GROMACS Copilot

Let LLM run your MDs.

The good news: 🎉 You now have more time to hang out with your cat! 🐱💖
The bad news: 😢 You'll miss out on GROMACS' legendary wisdom... 🧙‍♂️💬

Introduction

This agent automates MD simulations for proteins in water using GROMACS. It sets up the system, runs simulations, and analyzes RMSD, RMSF, Rg, H-bonds, etc.

Protein	Protein-Ligand Complex
A demo of output report	A demo of output report

How to Run

Before using a LLM

1. Install the package

pip install git+https://github.com/ChatMol/gromacs_copilot.git
conda install -c conda-forge acpype

2. Prepare a working dir and a input pdb

mkdir md_workspace && cd md_workspace
wget https://files.rcsb.org/download/1PGA.pdb
grep -v HOH 1PGA.pdb > 1pga_protein.pdb
cd ..

Using DeepSeek

gmx_copilot --workspace md_workspace/ \
--prompt "setup simulation system for 1pga_protein.pdb in the workspace" \
--api-key $DEEPSEEK_API_KEY \
--model deepseek-chat \
--url https://api.deepseek.com/chat/completions

Using OpenAI

gmx_copilot --workspace md_workspace/ \
--prompt "setup simulation system for 1pga_protein.pdb in the workspace" \
--api-key $OPENAI_API_KEY \
--model gpt-4o \
--url https://api.openai.com/v1/chat/completions

The agent handles system setup, simulation execution, and result analysis automatically. 🚀

License

This project is dual-licensed under:

• GPLv3 (Open Source License)
• Commercial License (For proprietary use)

For commercial licensing, read this.

Known issues

1. 🤖 LLM sometimes struggles with selecting the correct group index. Double-checking the selection is recommended.
2. ⚡ The interaction between LLM and gmx prompt input isn't always seamless. Running commands based on suggestions can help you get the correct results more easily.