bio-molecular-dynamics

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.