molecular-dynamics

Simulate molecular systems and analyze trajectories with OpenMM and MDAnalysis.

13|3|Updated Jun 10, 2026

Search Tags:#simulation #biophysics #molecular dynamics #OpenMM #MDAnalysis

Ready to run

npx skills add https://github.com/tassiovale/claude-code-kit --skill molecular-dynamics-tassiovale

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/tassiovale/claude-code-kit/tree/main/skills/molecular-dynamics
Command: npx skills add https://github.com/tassiovale/claude-code-kit --skill molecular-dynamics-tassiovale

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires openmm, mdanalysis, nglview, numpy, matplotlib, pandas, scipy, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill addresses complex molecular dynamics simulation needs for structural biology, drug binding, and biophysics by integrating OpenMM and MDAnalysis tools.

Core Features & Use Cases

OpenMM and MDAnalysis Integration: Simulate molecular systems and analyze trajectories with cutting-edge tools.
System Preparation: Set up protein and small molecule systems with force fields and solvation.
Energy Minimization: Remove steric clashes and prepare systems for MD simulations.
Equilibration and Production: Conduct NVT and NPT equilibration and production runs for accurate MD simulations.
Trajectory Analysis: Analyze trajectories for RMSD, RMSF, contact maps, and free energy surfaces.
Use Case: Utilize this Skill to study the stability of a protein after a mutation or to analyze ligand binding to a protein.

Quick Start

Run the molecular-dynamics skill to simulate and analyze a protein using OpenMM and MDAnalysis.

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 and analyze trajectories for structural biology?▼

You can run molecular dynamics simulations and analyze trajectories by integrating OpenMM for system preparation, energy minimization, and NVT/NPT production runs, followed by MDAnalysis to compute RMSD, RMSF, and contact maps.

What is the best way to prepare a protein system and remove steric clashes before MD simulations?▼

The best way to prepare a protein system for MD simulations is to apply force fields and solvation, then perform energy minimization using OpenMM to remove steric clashes and ensure structural stability before equilibration.

Does this molecular dynamics workflow support ligand binding analysis and free energy surface calculations?▼

Yes, the molecular dynamics workflow supports ligand binding analysis by utilizing MDAnalysis to evaluate trajectory data, calculate contact maps, and generate free energy surfaces for biophysics and drug discovery studies.

Can I use OpenMM and MDAnalysis to study protein stability after a mutation?▼

Yes, you can use OpenMM and MDAnalysis to study protein stability after a mutation by running production simulations and analyzing the resulting trajectories for RMSD and RMSF fluctuations.

What do I need to set up to simulate molecular systems with OpenMM and MDAnalysis?▼

You need OpenMM, MDAnalysis, and additional Python tools like NumPy, SciPy, Matplotlib, Pandas, and NGLView installed to handle system preparation, simulation execution, trajectory analysis, and molecular visualization.

How do I analyze MD simulation trajectories to calculate RMSD and RMSF?▼

You can analyze MD simulation trajectories to calculate RMSD and RMSF by loading the production run output into MDAnalysis, which processes the trajectory frames to measure structural deviations and fluctuations over time.