- name
- automd-gromacs
- description
- 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.
- metadata
- openclaw
- emoji
- 🧬
- category
- science
- requires
- bins
- install
- kind
- conda
- channel
- conda-forge
- package
- gromacs
- bins
- label
- Install GROMACS via conda
- kind
- manual
- url
- https://manual.gromacs.org/current/install-guide/index.html
- label
- Install GROMACS from source
- kind
- manual
- url
- https://pyyaml.org/wiki/PyYAMLDocumentation
- label
- Install PyYAML for the decision layer (
pip install pyyaml)
AutoMD-GROMACS
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/<skill>-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 \
--prettyDesign
- 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