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molecular-dynamics

Run end-to-end molecular dynamics simulations and trajectory analyses with OpenMM and MDAnalysis.

33.0k|3.2k|Updated Oct 19, 2025
Search Tags:#gpu-acceleration#molecular-dynamics#protein#trajectory-analysis#ligand#mdanalysis#openmm
One-click install
npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill molecular-dynamics-k-dense-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/scientific-skills/molecular-dynamics
Command: npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill molecular-dynamics-k-dense-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Molecular dynamics simulations enable detailed exploration of biomolecular dynamics, ligand binding, and conformational changes, but setting up reproducible workflows can be complex. This skill standardizes end-to-end workflows for system setup, energy minimization, equilibration, production runs, and trajectory analysis using OpenMM and MDAnalysis.

Core Features & Use Cases

  • End-to-end MD workflow: system preparation, energy minimization, NVT/NPT equilibration, and production runs on CPU/GPU.
  • Trajectory analysis suite: RMSD, RMSF, contact analysis, PCA, and free energy surfaces with MDAnalysis.
  • Force field guidance and tooling: recommendations for proteins, protein-ligand systems, and ligand parameterization with PDBFixer and GAFF2/OpenFF.
  • Extensibility: scripts and references to customize analyses; supports GPU acceleration for faster runs.
  • Use cases include protein stability studies, drug binding investigations, conformational sampling, and comparative analyses across mutants or ligands.

Quick Start

Install OpenMM and MDAnalysis, prepare your structure (optionally with PDBFixer), and run the OpenMM MD workflow to minimize, equilibrate, and produce trajectories for analysis.

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 for a protein using OpenMM?▼

You can run molecular dynamics simulations by preparing your structure, optionally using PDBFixer, then executing the OpenMM workflow for energy minimization, NVT/NPT equilibration, and production runs. The workflow supports both CPU and GPU acceleration.

What's the best way to analyze MD trajectories for RMSD and RMSF calculations?▼

The best way to analyze MD trajectories is using the MDAnalysis suite included in the workflow, which calculates RMSD, RMSF, contact analysis, PCA, and free energy surfaces from your production run outputs.

Can I use OpenMM for ligand binding and protein-ligand simulations?▼

Yes, OpenMM supports protein-ligand systems. The workflow provides force field guidance and tooling for ligand parameterization using GAFF2 or OpenFF, alongside system preparation for drug binding investigations.

Do I need GPU acceleration for molecular dynamics simulations?▼

GPU acceleration is optional but recommended for faster molecular dynamics runs. The workflow supports both CPU and GPU execution for energy minimization, equilibration, and production.

How do I prepare raw PDB structures before running molecular dynamics?▼

You prepare raw PDB structures using PDBFixer, an optional dependency, to clean and fix structures before passing them into the OpenMM system preparation, energy minimization, and equilibration workflow.

What analyses can I perform on molecular dynamics trajectories?▼

You can perform RMSD, RMSF, contact analysis, PCA, and free energy surface calculations on molecular dynamics trajectories using the integrated MDAnalysis suite, supporting protein stability studies and comparative mutant analyses.

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