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Let LLM run your MDs.
| Date | Stars |
|---|---|
| 2026-07-31 | 263 |
| 2026-08-02 | 263 |
| 2026-08-06 | 263 |
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Momentum
0.0
growth rate 0.00%/day
# 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.
<table>
<tr>
<td align="center"><b>Protein</b></td>
<td align="center"><b>Protein-Ligand Complex</b></td>
</tr>
<tr>
<td align="center">
<img src="assets/1pga_gmx_copilot_animation.gif" alt="1pga" width="300">
</td>
<td align="center">
<img src="assets/prot_lig.gif" alt="3wzm" width="300">
</td>
</tr>
<tr>
<td align="center">
<a href="./assets/report.pdf">A demo of output report</a>
</td>
<td align="center">
<a href="./assets/prot_lig_rmsf.pdf">A demo of output report</a>
</td>
</tr>
</table>
## How to Run
### Before using a LLM
1. Install the package
```bash
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
```
2. Prepare a working dir and a input pdb
```bash
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
```bash
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
```bash
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
```
### Using Gemini
```bash
gmx_copilot --workspace md_workspace/ \
--prompt "setup simulation system for 1pga_protein.pdb in the workspace" \
--api-key $GEMINI_API_KEY \
--model gemini-2.0-flash \
--url https://generativelanguage.googleapis.com/v1beta/chat/completions
```
3. Agent mode
The agent mode is good automation of a long acting trajectory of using tools.
```bash
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](COMMERCIAL_LICENSE.md).
## 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.Excerpt of 3,827 characters
Read on GitHubWould you bet a product on this? Bounded 0–100 and slow moving.
matched fp:660450ec2f2582bb, llm:Repository name 'ChatMol' and description 'Let LLM run your MDs.' indicates use of large language models to run molecular dynamics (MD) simulations (GROMACS).
matched fp:660450ec2f2582bb, llm:Repository name 'ChatMol' and description 'Let LLM run your MDs.' indicates use of large language models to run molecular dynamics (MD) simulations (GROMACS).
matched fp:660450ec2f2582bb, llm:Repository name 'ChatMol' and description 'Let LLM run your MDs.' indicates use of large language models to run molecular dynamics (MD) simulations (GROMACS).