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molecular-dynamics

Automate OpenMM molecular dynamics simulations and analyze trajectories with MDAnalysis.

22|4|Updated May 25, 2026
Search Tags:#molecular-dynamics#protein#trajectory-analysis#biophysics#ligand#mdanalysis#openmm
One-click install
npx skills add https://github.com/crazymsn/academic-skills --skill molecular-dynamics-crazymsn
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/crazymsn/academic-skills/tree/main/academic-skills/molecular-dynamics
Command: npx skills add https://github.com/crazymsn/academic-skills --skill molecular-dynamics-crazymsn

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Molecular dynamics simulations often require assembling complex systems, running lengthy productions, and extracting meaningful insights from trajectories. This skill provides a complete OpenMM/MDAnalysis workflow to streamline system setup, execution, and analysis.

Core Features & Use Cases

  • System preparation and force-field setup: build solvated systems with OpenMM and prepare topology.
  • Energy minimization and equilibration: minimize clashes and equilibrate with NVT and NPT ensembles.
  • Production runs and trajectory generation: run long MD simulations and export trajectories for analysis.
  • Trajectory analysis with MDAnalysis: compute RMSD, RMSF, radius of gyration, and protein–ligand contacts.
  • Use Cases: assess protein stability, ligand binding, and conformational sampling for biophysics studies.

Quick Start

Launch a complete OpenMM MD workflow by preparing a system, minimizing, equilibrating, running production, and analyzing the resulting trajectory 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 for protein stability studies?▼

Molecular dynamics simulations automate the assembly of complex systems, lengthy production runs, and trajectory analysis to extract meaningful insights for structural biology studies, eliminating the need to manually stitch together disparate simulation and analysis tools.

How do I analyze MD trajectories to compute RMSD and radius of gyration?▼

You can compute RMSD, RMSF, and radius of gyration by analyzing the exported MD trajectories with MDAnalysis to assess protein stability, ligand binding, and conformational sampling for biophysics studies.

Can I use OpenMM to prepare solvated systems and set up force fields for ligand binding investigations?▼

Yes, you can use OpenMM to build solvated systems and prepare topology for force-field setup, providing the necessary structural foundation for subsequent minimization, equilibration, and ligand binding investigations.

What is the best way to automate an end-to-end molecular dynamics workflow for biophysics research?▼

The best way to automate an end-to-end molecular dynamics workflow is to use a combined OpenMM and MDAnalysis approach that streamlines system preparation, execution, and trajectory analysis for structural biology investigations.

Does this OpenMM workflow support both NVT and NPT ensembles during equilibration?▼

Yes, the OpenMM workflow supports both NVT and NPT ensembles during the equilibration phase to stabilize thermodynamic properties before executing long production runs and trajectory generation.

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