Molecular Dynamics
k-dense-ai/scientific-agent-skillsMolecular dynamics simulations let you watch proteins and other molecules move in slow motion. This skill uses two powerful tools OpenMM and MDAnalysis. OpenMM runs the simulation on your computer or GPU. MDAnalysis helps you analyze the results like measuring how much a protein wiggles or how a drug binds.
You can set up a protein or small molecule system, add water and salt, and define force fields. Then run energy minimization to remove clashes and production simulations to see how the system evolves over time. After the simulation you can compute RMSD RMSF contact maps and free energy surfaces.
This is useful for structural biology drug binding and biophysics. Researchers use it to study protein stability drug binding and conformational changes. Even if you are new to simulations the step by step Python code makes it easy to get started.
Add Molecular Dynamics skill to your workflow
Global
mkdir -p ~/.claude/skills/molecular-dynamicsProject
mkdir -p .claude/skills/molecular-dynamicsSource Repository
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