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RamanEbrahimi
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molecular-dynamics

Automate molecular dynamics simulations and trajectory analysis with OpenMM and MDAnalysis.

3|Updated Apr 17, 2026
Search Tags:#simulation#molecular-dynamics#biophysics#OpenMM#MDAnalysis
One-click install
npx skills add https://github.com/RamanEbrahimi/raman-marketplace --skill molecular-dynamics-ramanebrahimi
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molecular-dynamics
Source: https://github.com/RamanEbrahimi/raman-marketplace/tree/main/plugins/agentic-research/skills/scientific-skills/molecular-dynamics
Command: npx skills add https://github.com/RamanEbrahimi/raman-marketplace --skill molecular-dynamics-ramanebrahimi

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the complex process of running and analyzing molecular dynamics simulations, providing an efficient solution for protein stability analysis, drug binding simulations, and biophysics research.

Core Features & Use Cases

  • Molecular Dynamics Simulation: Utilizes OpenMM and MDAnalysis to perform molecular dynamics simulations.
  • System Preparation: Automates the setup of protein and small molecule systems, force field definitions, and solvent box addition.
  • Energy Minimization and Equilibration: Handles energy minimization, NVT and NPT equilibration, and production runs.
  • Trajectory Analysis: Provides tools for RMSD, RMSF, contact maps, and free energy surface analysis.
  • Use Case: For a protein stability analysis, the skill can simulate protein dynamics, identify mutations affecting stability, and provide detailed RMSD and RMSF data.

Quick Start

Run the molecular-dynamics skill with the provided input file and parameters.

Frequently Asked Questions about molecular-dynamics

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

FAQPage Schema
How do I automate molecular dynamics simulations using OpenMM and MDAnalysis?▼

Automate molecular dynamics simulations by using this Skill to handle system preparation, force field application, energy minimization, and production runs with OpenMM and MDAnalysis. It streamlines protein setup and simulation execution automatically.

Can I calculate RMSD and RMSF from molecular dynamics trajectories?▼

Calculate RMSD and RMSF from molecular dynamics trajectories by using the trajectory analysis tools provided. The Skill computes RMSD, RMSF, contact maps, and free energy surfaces to analyze protein stability and dynamics.

What do I need to run protein stability analysis and drug binding simulations?▼

Run protein stability analysis and drug binding simulations by setting up protein systems with force fields and solvent boxes. This Skill requires OpenMM, MDAnalysis, nglview, pandas, and matplotlib to execute and analyze the simulations.

Does this Skill handle energy minimization, NVT, and NPT equilibration for protein systems?▼

Handle energy minimization, NVT, and NPT equilibration for protein systems automatically. The Skill manages the entire equilibration process and production runs to prepare your system for stable molecular dynamics trajectory analysis.

What is the best way to generate free energy surfaces and contact maps from MD simulations?▼

Generate free energy surfaces and contact maps from MD simulations by utilizing the integrated MDAnalysis tools. The Skill processes your simulation trajectories to produce detailed structural analysis and visualize molecular interactions.

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