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Gmx Vmd MCP Server

@egtai

リポジトリ

基本情報

カテゴリ

その他

ライセンス

MIT

トランスポート

stdio

作者

egtai

投稿者

EgT

Gmx Vmd MCP Server について

MCP service for GROMACS and VMD molecular dynamics simulations and visualization

Gmx Vmd MCP Server の設定

以下の設定を使って、このサーバーを MCP 対応クライアントに追加してください。

{
  "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 のツール

ツール一覧はまだありません

この掲載には表示できるツール一覧がまだありません。サーバーにツールがないという意味ではありません。対応機能はプロジェクトのドキュメントをご確認ください。

ツールは README から自動的に抽出されます。メンテナーは ## Tools という見出しの下に記載することで、このタブに反映できます。

概要

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

よくある質問

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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