gmx-vmd-mcp

egtai/gmx-vmd-mcp

3.4

If you are the rightful owner of gmx-vmd-mcp and would like to certify it and/or have it hosted online, please leave a comment on the right or send an email to henry@mcphub.com.

MCP-GMX-VMD is a service that integrates GROMACS molecular dynamics simulations with VMD visualization through a microservice architecture.

MCP-GMX-VMD is a sophisticated service designed to streamline the process of molecular dynamics simulations by integrating GROMACS with VMD for visualization. This tool leverages a microservice architecture to facilitate the setup, execution, analysis, and visualization of molecular dynamics simulations. Users can easily set up simulations, analyze trajectories, and visualize results in 3D, all within a modular and flexible framework built on the Model Context Protocol (MCP). The service supports custom workflow directories, allowing users to manage their simulation projects efficiently. With its modular architecture, MCP-GMX-VMD can be seamlessly integrated with other tools, enhancing its utility in computational chemistry and molecular biology research.

Features

  • Molecular Dynamics Simulations: Setup and run GROMACS simulations with an easy-to-use interface.
  • Trajectory Analysis: Analyze simulation trajectories (RMSD, RMSF, etc.).
  • 3D Visualization: Visualize molecular structures and simulation trajectories using VMD.
  • Custom Workflow Directories: Create and manage simulation workflows in user-specified directories.
  • Modular Architecture: Built on MCP for flexible integration with other tools.

Usages

usage with Claude Desktop

{
  "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"
      }
    }
  }
}

usage with Cursor IDE

{
  "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"
      }
    }
  }
}