概览
What is Gmx_vmd?
Gmx_vmd is a microservice that integrates GROMACS molecular dynamics simulations with VMD (Visual Molecular Dynamics) visualization. It facilitates molecular dynamics simulation setup, execution, analysis, and visualization through an easy-to-use API and natural language interfaces.
How to use Gmx_vmd?
Install Python 3.9+, GROMACS, and VMD, then clone the repository, create a virtual environment, install dependencies, and configure config.json. Start the server with python mcp_server.py. The service listens on localhost:8000 for HTTP requests. Optionally integrate with LLM assistants like Claude or Cursor IDE by adding an MCP configuration JSON file.
Key features of Gmx_vmd
- Setup and run GROMACS simulations with an easy-to-use interface
- Analyze simulation trajectories (RMSD, RMSF, etc.)
- Visualize molecular structures and trajectories using VMD
- Create and manage simulation workflows in custom directories
- Built on Model Context Protocol for flexible tool integration
Use cases of Gmx_vmd
- Set up a protein simulation in a water environment via natural language
- Analyze RMSD of a protein trajectory
- Visualize a protein structure showing secondary structure
- Calculate hydrogen bonds in an MD trajectory
- Create and manage simulation workflows in user-specified directories
FAQ from Gmx_vmd
What are the prerequisites for using Gmx_vmd?
Python 3.9+, GROMACS (installed and accessible in PATH), and VMD (Visual Molecular Dynamics, installed and accessible in PATH) are required.
How do I configure VMD and GROMACS paths?
Create a config.json file with the paths to the VMD and GROMACS executables, plus optional search paths for VMD.
Can I use custom directories for simulation workflows?
Yes, specify the workspace_dir parameter when creating a workflow to use a custom directory.
How do I integrate Gmx_vmd with an LLM assistant?
Add an MCP configuration JSON (e.g., claude_desktop_config.json or mcp.json) with the server command and environment variables, then restart the application.
What should I do if the VMD GUI closes immediately?
Launch VMD in a separate terminal window (default behavior) or use vmd -dispdev text for command-line operation without GUI.
