Skip to content

Latest commit

 

History

History
96 lines (79 loc) · 3.5 KB

README.md

File metadata and controls

96 lines (79 loc) · 3.5 KB

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
1pga 3wzm
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 # for protein-ligand complex
conda install -c conda-forge gmx_mmpbsa # for MM-PBSA/GBSA analysis
  1. 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
  1. Agent mode The agent mode is good automation of a long acting trajectory of using tools.
gmx_copilot --workspace md_workspace/ \
--prompt "run 1 ns production md for 1pga_protein.pdb in the workspace, and analyze rmsd" \
--mode agent

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.

Disclaimer

GROMACS Copilot is provided "as is" without warranty of any kind, express or implied. The authors and contributors disclaim all warranties including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. Users employ this software at their own risk.

The authors bear no responsibility for any consequences arising from the use, misuse, or misinterpretation of this software or its outputs. Results obtained through GROMACS Copilot should be independently validated prior to use in research, publications, or decision-making processes.

This software is intended for research and educational purposes only. Users are solely responsible for ensuring compliance with applicable laws, regulations, and ethical standards in their jurisdiction.