PLUMED2
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
What is PLUMED2?
PLUMED2 is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to plumed2 smart input generator - an mcp-based assistant for molecular dynamics enhanced sampling configurations that automatically generates optimized plumed input files, supporting metadynamics, umbre...
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
This server falls under the Data Science & ML category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- PLUMED2 Smart Input Generator - An MCP-based assistant for m
Use Cases
Maintainer
Works with
Installation
Manual Installation
npx plumed2Configuration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use PLUMED2
PLUMED2 MCP Server is an AI-assisted input generator for molecular dynamics enhanced sampling simulations. It provides tools to automatically generate, validate, and optimize PLUMED input files for methods including metadynamics, umbrella sampling, and funnel metadynamics, dramatically reducing the manual effort required to configure complex collective variable-based sampling workflows.
Prerequisites
- Python 3.11 or later installed
- pip package manager available
- PLUMED2 installed and accessible (for running the generated input files)
- Git installed to clone the repository
- An MCP-compatible client such as Claude Desktop or Cline
Clone the repository
Clone the PLUMED2 MCP server repository to your local machine.
git clone https://github.com/PhelanShao/plumed2-mcp-server.git
cd plumed2-mcp-server/plumed_mcp_serverInstall Python dependencies
Install the required Python packages listed in requirements.txt.
pip install -r requirements.txtRun the test suite to verify the installation
Run the bundled pytest tests to confirm that all tools are working correctly before connecting a client.
python -m pytest tests/ -vConfigure your MCP client
Add the PLUMED2 MCP server to your claude_desktop_config.json. The server is run directly with Python from the cloned directory.
{
"mcpServers": {
"plumed2": {
"command": "python",
"args": ["-m", "plumed_mcp_server.main"],
"cwd": "/path/to/plumed2-mcp-server",
"alwaysAllow": [
"generate_plumed_input",
"validate_plumed_syntax",
"optimize_plumed_performance",
"get_plumed_template"
]
}
}
}Restart Claude Desktop and start generating PLUMED inputs
After saving the config and restarting Claude Desktop, you can ask it to generate PLUMED input files by describing your simulation system and desired enhanced sampling method.
PLUMED2 Examples
Client configuration
claude_desktop_config.json entry for the PLUMED2 MCP server running from the cloned repository directory.
{
"mcpServers": {
"plumed2": {
"command": "python",
"args": ["-m", "plumed_mcp_server.main"],
"cwd": "/Users/yourname/plumed2-mcp-server",
"alwaysAllow": [
"generate_plumed_input",
"validate_plumed_syntax",
"optimize_plumed_performance",
"get_plumed_template"
]
}
}
}Prompts to try
Example prompts to use with the PLUMED2 MCP server for molecular dynamics simulation setup.
- "Generate a PLUMED input file for well-tempered metadynamics using the distance between atoms 1 and 50 as the collective variable"
- "Validate this PLUMED input file and identify any syntax errors: [paste your PLUMED input]"
- "Optimize this PLUMED configuration for a large system with 100,000 atoms"
- "Give me a PLUMED template for protein folding studies using the RMSD collective variable"
- "Create an umbrella sampling setup for the dihedral angle phi between residues 10-13"
- "Generate a funnel metadynamics input for a ligand-protein binding simulation"Troubleshooting PLUMED2
ModuleNotFoundError when starting the server
Ensure you installed dependencies from within the plumed_mcp_server subdirectory with pip install -r requirements.txt and that the correct Python interpreter is specified in the command field of the config.
Generated PLUMED input fails when run with PLUMED
Use the validate_plumed_syntax tool first to check for errors before running. Also confirm that your PLUMED version supports the collective variables and bias methods used in the generated file.
Server not appearing in Claude Desktop after configuration
Verify that the cwd path in the config points to the root of the cloned repository (not the plumed_mcp_server subdirectory) and that the Python interpreter can find the plumed_mcp_server module. Test by running: python -m plumed_mcp_server.main from the repo root.
Frequently Asked Questions about PLUMED2
What is PLUMED2?
PLUMED2 is a Model Context Protocol (MCP) server that 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 It connects AI assistants to external tools and data sources through a standardized interface.
How do I install PLUMED2?
Follow the installation instructions on the PLUMED2 GitHub repository. Clone the repo, install dependencies, and add the server config to your AI client.
Which AI clients work with PLUMED2?
PLUMED2 works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is PLUMED2 free to use?
Yes, PLUMED2 is open source and available under the GPL-3.0 license. You can use it freely in both personal and commercial projects.
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Set Up PLUMED2 in Your Editor
Choose your AI client for step-by-step setup instructions.
Quick Config Preview
Add this to your claude_desktop_config.json or .cursor/mcp.json
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