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molecular-dynamics

Run OpenMM molecular dynamics simulations and analyze trajectories with MDAnalysis.

4|Updated Mar 2, 2026
Search Tags:#trajectory analysis#molecular dynamics#mdanalysis#openmm#protein simulation#rmsd rmsf#protein-ligand contacts
One-click install
npx skills add https://github.com/shushuzn/Rairos --skill molecular-dynamics-shushuzn
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/shushuzn/Rairos/tree/main/skills/molecular-dynamics
Command: npx skills add https://github.com/shushuzn/Rairos --skill molecular-dynamics-shushuzn

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill helps you run molecular dynamics (MD) simulations and convert trajectories into quantitative insights about molecular motion, stability, and interactions.

Core Features & Use Cases

  • End-to-end MD workflows with OpenMM: build solvated systems from structures, run energy minimization, perform NVT/NPT equilibration, and execute production simulations with GPU acceleration when available.
  • Trajectory analysis with MDAnalysis: compute RMSD/RMSF, generate contact maps and protein–ligand contact histories, and support advanced analyses such as secondary structure and free-energy surfaces.
  • Practical modeling guidance: includes force field and water-model recommendations for proteins, ligands, membranes, and disordered systems, plus ligand parameterization approaches (e.g., OpenFF) to enable realistic simulations.
  • Use cases: assess mutation effects on protein stability, characterize drug binding and conformational sampling, and evaluate protein flexibility through RMSD/RMSF and interaction metrics.

Quick Start

Use the molecular-dynamics skill to simulate a PDB structure by running energy minimization and a short production MD run, then analyze the resulting trajectory for RMSD, RMSF, and protein–ligand contacts.

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 of a protein using OpenMM?▼

To run molecular dynamics simulations, build a solvated system from a PDB structure and use OpenMM to perform energy minimization, NVT/NPT equilibration, and production execution with GPU acceleration when available.

How do I calculate RMSD and RMSF from a protein simulation trajectory?▼

To calculate RMSD and RMSF from a trajectory, use MDAnalysis to process simulation frames and quantify molecular stability and protein flexibility over time.

What's the best way to analyze protein-ligand contacts during molecular dynamics?▼

The best way to analyze protein-ligand contacts is to use MDAnalysis to generate contact maps and track protein-ligand contact histories across trajectory frames to characterize drug binding.

Can I use OpenMM to assess mutation effects on protein stability?▼

Yes, you can use OpenMM to simulate protein conformational sampling and then analyze the resulting trajectories to assess mutation effects on protein stability through interaction metrics.

Do I need to parameterize ligands before running molecular dynamics simulations?▼

Yes, you need to parameterize ligands before running simulations, and this Skill provides practical modeling guidance including ligand parameterization approaches like OpenFF to enable realistic biomolecular systems.

How does MDAnalysis handle trajectory analysis for protein conformational sampling?▼

MDAnalysis handles trajectory analysis by evaluating simulation frames to compute RMSD/RMSF, generate contact maps, and support advanced analyses like secondary structure and free-energy surfaces for conformational sampling.

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