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molecular-dynamics

Automate OpenMM simulations and MDAnalysis trajectory analysis for molecular dynamics.

Updated May 8, 2026
Search Tags:#molecular dynamics#protein analysis#simulation analysis#OpenMM#MDAnalysis
One-click install
npx skills add https://github.com/Zeyuyang-0420/bio-ai-research-skills --skill molecular-dynamics-zeyuyang-0420
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/Zeyuyang-0420/bio-ai-research-skills/tree/main/categories/drug-discovery-molecular-modeling/molecular-dynamics
Command: npx skills add https://github.com/Zeyuyang-0420/bio-ai-research-skills --skill molecular-dynamics-zeyuyang-0420

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires openmm, mdanalysis, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies the analysis of molecular dynamics simulations, making it easier to extract insights from complex simulation data.

Core Features & Use Cases

  • OpenMM Simulation: Run and analyze molecular dynamics simulations with OpenMM, including energy minimization and production MD.
  • MDAnalysis Analysis: Utilize MDAnalysis for trajectory analysis, such as RMSD and RMSF calculations.
  • Use Case: A scientist uses this Skill to analyze protein-ligand interactions in drug discovery, optimizing the design of new molecules.

Quick Start

Run a molecular dynamics simulation for your protein using OpenMM and analyze the RMSD with MDAnalysis.

Frequently Asked Questions about molecular-dynamics

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

FAQPage Schema
How do I analyze molecular dynamics simulations using OpenMM and MDAnalysis?▼

To analyze molecular dynamics simulations, you can use this Skill to run OpenMM for energy minimization and production MD, then calculate trajectory metrics like RMSD and RMSF with MDAnalysis to extract structural insights.

Can I calculate RMSD and RMSF for protein-ligand interactions in drug discovery?▼

Yes, you can calculate RMSD and RMSF for protein-ligand interactions by leveraging MDAnalysis-based trajectory analysis, enabling you to optimize molecular design in structural biology and drug discovery workflows.

What do I need to run molecular dynamics simulations for structural biology workflows?▼

You need OpenMM and MDAnalysis installed in your environment to run molecular dynamics simulations and perform trajectory analysis, specifically catering to structural biology and biophysics workflows.

How does automating trajectory analysis simplify biophysics workflows?▼

Automating trajectory analysis simplifies biophysics workflows by streamlining the extraction of insights from complex simulation data, reducing manual overhead when running OpenMM simulations and calculating structural metrics.

Are there limitations when using OpenMM for energy minimization and production MD?▼

OpenMM for energy minimization and production MD is limited to environments where OpenMM and MDAnalysis dependencies are supported, focusing primarily on structural biology and biophysics simulation analysis workflows.

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