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Molecular Dynamics Toolkit

molecular-dynamics

K-Dense-AI/claude-scientific-skills

Run OpenMM-powered molecular dynamics simulations and MDAnalysis trajectory workflows to build protein or small-molecule systems, minimize energy, equilibrate conditions, and characterize RMSD/RMSF, contacts, and free-energy surfaces for structural biology or drug studies.

Molecular Dynamics Simulation Workflow

molecular-dynamics

K-Dense-AI/scientific-agent-skills

A comprehensive toolkit for running and analyzing molecular dynamics (MD) simulations. This skill covers the entire workflow: system setup, force field definition, energy minimization, and equilibration using industry-standard tools like OpenMM and MDAnalysis. Essential for structural biology, drug binding studies, and biophysics research.

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