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bio-molecular-dynamics

Execute and analyze molecular dynamics simulations with OpenMM and MDAnalysis.

Updated Mar 13, 2026
Search Tags:#simulation#biophysics#computational chemistry#molecular dynamics#mdanalysis#openmm
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill bio-molecular-dynamics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-molecular-dynamics
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/bio-molecular-dynamics
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill bio-molecular-dynamics

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the complex process of setting up, running, and analyzing molecular dynamics simulations, making advanced biophysical research accessible.

Core Features & Use Cases

  • Simulation Setup: Prepare protein and small molecule systems, define force fields, and solvate.
  • MD Simulation: Run energy minimization, NVT, and NPT equilibration, followed by production runs using OpenMM.
  • Trajectory Analysis: Compute RMSD, RMSF, analyze contacts, and visualize molecular motion using MDAnalysis.
  • Use Case: Investigate how a specific mutation affects protein stability by simulating its dynamics and analyzing conformational changes.

Quick Start

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

Frequently Asked Questions about bio-molecular-dynamics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run molecular dynamics simulations and analyze trajectories using OpenMM and MDAnalysis?▼

To run molecular dynamics simulations, you prepare protein systems, apply force fields, execute energy minimization and equilibration, then compute trajectory analysis like RMSD and RMSF using OpenMM and MDAnalysis.

What is the process for preparing a protein system for molecular dynamics simulation?▼

System preparation for molecular dynamics involves loading a protein PDB file, defining appropriate force fields, solvating the molecule, and running initial energy minimization before equilibration.

Can I analyze protein stability and conformational changes from a molecular dynamics trajectory?▼

Yes, you can analyze protein stability by computing RMSD, RMSF, and contact maps from the molecular dynamics trajectory to observe conformational changes caused by mutations.

Do I need Python and specific libraries installed to execute MDAnalysis and OpenMM workflows?▼

Yes, you need a Python environment with OpenMM and MDAnalysis libraries installed to execute deterministic molecular dynamics simulation tasks and trajectory analysis workflows.

How do I calculate RMSD and RMSF to measure molecular motion in biophysics simulations?▼

You calculate RMSD and RMSF to measure molecular motion by loading the simulation trajectory into MDAnalysis and running the built-in analysis modules on the atomic coordinates.

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