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molecular-dynamics

Prepare, run, and analyze biomolecular MD simulations with OpenMM and MDAnalysis trajectories.

Updated Jul 1, 2026
Search Tags:#trajectory analysis#rmsd#molecular dynamics#mdanalysis#openmm#protein simulation#free energy
One-click install
npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill molecular-dynamics-jasrajtulsi
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/jasrajtulsi/GRAD-SCOPE/tree/main/.claude/skills/molecular-dynamics
Command: npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill molecular-dynamics-jasrajtulsi

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill helps you set up, run, and interpret molecular dynamics simulations so you can study how biomolecular systems move, stabilize, bind, or change over time without stitching together multiple tools manually.

Core Features & Use Cases

  • System Preparation: Build solvated protein or protein-ligand systems, add hydrogens, choose force fields, and prepare structures for simulation.
  • Simulation Workflow: Perform energy minimization, NVT equilibration, NPT production, and checkpointed runs using OpenMM.
  • Trajectory Analysis: Measure RMSD, RMSF, contacts, hydrogen bonds, radius of gyration, secondary structure, PCA, and free energy surfaces with MDAnalysis.
  • Use Case: If a mutation appears to destabilize a protein or a ligand seems to change binding pose, this Skill can help you simulate the system and quantify the structural changes over time.

Quick Start

Use the molecular-dynamics skill to prepare an OpenMM simulation from a PDB file, run equilibration and production, and analyze the resulting trajectory for stability and binding behavior.

Frequently Asked Questions about molecular-dynamics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run molecular dynamics simulations for a protein from a PDB file?▼

To run molecular dynamics simulations, you prepare a solvated protein system from a PDB file, perform energy minimization, NVT equilibration, and NPT production using OpenMM, then analyze the resulting trajectory for stability and binding behavior.

What trajectory analysis metrics can I calculate for my biomolecular simulation?▼

Trajectory analysis metrics include RMSD, RMSF, contacts, hydrogen bonds, radius of gyration, secondary structure, PCA, and free energy surfaces, calculated using MDAnalysis to quantify structural changes over time.

Can I use OpenMM and MDAnalysis to simulate protein-ligand binding and membrane systems?▼

Yes, you can use OpenMM and MDAnalysis to simulate protein-ligand binding and membrane systems, supporting protein, ligand, membrane, and nucleic acid workflows across system preparation, equilibration, production, and trajectory analysis.

What's the best way to quantify if a mutation destabilizes a protein during molecular dynamics?▼

The best way to quantify if a mutation destabilizes a protein is to simulate the system, then measure structural changes over time using RMSD, RMSF, radius of gyration, and hydrogen bond analysis from the production trajectory.

Do I need OpenMM and MDAnalysis installed to prepare and analyze biomolecular trajectories?▼

Yes, you need OpenMM installed to run energy minimization, equilibration, and production simulations, and MDAnalysis to handle trajectory files and calculate metrics like RMSD, RMSF, and free energy surfaces.

Why use checkpointed runs for molecular dynamics simulations of biomolecules?▼

Checkpointed runs ensure reproducible analysis by saving simulation state during NVT equilibration and NPT production, allowing recovery from interruptions and consistent trajectory generation for biomolecular systems.

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