molecular-dynamics

Simulate and analyze molecular dynamics with OpenMM and MDAnalysis.

Updated May 17, 2026

Search Tags:#simulation #molecular-dynamics #biophysics #mdanalysis #protein simulation

Ready to run

npx skills add https://github.com/galeep/plugin-place --skill molecular-dynamics-galeep

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/galeep/plugin-place/tree/main/plugins/sci-engineering-simulation/skills/molecular-dynamics
Command: npx skills add https://github.com/galeep/plugin-place --skill molecular-dynamics-galeep

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires openmm, mdanalysis, nglview, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies the analysis and simulation of molecular systems by providing an interface to OpenMM and MDAnalysis tools, streamlining molecular dynamics simulations for biophysics, drug binding, and structural biology applications.

Core Features & Use Cases

Simulation Engine: Accesses high-performance OpenMM and MDAnalysis for molecular dynamics simulations.
Force Fields: Offers predefined force field configurations for proteins, small molecules, membranes, and nucleic acids.
Data Analysis: Enables detailed analysis of molecular systems, including RMSD, RMSF, contact maps, and free energy surfaces.
Use Case: Ideal for studying protein stability, drug binding, conformational changes, and protein-protein interactions.

Quick Start

Execute 'molecular-dynamics run -f AMBER14 -p protein.pdb' to run a simulation on the protein 'protein.pdb' using the AMBER14 force field.

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 protein stability using OpenMM?▼

Run molecular dynamics simulations for protein stability by executing the command with OpenMM and specifying a force field like AMBER14 along with your protein PDB file. The Skill handles system preparation, energy minimization, and equilibration automatically.

What analysis can I perform on molecular dynamics trajectories with MDAnalysis?▼

Molecular dynamics trajectory analysis with MDAnalysis includes calculating RMSD, RMSF, contact maps, and free energy surfaces. These metrics help study conformational changes, protein-protein interactions, and drug binding events.

Can I simulate small molecules and nucleic acids, or does this only support proteins?▼

You can simulate small molecules, nucleic acids, and membranes in addition to proteins. The Skill provides predefined force field configurations for these molecule types to support diverse biophysics and structural biology workflows.

Does this molecular dynamics workflow include visualization for trajectory analysis?▼

Molecular dynamics trajectory visualization is supported optionally through NGLView. While OpenMM and MDAnalysis handle the core simulation and analysis, NGLView integrates to provide visual representation of the molecular systems.

What force fields are available for biophysics simulations involving drug binding?▼

Biophysics simulations for drug binding use predefined force field configurations, explicitly including AMBER14. These force fields parameterize proteins, small molecules, membranes, and nucleic acids for accurate molecular dynamics calculations.

Do I need OpenMM and MDAnalysis installed to use this molecular dynamics Skill?▼

OpenMM and MDAnalysis are required dependencies to run molecular dynamics simulations and analyze trajectories. NGLView is an optional dependency needed only if you want to visualize the molecular systems during your workflow.