MCP-GMX-VMD
by egtai
MCP-GMX-VMD integrates GROMACS molecular dynamics simulations with VMD visualization through a microservice architecture. This tool facilitates molecular dynamics simulation setup, execution, analysis, and visualization.
Last updated: N/A
What is MCP-GMX-VMD?
MCP-GMX-VMD is a service that combines GROMACS for molecular dynamics simulations and VMD for visualization using a microservice architecture. It provides an interface to set up, run, analyze, and visualize molecular dynamics simulations.
How to use MCP-GMX-VMD?
To use MCP-GMX-VMD, you need to clone the repository, set up a virtual environment, install the dependencies, and configure the service with the paths to your GROMACS and VMD installations. Then, you can start the server and interact with it using HTTP requests to create workflows, prepare simulations, analyze trajectories, and visualize structures. LLM integration is also available by configuring Claude or Cursor IDE.
Key features of MCP-GMX-VMD
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 (Microservice Communication Protocol) for flexible integration with other tools
Use cases of MCP-GMX-VMD
Setting up and running molecular dynamics simulations of proteins, lipids, and other biomolecules.
Analyzing simulation trajectories to understand the dynamics and behavior of molecular systems.
Visualizing molecular structures and simulation trajectories in 3D to gain insights into molecular interactions.
Integrating molecular dynamics simulations with LLMs for natural language control and automation.
FAQ from MCP-GMX-VMD
How do I specify a custom directory for my simulation workflow?
How do I specify a custom directory for my simulation workflow?
You can specify the workspace_dir parameter when creating a workflow using the /workflow/create endpoint.
How do I apply a built-in visualization template?
How do I apply a built-in visualization template?
You can use the /visualization/apply-template endpoint and specify the template_name parameter.
What should I do if VMD GUI closes immediately after launch?
What should I do if VMD GUI closes immediately after launch?
Try launching VMD in a separate terminal window, use vmd -dispdev text for command-line operation, or check VMD installation and permissions.
How do I resolve permission issues with custom directories?
How do I resolve permission issues with custom directories?
Use the chmod -R 755 /path/to/your/custom/directory command to set appropriate permissions for the directory.
How do I integrate MCP-GMX-VMD with LLMs?
How do I integrate MCP-GMX-VMD with LLMs?
You can integrate it with LLM assistants like Claude or Cursor IDE by configuring the mcp.json file with the correct paths and restarting the application.