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 validation and performance optimization.
{
"mcpServers": {
"plumed2-mcp-server": {
"command": "<see-readme>",
"args": []
}
}
}No install config available. Check the server's README for setup instructions.
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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 validation and performance optimization.
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GPL-3.0. View license →
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Last commit 311 days ago. 10 stars.
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Transport: stdio. Works with Claude Desktop, Cursor, Claude Code, and most MCP clients.
No automated test available for this server. Check the GitHub README for setup instructions.
No known vulnerabilities.
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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.
cd plumed_mcp_server
pip install -r requirements.txt
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.
generate_plumed_inputGenerate complete PLUMED input files based on simulation requirements.
Parameters:
collective_variables (required): List of collective variables to computebias_methods (optional): List of bias methods to applyoutput_config (optional): Output configuration settingssystem_info (optional): System information for optimizationmolinfo_config (optional): Molecular information settingsgroup_definitions (optional): Custom group definitionsvalidate_plumed_syntaxValidate PLUMED input syntax and check for common errors.
Parameters:
plumed_input (required): PLUMED input content to validatenumber_of_replicas (optional): Number of replicas for @replicas syntax validationoptimize_plumed_performanceGet performance optimization suggestions for PLUMED simulations.
Parameters:
plumed_input (required): PLUMED input content to analyzesystem_info (optional): System information (number of atoms, simulation length, etc.)get_plumed_templateRetrieve pre-defined or custom PLUMED templates.
Parameters:
template_name (required): Name of the template to retrievesystem_type (optional): Type of system for template customizationPrompt 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)