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molecular-dynamics

Run end-to-end molecular dynamics simulations and trajectory analysis with OpenMM and MDAnalysis.

1|2|Updated Apr 29, 2026
Search Tags:#trajectory analysis#biophysics#molecular dynamics#mdanalysis#openmm#protein simulations#drug binding
One-click install
npx skills add https://github.com/fuzzy-dynamics/strings --skill molecular-dynamics-fuzzy-dynamics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/fuzzy-dynamics/strings/tree/main/packages/skills/molecular-dynamics
Command: npx skills add https://github.com/fuzzy-dynamics/strings --skill molecular-dynamics-fuzzy-dynamics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Molecular dynamics simulations are powerful but require setup, execution, and analysis that involve multiple tools and custom scripting. This skill provides an end-to-end workflow by combining OpenMM for system preparation, minimization, and production runs with MDAnalysis for trajectory analysis, enabling researchers to streamline experiments and derive insights efficiently.

Core Features & Use Cases

  • End-to-end MD pipeline: system setup, energy minimization, NVT/NPT equilibration, production runs, and trajectory analysis.
  • Trajectory analysis: RMSD, RMSF, radius of gyration, protein-ligand contacts, and free energy surfaces from MD trajectories.
  • Applicability: structural biology, drug discovery, and biophysics research requiring rigorous MD simulations and analysis.

Quick Start

Prepare a system, run a short MD, and analyze the trajectory to extract RMSD and RMSF.

Frequently Asked Questions about molecular-dynamics

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

FAQPage Schema
How do I run end-to-end molecular dynamics simulations and trajectory analysis?▼

End-to-end molecular dynamics simulations and trajectory analysis are facilitated by combining OpenMM for system preparation and production runs with MDAnalysis for downstream trajectory analysis.

Can I analyze protein stability and drug binding using OpenMM and MDAnalysis?▼

Yes, protein stability and drug binding studies are supported through MDAnalysis workflows that calculate RMSD, RMSF, radius of gyration, and protein-ligand contacts from simulation trajectories.

What do I need to set up biomolecular workflows for protein simulations?▼

You need OpenMM and MDAnalysis installed via conda or pip to execute biomolecular workflows from system prep to production, with optional ligand parameterization using GAFF2 or OpenFF.

How does this approach handle conformational sampling and free energy surfaces?▼

Conformational sampling and free energy surfaces are handled through integrated OpenMM production runs and MDAnalysis trajectory analysis, enabling rigorous biophysics research and structural biology insights.

Are there limitations when parameterizing ligands for molecular dynamics simulations?▼

Ligand parameterization for molecular dynamics simulations is optional and supports GAFF2 or OpenFF, but requires proper system setup and OpenMM installation via conda or pip to function correctly.

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