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Gmx Vmd MCP Server

MCP service for GROMACS and VMD molecular dynamics simulations and visualization

Local serverstdioPython

What is the Gmx Vmd MCP Server?

MCP service for GROMACS and VMD molecular dynamics simulations and visualization

The short version

MCP-GMX-VMD is a service that integrates GROMACS molecular dynamics simulations with VMD (Visual Molecular Dynamics) visualization through a microservice architecture. This tool facilitates molecular dynamics simulation setup, execution, analysis, and visualization.

  • Molecular Dynamics Simulations — Setup and run GROMACS simulations with an easy-to-use interface
  • Trajectory Analysis — Analyze simulation trajectories (RMSD, RMSF, etc.)
  • 3D Visualization — Visualize molecular structures and simulation trajectories using VMD
  • Custom Workflow Directories — Create and manage simulation workflows in user-specified directories
  • Modular Architecture — Built on MCP (Model Context Protocol ) for flexible integration with other tools

What it needs from you

  • Python 3.9+ - GROMACS (installed and accessible in PATH) - VMD (Visual Molecular Dynamics, installed and accessible in PATH) - (Optional) Python VMD module for enhanced visualization capabilities

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Maintainer setup documentation.

Configuration

  • Python 3.9+ - GROMACS (installed and accessible in PATH) - VMD (Visual Molecular Dynamics, installed and accessible in PATH) - (Optional) Python VMD module for enhanced visualization capabilities
VariableDescriptionRequired
PYTHONPATHPython module search path for a local installation.Optional
MCP_DEBUGConfiguration value read at startup.Optional
PYTHONUNBUFFEREDConfiguration value read at startup.Optional

Frequently asked questions

Python 3.9+, GROMACS (installed and accessible in PATH), and VMD (Visual Molecular Dynamics, installed and accessible in PATH) are required.

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