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molecular-dynamics

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

Updated Mar 10, 2026
Search Tags:#simulation#cheminformatics#biophysics#molecular dynamics#OpenMM#MDAnalysis
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill molecular-dynamics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/molecular-dynamics
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill molecular-dynamics

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill enables users to set up, run, and analyze molecular dynamics simulations, providing insights into protein stability, drug binding, and molecular interactions.

Core Features & Use Cases

  • Simulation Setup: Prepare protein and small molecule systems using standard force fields and water models.
  • Simulation Execution: Run energy minimization, NVT, and NPT equilibration, followed by production MD using OpenMM.
  • Trajectory Analysis: Analyze simulation results using MDAnalysis for RMSD, RMSF, contact maps, and more.
  • Use Case: Investigate how a specific mutation affects the stability and conformational dynamics of a target protein by simulating its behavior in a solvated environment.

Quick Start

Use the molecular-dynamics skill to prepare a system from 'protein.pdb', minimize its energy, and run 100 ps of NPT equilibration.

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 and MDAnalysis?▼

Molecular dynamics simulations using OpenMM and MDAnalysis involve preparing protein systems, running energy minimization, NVT and NPT equilibration, executing production MD, and analyzing trajectories for RMSD and RMSF.

What's the best way to analyze protein stability and conformational changes from a trajectory?▼

Trajectory analysis for protein stability and conformational changes uses MDAnalysis to compute RMSD, RMSF, and contact maps from simulation results, providing insights into molecular interactions and structural dynamics.

Do I need PDBFixer and openff-toolkit to set up small molecule systems for molecular dynamics?▼

PDBFixer and openff-toolkit are required dependencies for preparing protein and small molecule systems, applying standard force fields and water models before running OpenMM simulations.

Can I investigate ligand binding and drug discovery interactions with this molecular dynamics workflow?▼

Ligand binding and drug discovery interactions can be investigated using this workflow by simulating molecular behavior in a solvated environment to study how specific mutations or drugs affect target protein dynamics.

How does energy minimization and NPT equilibration work before production molecular dynamics?▼

Energy minimization and NPT equilibration prepare the solvated system by relaxing steric clashes and stabilizing pressure and temperature before executing production molecular dynamics simulations with OpenMM.

Why use MDAnalysis for trajectory analysis instead of other tools in the same category?▼

MDAnalysis enables trajectory analysis by computing RMSD, RMSF, and contact maps, distinguishing it from other category tools through native integration with OpenMM workflows for structural biology and biophysics research.

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