| name | automd-gromacs |
| description | 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. |
| version | 2.1.0 |
| author | Guo Xuan |
| organization | Hong Kong University of Science and Technology (Guangzhou) |
| homepage | https://github.com/Billwanttobetop/automd-gromacs |
| metadata | {"openclaw":{"emoji":"🧬","category":"science","requires":{"bins":["gmx"]},"install":[{"id":"conda","kind":"conda","channel":"conda-forge","package":"gromacs","bins":["gmx"],"label":"Install GROMACS via conda"},{"id":"manual","kind":"manual","url":"https://manual.gromacs.org/current/install-guide/index.html","label":"Install GROMACS from source"}]}} |
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
- Read the index:
read references/SKILLS_INDEX.yaml
- Choose a skill (setup, freeenergy, umbrella, etc.)
- Execute:
bash scripts/<skill>.sh <args>
- 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
