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molecular-dynamics

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

Updated Mar 10, 2026
Search Tags:#simulation#biophysics#structural biology#molecular dynamics#mdanalysis#openmm
One-click install
npx skills add https://github.com/felixboehm/biochem-allergy --skill molecular-dynamics-felixboehm
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/molecular-dynamics
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill molecular-dynamics-felixboehm

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides a comprehensive toolkit for simulating the time evolution of molecular systems and analyzing the resulting trajectories, enabling deep insights into molecular behavior.

Core Features & Use Cases

  • Molecular Dynamics Simulation: Set up, run, and analyze simulations using OpenMM and MDAnalysis.
  • System Preparation: Prepare protein and small molecule systems, including solvation and parameterization.
  • Trajectory Analysis: Perform RMSD, RMSF, contact analysis, and secondary structure assignments.
  • Use Case: Investigate how a specific mutation affects protein stability by running a molecular dynamics simulation and analyzing the conformational changes.

Quick Start

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

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?▼

To run molecular dynamics simulations, you prepare and solvate your protein system, perform energy minimization, equilibrate in NVT and NPT ensembles, and execute production runs using OpenMM and MDAnalysis.

Can I calculate RMSD and RMSF from molecular dynamics trajectories?▼

Yes, you can perform detailed trajectory analysis including RMSD, RMSF, contact maps, and secondary structure assignments to evaluate conformational changes using MDAnalysis.

What's the best way to prepare a protein system for a molecular dynamics simulation?▼

System preparation for molecular dynamics involves solvation and parameterization of your protein or small molecule, followed by energy minimization to remove steric clashes before equilibration.

Does this workflow support investigating how a specific mutation affects protein stability?▼

Yes, you can investigate how a specific mutation affects protein stability by running a molecular dynamics simulation and analyzing the resulting conformational changes in the trajectory.

What is needed for NVT and NPT equilibration in biophysics simulations?▼

NVT and NPT equilibration in biophysics simulations requires a prepared and energy-minimized molecular system, stabilizing temperature and pressure before executing the final production run.

When do I need trajectory analysis for structural biology research?▼

You need trajectory analysis for structural biology research when evaluating molecular behavior over time, such as calculating RMSF to measure protein flexibility or generating contact maps to map interactions.

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