup, equilibration, production runs, trajectory analysis, or MM/PBSA-style post-processing. Gromacs is an agent skill from ZimoLiao/scholaraio. Use when working on biomolecular molecular dynamics with GROMACS, including system setup, equilibration, production runs, trajectory analysis, or MM/PBSA-style post-processing.

When should I use Gromacs?

Gromacs fits situations like: working on biomolecular molecular dynamics with GROMACS; including system setup; production runs; trajectory analysis.

How do I install Gromacs in Claude Code?

Run `npx skills add ZimoLiao/scholaraio --skill gromacs -a claude-code`. Or copy the skill folder (.claude/skills/gromacs in ZimoLiao/scholaraio) into .claude/skills/gromacs in your project. Claude Code loads it when a task matches its description.

How do I install Gromacs in Codex?

Run `npx skills add ZimoLiao/scholaraio --skill gromacs -a codex`. Or copy the skill folder (.claude/skills/gromacs in ZimoLiao/scholaraio) into .agents/skills/gromacs in your project. Codex loads it when a task matches its description.

Can I use Gromacs in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ZimoLiao/scholaraio --skill gromacs -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gromacs, .gemini/skills/gromacs, .github/skills/gromacs and .opencode/skills/gromacs in your project.

What does Gromacs need to run?

Going by SKILL.md and its folder, Gromacs needs the command-line tools its instructions call (conda and pip). Our summary lists: Python 3.

Does Gromacs access the network?

SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Gromacs safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Gromacs use?

Gromacs is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Gromacs use?

About 848 tokens (SKILL.md is roughly 3.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Gromacs?

Skills that share tags, products or a category with Gromacs: Astropy (zLanqing/codex-claude-academic-skills, 4.7k stars), Pymatgen (zLanqing/codex-claude-academic-skills, 4.7k stars), Cantera Ignition Delay (K-Dense-AI/scientific-agent-skills, 48k stars) and Weather (trpc-group/trpc-agent-go, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Gromacs?

ZimoLiao (a GitHub user) maintains it in ZimoLiao/scholaraio, which has 577 GitHub stars. The repository holds 43 skills in this directory. The repository was last updated on September 25, 2026.

Source: ZimoLiao/scholaraio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.