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Auto CGUI Agentic Pipeline

This project provides an agentic pipeline for automating CHARMM-GUI workflows and running molecular dynamics simulations using NAMD, with support for Retrieval-Augmented Generation (RAG) via LlamaIndex and Google Gemini.

1. Configuration

Before running the pipeline, update the configuration file:

Edit auto_cgui_master/config.yml with your CHARMM-GUI credentials and browser type. Example:

BASE_URL: https://charmm-gui.org/
CGUSER: your cgui email goes here
CGPASS: your plain text password goes here
BROWSER_TYPE: firefox
  • BASE_URL: URL for CHARMM-GUI (default: https://charmm-gui.org/)
  • CGUSER: Your CHARMM-GUI email/username
  • CGPASS: Your CHARMM-GUI password
  • BROWSER_TYPE: firefox or chrome

2. Installation

Install the following dependencies:

Python

  • Python 3.8 or any version compatible with the multiprocessing requirements of Selenium/Splinter

Python Libraries

Install these with pip:

  • selenium
  • splinter
  • pyyaml
  • mdtraj
  • requests
  • pdbfixer
  • openmm
  • yaml
  • llama_index
  • llama-index-llms-google-genai
  • llama-index-embeddings-google-genai

Example installation command:

pip install selenium splinter pyyaml mdtraj requests pdbfixer openmm PyYAML llama_index llama-index-llms-google-genai llama-index-embeddings-google-genai

System Requirements

  • geckodriver (required if using Firefox)
    • Download and add to your PATH.

3. Running the Agentic Pipeline

The main entry point for the agentic pipeline is the Jupyter notebook:

new_rag/namd_agent_master.ipynb

Open this notebook in Jupyter and follow the instructions in the cells to:

  • Generate and clean YAML configuration files for CHARMM-GUI jobs
  • Run CHARMM-GUI workflows (solution or bilayer)
  • Launch and monitor NAMD simulations
  • Perform post-processing and analysis
  • Use RAG (Retrieval-Augmented Generation) with LlamaIndex and Google Gemini for enhanced automation

Note:

  • The notebook expects the Google Gemini API key to be set in the environment variable GOOGLE_API_KEY for LlamaIndex integration.
  • Ensure all dependencies are installed and the config file is updated before running the notebook.

4. Additional Notes

  • For advanced usage or troubleshooting, refer to the code and comments in namd_agent_master.ipynb.
  • For legacy CHARMM-GUI automation and test case development, see the auto_cgui_master/README.md.

For questions or issues, please open an issue or contact the project maintainer.