Automd Gromacs

AutoMD-GROMACS: AI-friendly molecular dynamics automation for GROMACS with workflow, enhanced sampling, special-system simulation, advanced analysis, and publication-ready visualization. Built-in troubleshooting and token-optimized execution. Part of the AutoMD series.

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: 5.1.1
• 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

1. Read references/SKILLS_INDEX.yaml — structured index of all workflows
2. If the target method is unclear, run the decision layer:

   python3 scripts/decision/method-selector.py --goal "..." --system-type "..." --target-observable "..." --pretty
   

3. Execute the recommended script (e.g. bash scripts/advanced/freeenergy.sh --input ...)
4. On failure: look up the error code in the matching file under references/troubleshoot/ (e.g. freeenergy errors → references/troubleshoot/freeenergy-errors.md)

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
• Reusable MDP templates in references/templates/ (em, nvt, npt, production, membrane, freeenergy)

Project Info

• Version: 5.1.1
• 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