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molecular-dynamics

Analyzes and simulates MD workflows using OpenMM and MDAXA for Python-based setups and RMSD/RMSF trajectory analysis.

321|26|Updated Mar 10, 2026
Search Tags:#molecular-dynamics#protein-ligand#trajectory-analysis#rmsd#mdanalysis#rmsf#openmm
One-click install
npx skills add https://github.com/mkurman/tamux --skill molecular-dynamics-mkurman
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/mkurman/tamux/tree/main/skills/scientific-skills/molecular-dynamics
Command: npx skills add https://github.com/mkurman/tamux --skill molecular-dynamics-mkurman

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Molecular dynamics simulations enable detailed exploration of the time evolution of molecular systems by solving Newton's equations of motion. This Skill provides a workflow and analysis toolkit using OpenMM and MDAnalysis to set up protein/small molecule systems, apply force fields, minimize energy, equilibrate, run production MD, and analyze trajectories (RMSD, RMSF, contacts, and free energy surfaces).

Core Features & Use Cases

  • System setup and force field preparation for proteins and ligands.
  • Energy minimization, NVT/NPT equilibration, and production MD to generate trajectories.
  • Trajectory analysis including RMSD, RMSF, residue-level analysis, and protein-ligand contacts.
  • Use Case: Explore protein stability, ligand binding, and conformational changes.

Quick Start

Install the required Python packages, prepare a system (protein or small molecule) with a PDB, and run a short OpenMM MD workflow to generate a trajectory.

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 Python?▼

You can run molecular dynamics simulations by preparing a PDB file, applying force fields, and executing Python scripts for energy minimization, NVT/NPT equilibration, and production MD using OpenMM to generate trajectories.

How do I calculate RMSD and RMSF from a trajectory file?▼

You can calculate RMSD and RMSF from a trajectory by integrating MDAnalysis with your workflow to perform trajectory analysis, measuring protein stability, residue-level fluctuations, and conformational changes.

What do I need to set up protein and ligand systems for MD simulations?▼

To set up protein and ligand systems, you need a PDB file of your molecular structure and the required Python packages installed to apply force fields and prepare the system for simulation.

Can I analyze protein-ligand binding contacts and free energy surfaces?▼

Yes, you can analyze protein-ligand binding contacts and free energy surfaces by processing the generated trajectories with MDAnalysis to study detailed molecular interactions and conformational stability.

Does this molecular dynamics workflow support membrane and small molecule systems?▼

Yes, the workflow supports setup, execution, and analysis of MD runs across proteins, small molecules, and membranes, allowing you to study diverse conformational dynamics and ligand binding.

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