PLUMED2 MCP Server / PLUMED2 MCP 服务器

Name: PLUMED2 MCP Server / PLUMED2 MCP 服务器
Author: PhelanShao

@PhelanShao

PLUMED2 MCP Server / PLUMED2 MCP 服务器について

PLUMED2 Smart Input Generator - An MCP-based assistant for molecular dynamics enhanced sampling configurations that automatically generates optimized PLUMED input files, supporting metadynamics, umbrella sampling, and other enhanced sampling methods with built-in syntax validatio

#plumed2 #molecular-dynamics #input-generator

基本情報

カテゴリ

その他

ライセンス

GPL-3.0 license

ランタイム

python

トランスポート

stdio

公開者

PhelanShao

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": {
    "plumed2-mcp-server": {
      "command": "python",
      "args": [
        "-m",
        "pytest",
        "tests/",
        "-v"
      ]
    }
  }
}

ツール

ツールは検出されませんでした

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 PLUMED2 MCP Server?

The PLUMED2 MCP Server is a Model Context Protocol (MCP) server that provides AI assistants with tools for generating, validating, and optimizing PLUMED input files for molecular dynamics simulations. It is designed for researchers and developers who want to integrate PLUMED expertise into AI workflows.

How to use PLUMED2 MCP Server?

Install Python 3.11 or higher, install dependencies via pip install -r requirements.txt, then add a JSON configuration to your MCP client (e.g., Claude Desktop, Cline) specifying the command python -m plumed_mcp_server.main. The server exposes four tools: generate_plumed_input, validate_plumed_syntax, optimize_plumed_performance, and get_plumed_template. AI assistants invoke these tools based on natural language prompts.

Key features of PLUMED2 MCP Server

Generate complete PLUMED input files with collective variables and bias methods
Access pre-defined templates for common simulation scenarios (protein folding, drug binding, phase transitions, nucleation)
Get intelligent performance optimization suggestions for large systems
Validate PLUMED syntax with detailed error reporting and reference checking
Fully English codebase with professional documentation

Use cases of PLUMED2 MCP Server

Generate a metadynamics input file for a protein using distance collective variables
Validate a user‑written PLUMED input for syntax errors and common mistakes
Obtain performance optimization tips for a PLUMED simulation on a 100,000‑atom system
Retrieve a ready‑to‑use template for protein folding simulations
Speed up workflow creation for drug binding, phase transitions, or nucleation studies

FAQ from PLUMED2 MCP Server

What is the PLUMED2 MCP Server used for?

It provides AI assistants with the ability to generate, validate, and optimize PLUMED input files for molecular dynamics simulations, integrating PLUMED expertise directly into AI workflows.

What are the installation prerequisites?

Python 3.11 or higher and the pip package manager are required. All dependencies are listed in requirements.txt.

How do I configure an MCP client to use this server?

Add a JSON entry to your MCP client settings with "command": "python", "args": ["-m", "plumed_mcp_server.main"], and set "cwd" to the installation directory. The alwaysAllow array lists the four permitted tools.

What tools does the server provide?

It offers four tools: generate_plumed_input (create input files), validate_plumed_syntax (check syntax), optimize_plumed_performance (suggest improvements), and get_plumed_template (retrieve templates). Each tool accepts specific parameters.