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molecular-dynamics

Simulate biomolecular dynamics with OpenMM and analyze trajectories using MDAnalysis.

Updated May 24, 2026
Search Tags:#trajectory analysis#protein-ligand#molecular dynamics#mdanalysis#openmm#free energy#rmsd rmsf
One-click install
npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill molecular-dynamics-estrella-231
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/Estrella-231/Mathematical_modeling_tongmeng/tree/main/.agents/skills/molecular-dynamics
Command: npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill molecular-dynamics-estrella-231

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Molecular dynamics simulation helps you understand how proteins and small molecules move over time at an atomistic level, turning structural hypotheses into measurable dynamical observables.

Core Features & Use Cases

  • Run MD with OpenMM: Build solvated systems from PDB, choose force fields, perform energy minimization, and run NVT/NPT equilibration plus production with GPU acceleration when available.
  • Analyze trajectories with MDAnalysis: Compute RMSD/RMSF, track protein–ligand contacts, and support additional analyses such as secondary structure, hydrogen bonds, PCA, and free energy surfaces.
  • Force-field and workflow guidance: Provide practical recommendations for common biological system types (proteins, disordered proteins, membrane proteins, nucleic acids, and ligand parameterization via OpenFF).

Quick Start

Use the molecular-dynamics skill to minimize, equilibrate, run a production MD trajectory, and then compute RMSD/RMSF and protein–ligand contact patterns from your output files.

Frequently Asked Questions about molecular-dynamics

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

FAQPage Schema
How do I compute RMSD and RMSF from a molecular dynamics trajectory?▼

Use MDAnalysis to load compatible topology and trajectory formats, calculating RMSD and RMSF to quantify structural deviations and flexibility over time, tracking protein stability and conformational changes.

How do I run molecular dynamics simulations using OpenMM for protein-ligand binding?▼

Build a solvated system from a PDB file, choose a force field, perform energy minimization, and run NVT/NPT equilibration plus production with GPU acceleration when available to simulate protein-ligand binding dynamics.

Can I analyze hydrogen bonds and secondary structure from MD trajectories?▼

Yes, MDAnalysis supports additional analyses such as secondary structure, hydrogen bonds, PCA, and free energy surfaces alongside standard RMSD and RMSF calculations for biomolecular dynamics.

What force fields work best for membrane proteins and disordered proteins in OpenMM?▼

The workflow provides practical force-field recommendations for common biological system types including proteins, disordered proteins, membrane proteins, and nucleic acids, with ligand parameterization via OpenFF.

What file formats do I need for MDAnalysis trajectory analysis after simulation?▼

You need compatible topology and trajectory formats generated from the OpenMM production run, ensuring files contain atomic coordinates and connectivity information required for loading and analyzing structural dynamics.

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