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Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization…
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:
don't have the plugin yet? install it then click "run inline in claude" again.