iflow-mcp_phelanshao-plumed2-mcp-server

# PLUMED2 MCP Server / PLUMED2 MCP 服务器 [English](#english) | [中文](#中文) --- ## English ### 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 ```bash 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.): ```json { "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` (op…