PLUMED2 MCP Server / PLUMED2 MCP 服务器

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Overview

The PLUMED2 MCP Server is a Model Context Protocol (MCP) server that provides AI assistants with powerful tools for generating, validating, and optimizing PLUMED input files for molecular dynamics simulations. This server enables seamless integration of PLUMED expertise into AI workflows.

Features

• 🔧 Input File Generation: Generate complete PLUMED input files with collective variables, bias methods, and output configurations
• 📋 Template System: Access pre-defined templates for common simulation scenarios (protein folding, drug binding, phase transitions, nucleation)
• ⚡ Performance Optimization: Get intelligent suggestions to optimize PLUMED performance for large systems
• ✅ Syntax Validation: Validate PLUMED syntax with detailed error reporting and reference checking
• 🌐 International: Fully English codebase with professional documentation

Installation

Prerequisites

• Python 3.11 or higher
• pip package manager

Install Dependencies

cd plumed_mcp_server
pip install -r requirements.txt

MCP Client Configuration

Add the following configuration to your MCP client settings (e.g., Claude Desktop, Cline, etc.):

{
  "mcpServers": {
    "plumed2": {
      "command": "python",
      "args": [
        "-m", "plumed_mcp_server.main"
      ],
      "cwd": "/path/to/plumed_mcp_server",
      "alwaysAllow": [
        "generate_plumed_input",
        "validate_plumed_syntax", 
        "optimize_plumed_performance",
        "get_plumed_template"
      ]
    }
  }
}

Note: Replace /path/to/plumed_mcp_server with the actual path to your installation directory.

Available Tools

1. generate_plumed_input

Generate complete PLUMED input files based on simulation requirements.

Parameters:

• collective_variables (required): List of collective variables to compute
• bias_methods (optional): List of bias methods to apply
• output_config (optional): Output configuration settings
• system_info (optional): System information for optimization
• molinfo_config (optional): Molecular information settings
• group_definitions (optional): Custom group definitions

2. validate_plumed_syntax

Validate PLUMED input syntax and check for common errors.

Parameters:

• plumed_input (required): PLUMED input content to validate
• number_of_replicas (optional): Number of replicas for @replicas syntax validation

3. optimize_plumed_performance

Get performance optimization suggestions for PLUMED simulations.

Parameters:

• plumed_input (required): PLUMED input content to analyze
• system_info (optional): System information (number of atoms, simulation length, etc.)

4. get_plumed_template

Retrieve pre-defined or custom PLUMED templates.

Parameters:

• template_name (required): Name of the template to retrieve
• system_type (optional): Type of system for template customization

Usage Examples

Example 1: Generate a Simple Distance CV with Metadynamics

Prompt to AI:

Generate a PLUMED input file for metadynamics simulation of a protein. I want to use the distance between atoms 1 and 2 as a collective variable, with metadynamics bias. Include output every 100 steps.

Expected AI Response: The AI will use the generate_plumed_input tool with parameters like:

{
  "collective_variables": [
    {
      "type": "DISTANCE",
      "label": "d1",
      "atoms": [1, 2]
    }
  ],
  "bias_methods": [
    {
      "type": "METAD",
      "arg": "d1",
      "sigma": 0.1,
      "height": 1.0,
      "pace": 500
    }
  ],
  "output_config": {
    "stride": 100,
    "file": "colvar.dat"
  }
}

Generated Output:

# PLUMED input file generated by PLUMED2 MCP Server
# Collective Variables
d1: DISTANCE ATOMS=1,2

# Bias Methods  
METAD ARG=d1 SIGMA=0.1 HEIGHT=1.0 PACE=500

# Output
PRINT ARG=d1 

... [View full README on GitHub](https://github.com/PhelanShao/plumed2-mcp-server#readme)