Gmx_vmd

Name: Gmx_vmd
Author: egtai

@egtai

Repository

About Gmx_vmd

MCP service for GROMACS and VMD molecular dynamics simulations and visualization

Basic information

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "gmx_vmd": {
      "command": "{{PATH_TO_UV}}",
      "args": [
        "--directory",
        "{PATH_TO_SRC}/mcp-gmx-vmd",
        "run",
        "mcp",
        "run",
        "mcp_server.py"
      ],
      "env": {
        "PYTHONPATH": "{PATH_TO_SRC}/mcp-gmx-vmd",
        "MCP_DEBUG": "1",
        "PYTHONUNBUFFERED": "1"
      }
    }
  }
}

Tools

No tools detected

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

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.

Comments

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