📦 AutoMD-GROMACS — 技能工具

技能文档

AutoMD-GROMACS is an AI-oriented automation toolkit for GROMACS. It packages decision-layer routing, end-to-end simulation workflows, enhanced sampling, special-system simulation, advanced analysis, and publication-ready visualization into a public OpenClaw skill with troubleshooting references.

Project metadata:

• Version: 5.0.0
• Author: Guo Xuan
• Organization: Hong Kong University of Science and Technology (Guangzhou)
• Homepage: https://github.com/Billwanttobetop/automd-gromacs

Scope

• Decision layer: method routing before execution via method-selector
• Core workflow: setup, equilibration, production, preprocessing, utilities
• Enhanced sampling: umbrella, free energy, replica exchange, metadynamics, steered MD, enhanced sampling, accelerated MD
• Special systems: membrane, ligand, coarse-grained, electric field, non-equilibrium, QM/MM
• Validation and analysis: trajectory, binding, property, membrane, scattering, free-energy, protein-focused analyses
• Visualization: publication-ready plotting and structure/trajectory rendering

Quick Start

• Read references/SKILLS_INDEX.yaml
• If the method is not chosen yet, use scripts/decision/method-selector.py
• Run the recommended script under scripts/
• If something fails, read references/troubleshoot/-errors.md

Example:

python3 scripts/decision/method-selector.py \
  --goal "binding free energy from a docked complex" \
  --system-type protein-ligand \
  --target-observable binding-free-energy \
  --pretty

Design

• Decision -> execution -> validation as the public product stack
• Executable workflows over tutorial prose
• Layered disclosure for low token overhead
• Embedded domain knowledge from GROMACS practice
• Auto-repair and troubleshooting guidance by default

Project Info

• Version: 5.0.0
• Based on: GROMACS 2026.1
• Runtime needs: python3, PyYAML, gmx
• License: MIT
• Homepage: https://github.com/Billwanttobetop/automd-gromacs

Get started: read references/SKILLS_INDEX.yaml