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 via CLI (Recommended)
clawhub install openclaw/skills/skills/billwanttobetop/automd-gromacsAutoMD-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
Metadata
Not sure this is the right skill?
Describe what you want to build — we'll match you to the best skill from 16,000+ options.
Find the right skillPaste this into your clawhub.json to enable this plugin.
{
"plugins": {
"official-billwanttobetop-automd-gromacs": {
"enabled": true,
"auto_update": true
}
}
}Related Skills
auto-proteomics
Public OpenClaw skill for low-token routing and downstream analysis of processed DDA LFQ proteomics inputs. Use when the user already has protein-level quantification tables such as MaxQuant-style `proteinGroups.txt` and needs a clear two-group downstream workflow.
Automd Viz
Skill by billwanttobetop
Phylo Tree
Skill by billwanttobetop
protein-phylogeny
Comprehensive protein family phylogenetic analysis workflow with quality control, conservation analysis, coevolution network analysis, and publication-ready visualization. Use when: (1) analyzing protein family evolution, (2) building phylogenetic trees from sequences, (3) identifying conserved/coevolved residues, (4) generating publication-quality figures and reports, (5) quality-controlling sequence datasets, or (6) performing systematic evolutionary analysis of enzyme families, protein superfamilies, or any homologous protein groups.
protein-qc-strict
Strictest protein sequence analysis quality control workflow (3365→456 sequences). Includes literature validation, CD-HIT redundancy removal, complexity check, motif verification, MSA quality assessment, and conservation/coevolution analysis. Based on real research experience with IRED enzyme family.