molecular-dynamics

Name: molecular-dynamics
Rating: 5 (1 reviews)
Author: bg-szy

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

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Updated 18 days ago

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Molecular Dynamics

Overview

Molecular dynamics (MD) simulation computationally models the time evolution of molecular systems by integrating Newton's equations of motion. This skill covers two complementary tools:

OpenMM (https://openmm.org/): High-performance MD simulation engine with GPU support, Python API, and flexible force field support
MDAnalysis (https://mdanalysis.org/): Python library for reading, writing, and analyzing MD trajectories from all major simulation pack

[Description truncada. Veja o README completo no GitHub.]

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