scicomp-molecular-mcp

MCP server for classical molecular dynamics simulations.

Overview

This server provides tools for molecular dynamics simulations with support for various ensembles and interaction potentials:

• Particle systems - Create and manage systems of interacting particles
• Interaction potentials - Lennard-Jones and Coulomb interactions
• Ensembles - NVE (microcanonical), NVT (canonical), NPT (isothermal-isobaric)
• Analysis tools - Radial distribution functions, mean squared displacement, phase transitions
• Visualization - Trajectory rendering and density field visualization
• GPU acceleration - Optional CUDA acceleration for large systems

Installation & Usage

# Run directly with uvx (no installation required)
uvx scicomp-molecular-mcp

# Or install with pip
pip install scicomp-molecular-mcp

# With GPU support
pip install scicomp-molecular-mcp[gpu]

# Run as command
scicomp-molecular-mcp

Available Tools

System Setup

• create_particles - Initialize particle system with temperature
• add_potential - Add Lennard-Jones or Coulomb interactions

Simulation

• run_md - NVE ensemble (constant energy, volume)
• run_nvt - NVT ensemble (constant temperature, volume)
• run_npt - NPT ensemble (constant temperature, pressure)
• get_trajectory - Retrieve simulation trajectory data

Analysis

• compute_rdf - Radial distribution function analysis
• compute_msd - Mean squared displacement
• analyze_temperature - Thermodynamic properties
• detect_phase_transition - Identify phase transitions
• density_field - Compute density field visualization

Visualization

• render_trajectory - Animate particle trajectories

Configuration

Enable GPU acceleration with environment variable:

MCP_USE_GPU=1 scicomp-molecular-mcp

Examples

See the API documentation for detailed examples and simulation protocols.

Part of Math-Physics-ML MCP System

Part of a comprehensive system for scientific computing. See the documentation for the complete ecosystem.