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Run, analyze, and visualize GROMACS molecular dynamics workflows with natural language.
Copy the install command and let the AI configure it · recommended for beginners
No copy-paste install info for "MCP-GMX-VMD" yet — see the docs or source repo.
Set up a GROMACS molecular dynamics workflow for a protein-ligand complex, including system preparation, solvation, ion addition, energy minimization, equilibration, and a 100 ns production run. Explain the output files for each step.
A structured simulation workflow with key command guidance, output files, and execution order.
Analyze this GROMACS simulation trajectory, focusing on RMSD, RMSF, hydrogen-bond changes, and conformational stability, then suggest suitable 3D visualizations in VMD.
Interpretation of key metrics, stability conclusions, and VMD visualization suggestions for structural changes.
Starting from an existing topology and initial structure, run a molecular dynamics job, organize the analysis results automatically, and generate visualization steps in VMD to inspect ligand binding-site changes.
Executable task steps, an organized analysis plan, and VMD instructions for inspecting binding-site changes.
Access multiple scientific MCP tools through one unified integration interface.
Control ChimeraX for molecular visualization, analysis, screenshots, and session management.
Control PyMOL with natural language for protein structure analysis and visualization.
Analyze hardware simulation VCD and GTKWave files for signals, buses, and groups.
Automate COMSOL multiphysics modeling, solving, and result visualization through MCP.
Run hollow-fiber gas membrane simulations via MCP with flexible thermodynamic models.