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OpenMM MCP Server

@PhelanShao

代码仓库

基本信息

分类

其他

许可证

View license

传输方式

stdio

作者

PhelanShao

关于 OpenMM MCP Server

OpenMM, an open-source platform for molecular dynamics (MD) simulations, is supported by an MCP server that offers a structured communication interface for task submission, management, and execution.

#openmm#molecular-dynamics#simulation-server

OpenMM 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": {
    "openmm-mcp-server": {
      "command": "python",
      "args": [
        "test_mcp_server.py"
      ]
    }
  }
}

OpenMM 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 OpenMM MCP Server?

It is a Model Context Protocol server that integrates OpenMM molecular dynamics and Abacus DFT engines, providing a natural language interface for molecular simulations through LLM integration. It is designed for researchers, computational chemists, and developers who want to run complex simulations via conversational commands.

How to use OpenMM MCP Server?

Clone the repository, install Python dependencies (pip install -r requirements.txt), and optionally install OpenMM (conda install -c conda-forge openmm). Configure the server in your LLM client (e.g., Roo Code) by adding the provided JSON snippet to your MCP settings, pointing to run_openmm_server.py. Then use natural language commands (e.g., “Run a molecular dynamics simulation of a water molecule at 300K for 10000 steps”) to invoke tools like create_md_simulation, create_dft_calculation, or control_simulation.

Key features of OpenMM MCP Server

  • Complete OpenMM integration with advanced integrators, barostats, and constraints
  • DFT calculations using the Abacus engine
  • Pre-configured templates for protein, membrane, and other simulations
  • GPU acceleration via CUDA and OpenCL platforms
  • Asynchronous task management with persistence and monitoring
  • Natural language interface for complex simulation commands

Use cases of OpenMM MCP Server

  • Set up a protein production simulation for 100 ns at 310 K using Amber19 and TIP3P-FB water
  • Create a POPC membrane protein simulation for 50 ns with surface tension control
  • Perform enhanced sampling methods like metadynamics or free energy calculations
  • Run a simple water box simulation at 300 K for testing and validation
  • Combine molecular dynamics with DFT calculations for hybrid QM/MM workflows

常见问题

1

What happens if OpenMM is not installed?

The server runs in “mock mode” for testing. To run actual simulations, install OpenMM via `conda install -c conda-forge openmm`.

2

How do I integrate this server with Roo Code or Claude?

Add the provided JSON configuration to your MCP settings, replacing the path in `"cwd"` with the actual project directory, and include the listed tools under `alwaysAllow`.

3

Which force fields and water models are supported?

Force fields: Amber14, Amber19, CHARMM36. Water models: TIP3P, TIP3P-FB, TIP4P-Ew, SPC/E.

4

What compute platforms can I use?

CUDA (NVIDIA GPU, fastest), OpenCL (general GPU), CPU, and Reference (for debugging).

5

Which environment variables can I set?

`TASK_DATA_DIR`, `MAX_CONCURRENT_TASKS`, `DEFAULT_OPENMM_PLATFORM`, `LOG_LEVEL`, and `LOG_FILE`.

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