molecular-dynamics
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 packages
Installation:
conda install -c conda-forge openmm mdanalysis nglview
# or
pip install openmm mdanalysis
When to Use This Skill
Use molecular dynamics when:
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