egtai/gmx-vmd-mcp
If you are the rightful owner of gmx-vmd-mcp and would like to certify it and/or have it hosted online, please leave a comment on the right or send an email to henry@mcphub.com.
MCP-GMX-VMD is a service that integrates GROMACS molecular dynamics simulations with VMD visualization through a microservice architecture.
MCP-GMX-VMD is a sophisticated service designed to streamline the process of molecular dynamics simulations by integrating GROMACS with VMD for visualization. This tool leverages a microservice architecture to facilitate the setup, execution, analysis, and visualization of molecular dynamics simulations. Users can easily set up simulations, analyze trajectories, and visualize results in 3D, all within a modular and flexible framework built on the Model Context Protocol (MCP). The service supports custom workflow directories, allowing users to manage their simulation projects efficiently. With its modular architecture, MCP-GMX-VMD can be seamlessly integrated with other tools, enhancing its utility in computational chemistry and molecular biology research.
Features
- 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 for flexible integration with other tools.
Usages
usage with Claude Desktop
{ "mcpServers": { "gmx_vmd": { "command": "{{PATH_TO_UV}}", "args": [ "--directory", "{PATH_TO_SRC}/mcp-gmx-vmd", "run", "mcp", "run", "mcp_server.py" ], "env": { "PYTHONPATH": "{PATH_TO_SRC}/mcp-gmx-vmd", "MCP_DEBUG": "1", "PYTHONUNBUFFERED": "1" } } } }
usage with Cursor IDE
{ "mcpServers": { "gmx_vmd": { "command": "{{PATH_TO_UV}}", "args": [ "--directory", "{PATH_TO_SRC}/mcp-gmx-vmd", "run", "mcp", "run", "mcp_server.py" ], "env": { "PYTHONPATH": "{PATH_TO_SRC}/mcp-gmx-vmd", "MCP_DEBUG": "1", "PYTHONUNBUFFERED": "1" } } } }