molecular-dynamics

Automates end-to-end molecular dynamics workflows for OpenMM and MDAnalysis.

1|Updated Mar 19, 2026

Search Tags:#simulation #molecular-dynamics #trajectory-analysis #mdanalysis #openmm #protein-dynamics

Ready to run

npx skills add https://github.com/JosephWoodall/noosphere --skill molecular-dynamics-josephwoodall

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/molecular-dynamics
Command: npx skills add https://github.com/JosephWoodall/noosphere --skill molecular-dynamics-josephwoodall

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Molecular dynamics simulations are often tedious to set up, run, and analyze, leading to slow progress in structural biology and drug design workflows.

Core Features & Use Cases

OpenMM-based setup & production: System preparation, minimization, NVT/NPT equilibration, and production runs.
Trajectory analysis with MDAnalysis: RMSD, RMSF, contacts, and other metrics for conformational insights.
End-to-end workflow: From structure preparation to results interpretation for protein dynamics and ligand binding studies.

Quick Start

Run a complete MD workflow for a given PDB using OpenMM to minimize, equilibrate, produce trajectories, and analyze 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 run molecular dynamics simulations using OpenMM?▼

To run molecular dynamics simulations with OpenMM, you can automate the entire workflow from system setup and minimization to NVT/NPT equilibration and production runs. This provides complete trajectory generation for structural biology studies.

What's the best way to analyze protein dynamics trajectories?▼

The best way to analyze protein dynamics trajectories is using MDAnalysis to calculate RMSD, RMSF, and contact metrics. This provides conformational insights into protein behavior and ligand binding interactions.

Do I need both OpenMM and MDAnalysis to run end-to-end MD workflows?▼

Yes, you need both OpenMM and MDAnalysis libraries to run end-to-end MD workflows. OpenMM handles system preparation and production runs, while MDAnalysis performs trajectory analysis for complete simulation coverage.

Can I use this molecular dynamics workflow for drug discovery applications?▼

Yes, you can use this molecular dynamics workflow for drug discovery applications. It supports structural biology and ligand binding studies by simulating protein dynamics and analyzing conformational changes.

What steps are involved in an OpenMM molecular dynamics production run?▼

An OpenMM molecular dynamics production run involves system preparation, energy minimization, NVT and NPT equilibration phases, and the final production simulation. This generates trajectory data ready for analysis.

Why does my MDAnalysis trajectory analysis return empty RMSD results?▼

MDAnalysis trajectory analysis may return empty RMSD results if the production run did not complete properly or the trajectory file is misaligned with the topology. Ensure system setup and equilibration steps finish successfully before analysis.