Gmx_vmd

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.