biomolecular-md
Biomolecular molecular dynamics simulations using OpenMM for proteins, solvated molecular systems, drug-protein interactions, and soft matter. Covers force field assignment (AMBER, CHARMM, OpenFF), explicit solvent models, free energy calculations, and trajectory analysis with mdtraj.
npx skills add majiayu000/claude-skill-registry --skill biomolecular-md --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
--- name: biomolecular-md description: Biomolecular MD (1 sub-skills: openmm-simulation) --- # Biomolecular MD Biomolecular molecular dynamics simulations using OpenMM for proteins, solvated molecular systems, drug-protein interactions, and soft matter. Covers force field assignment (AMBER, CHARMM, OpenFF), explicit solvent models, free energy calculations, and trajectory analysis with mdtraj. ## Sub-Skills | Sub-Skill | Directory | Description | |---|---|---| | OpenMM Simulation | `openmm-simulation/` | Full biomolecular MD workflows: protein-in-water from PDB, small molecule solvation with Open Force Field, temperature annealing, equilibration protocols (NVT/NPT), and trajectory analysis with mdtraj | ## Method Decision Guide ``` What biomolecular simulation do you need? Protein folding / dynamics / conformational sampling? --> openmm-simulation/ (Workflow 1: Protein in Water from PDB) Small molecule solvation free energy / drug-like molecule in water? --> openmm-simulation/ (Workflow 2: Small Molecule Solvation with OpenFF) Temperature-driven conformational changes / simulated annealing? --> openmm-simulation/ (Workflow 3: Temperature Annealing) Drug-protein binding / ligand-rec
- Sub-Skills
- Method Decision Guide
What does the biomolecular-md skill do?
Biomolecular molecular dynamics simulations using OpenMM for proteins, solvated molecular systems, drug-protein interactions, and soft matter. Covers force field assignment (AMBER, CHARMM, OpenFF), explicit solvent models, free energy calculations, and trajectory analysis with mdtraj.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill biomolecular-md --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.