molecular-dynamics

What problem does it solve?

This Skill enables users to set up, run, and analyze molecular dynamics simulations, providing insights into protein stability, drug binding, and molecular interactions.

Core Features & Use Cases

• Simulation Setup: Prepare protein and small molecule systems using standard force fields and water models.
• Simulation Execution: Run energy minimization, NVT, and NPT equilibration, followed by production MD using OpenMM.
• Trajectory Analysis: Analyze simulation results using MDAnalysis for RMSD, RMSF, contact maps, and more.
• Use Case: Investigate how a specific mutation affects the stability and conformational dynamics of a target protein by simulating its behavior in a solvated environment.

Quick Start

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