PLUMED2 MCP Server / PLUMED2 MCP 服务器
@PhelanShao
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
概览
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.
How can I verify the installation is correct?
Run python -m pytest tests/ -v from the project directory. All 33 tests should pass, indicating a successful installation.
