From 2cd68774c2e736763ccb2865e9dadc65987fc7bf Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 17 Feb 2026 17:36:52 +0000
Subject: [PATCH 1/2] Initial plan


From 90fa75cbead77a2f19f4feb34a14f40f26c5e11f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 17 Feb 2026 17:38:55 +0000
Subject: [PATCH 2/2] Create comprehensive organization README for ChatMol

Co-authored-by: JinyuanSun <33344948+JinyuanSun@users.noreply.github.com>
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-# .github
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+# ChatMol Organization
+
+[![GitHub Stars](https://img.shields.io/github/stars/ChatMol?style=social)](https://github.com/ChatMol)
+[![Website](https://img.shields.io/badge/website-chatmol.org-blue)](https://chatmol.org)
+
+**Empowering molecular science with AI**
+
+ChatMol is an open-source organization dedicated to bridging the gap between large language models (LLMs) and molecular biology research. We develop tools that enable scientists to leverage AI capabilities for molecular design, simulation, and analysis through natural language interfaces.
+
+## 🎯 Mission
+
+We aim to make advanced molecular modeling and computational chemistry accessible to researchers by creating AI-powered tools that understand natural language commands and automate complex scientific workflows.
+
+## 🚀 Key Projects
+
+### [ChatMol](https://github.com/ChatMol/ChatMol)
+![Stars](https://img.shields.io/github/stars/ChatMol/ChatMol?style=social)
+
+Started as a PyMOL plugin, ChatMol has evolved into a comprehensive molecular design assistant. It translates natural language into PyMOL commands and provides:
+- PyMOL plugin for natural language control
+- Interactive Streamlit interface
+- Python package for molecular modeling
+- Automated structure prediction and analysis
+- Molecular docking capabilities
+- Sequence design tools
+- Small molecule analysis & generation
+
+**Featured in:** ACL 2024 Workshop on Language and Molecules (Oral Presentation)
+
+### [GROMACS Copilot](https://github.com/ChatMol/gromacs_copilot)
+![Stars](https://img.shields.io/github/stars/ChatMol/gromacs_copilot?style=social)
+
+*Let LLM run your MDs.*
+
+Automates molecular dynamics (MD) simulations using GROMACS through natural language commands. Features include:
+- Automated system setup for proteins and protein-ligand complexes
+- MD simulation execution
+- Analysis of RMSD, RMSF, Rg, H-bonds, and more
+- Support for multiple LLM providers (OpenAI, DeepSeek, Gemini)
+- Agent mode for long-running simulation workflows
+
+### [Molecule-MCP](https://github.com/ChatMol/molecule-mcp)
+![Stars](https://img.shields.io/github/stars/ChatMol/molecule-mcp?style=social)
+
+A Model Context Protocol (MCP) server that connects molecular science tools to Claude AI, enabling:
+- Direct integration with PyMOL and ChimeraX
+- Natural language control of molecular visualization software
+- Seamless interaction between AI and molecular modeling tools
+
+### [nano_cowork](https://github.com/ChatMol/nano_cowork)
+
+A minimal version of collaborative workflow tools for molecular research.
+
+## 🌐 Resources
+
+- **Website:** [chatmol.org](https://chatmol.org)
+- **Web Interface:** [xp.chatmol.org/chatmol.html](http://xp.chatmol.org/chatmol.html)
+- **Documentation:** Available in each project repository
+- **Paper:** [ACL 2024 L+M Workshop](https://aclanthology.org/2024.langmol-1.7/)
+
+## 🤝 Community & Support
+
+We welcome contributions from the community! Whether you're interested in:
+- Developing new features
+- Improving documentation
+- Reporting bugs
+- Suggesting enhancements
+
+Feel free to open issues or submit pull requests in the respective project repositories.
+
+## 🙏 Acknowledgements
+
+ChatMol is supported by:
+- [ChemXAI](https://www.chemxai.com/)
+- [WeComput](https://www.wecomput.com/)
+- [Levinthal](https://www.levinthal.bio/)
+
+## 📄 License
+
+Most ChatMol projects are released under the MIT License. Please check individual repositories for specific licensing information.
+
+---
+
+*Making molecular science more accessible through AI-powered tools*
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