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Skills automd-gromacs

AutoMD-GROMACS: Automated molecular dynamics simulation workflow - 13 Skills covering system setup, equilibration, production, analysis, free energy, ligand binding, membrane proteins, umbrella sampling, PCA, and workflows. Built-in auto-repair, 84.7% token savings. Part of the AutoMD series.

install
source · Clone the upstream repo
git clone https://github.com/openclaw/skills
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/openclaw/skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/billwanttobetop/automd-gromacs" ~/.claude/skills/clawdbot-skills-automd-gromacs && rm -rf "$T"
manifest: skills/billwanttobetop/automd-gromacs/SKILL.md
source content

AutoMD-GROMACS

Automated molecular dynamics simulation workflow for GROMACS, optimized for AI agents with built-in auto-repair and manual knowledge. Part of the AutoMD series for automated MD simulations.

Quick Start

  1. Read the index: 
    read references/SKILLS_INDEX.yaml
  2. Choose a skill (setup, freeenergy, umbrella, etc.)
  3. Execute: 
    bash scripts/<skill>.sh <args>
  4. If errors occur: 
    read references/troubleshoot/<skill>-errors.md

13 Skills Overview

Basic (P0): setup, equilibration, production, analysis
Advanced (P1): freeenergy, umbrella, membrane, ligand
Extended (P2): pca, workflow
Utility (P3): protein, utils, run

Architecture

3-layer progressive disclosure:

  • Layer 1: SKILL.md (this file) - quick overview
  • Layer 2: references/SKILLS_INDEX.yaml - structured index
  • Layer 3: scripts/.sh + references/troubleshoot/.md - executable scripts + troubleshooting

Design Principles

  • Executable > Readable: Direct runnable commands, not tutorials
  • Structured > Textual: YAML/scripts, not long docs
  • Embedded Facts > External References: 90+ manual knowledge points embedded
  • Auto-Repair > Manual Intervention: 8+ auto-repair functions

Token Optimization

  • Normal flow: 2,300 tokens (vs traditional 15,000)
  • 84.7% savings, 100% technical accuracy maintained

Project Info

  • Version: 2.1.0
  • Based on: GROMACS 2026.1
  • License: MIT
  • Verified: Real system validation (LYSOZYME 38376 atoms)

Get started: 

read references/SKILLS_INDEX.yaml