molecular-dynamics

Run molecular dynamics simulations and analyze trajectories with OpenMM and MDAnalysis.

2|Updated Jun 4, 2026

Search Tags:#simulation #biophysics #structural biology #molecular dynamics #mdanalysis #openmm

Ready to run

npx skills add https://github.com/Lord1Egypt/scientific-agent-toolkit --skill molecular-dynamics-lord1egypt

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/Lord1Egypt/scientific-agent-toolkit/tree/main/scientific-skills/molecular-dynamics
Command: npx skills add https://github.com/Lord1Egypt/scientific-agent-toolkit --skill molecular-dynamics-lord1egypt

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires openmm, mdanalysis, nglview, numpy, matplotlib, pdbfixer, openff-toolkit, and includes references (resource) components.

What problem does it solve?

This skill addresses the complexity of setting up, running, and analyzing molecular dynamics simulations, which are often prone to configuration errors and require specialized knowledge of force fields and trajectory analysis.

Core Features & Use Cases

Simulation Setup: Automates system preparation, energy minimization, and equilibration for protein and small molecule systems.
Trajectory Analysis: Provides robust tools for calculating RMSD, RMSF, protein-ligand contacts, and free energy surfaces.
Use Case: Researchers can use this to model protein-ligand binding modes or study the conformational flexibility of a protein over time to understand drug binding mechanisms.

Quick Start

Use the molecular-dynamics skill to prepare a PDB file for simulation and run an NVT equilibration.

Frequently Asked Questions about molecular-dynamics

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

FAQPage Schema

How do I set up and run molecular dynamics simulations for protein-ligand binding studies?▼

Molecular dynamics simulations for protein-ligand binding studies require automated system preparation, energy minimization, and NVT equilibration. This skill automates these steps using OpenMM, allowing you to prepare PDB files and run equilibration directly.

What's the best way to calculate RMSD and RMSF from molecular dynamics trajectories?▼

To calculate RMSD and RMSF from molecular dynamics trajectories, use MDAnalysis. This skill provides robust trajectory analysis tools to extract these metrics, alongside protein-ligand contacts and free energy surfaces for structural biology workflows.

Can I use OpenMM and MDAnalysis to perform conformational sampling and free energy estimation?▼

Yes, you can use OpenMM and MDAnalysis to perform conformational sampling and free energy estimation. This skill supports these workflows for modeling conformational flexibility and understanding drug binding mechanisms over time.

Do I need PDBFixer and openff-toolkit to prepare PDB files for molecular dynamics simulation?▼

Yes, preparing PDB files for molecular dynamics simulation requires PDBFixer and openff-toolkit. These dependencies handle system preparation and parameterization, ensuring your protein and small molecule systems are correctly configured before running OpenMM.

Why does automated molecular dynamics setup prevent configuration errors during simulation?▼

Automated molecular dynamics setup prevents configuration errors by standardizing force field selection and trajectory analysis. This skill addresses the complexity of system preparation, ensuring accurate computational modeling for complex molecular systems.

Does this molecular dynamics skill support visualization of trajectory analysis results?▼

Yes, this molecular dynamics skill supports visualization of trajectory analysis results. It integrates nglview and matplotlib to render molecular structures and plot data, enabling you to visualize simulation outputs and analyze conformational changes.