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Gmx Vmd MCP Server

@egtai

代码仓库

基本信息

分类

其他

许可证

MIT

传输方式

stdio

作者

egtai

提交者

EgT

关于 Gmx Vmd MCP Server

MCP service for GROMACS and VMD molecular dynamics simulations and visualization

Gmx Vmd MCP Server 配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

{
  "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"
      }
    }
  }
}

Gmx Vmd MCP Server 工具

工具列表暂未提供

当前收录暂时没有可展示的工具列表，不代表服务没有工具。请查阅项目文档了解支持的能力。

工具是从 README 中自动提取的。维护者可以在 ## Tools 标题下列出工具,即可填充这部分内容。

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

常见问题

1

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.

2

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.

3

Can I use custom directories for simulation workflows?

Yes, specify the `workspace_dir` parameter when creating a workflow to use a custom directory.

4

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.

5

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.

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