Molecular Dynamics
Skill Verifiziert AktivRun 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.
To enable AI agents to perform complex molecular dynamics simulations and analyze the resulting trajectories for scientific research in areas like structural biology, drug binding, and biophysics.
Funktionen
- Set up protein/small molecule systems with OpenMM
- Run energy minimization and production MD simulations
- Analyze MD trajectories with MDAnalysis (RMSD, RMSF, contacts)
- Visualize simulation data and analysis results
Anwendungsfälle
- Investigating protein stability and conformational changes
- Characterizing ligand binding modes and residence times
- Studying protein-protein interactions and their dynamics
- Estimating free energies of binding or conformational changes
Nicht-Ziele
- Performing ab initio quantum chemistry calculations
- Directly controlling hardware resources for simulation
- Interfacing with laboratory automation hardware
Workflow
- Prepare simulation system from PDB
- Perform energy minimization
- Run NVT equilibration
- Run NPT production simulation
- Load trajectory with MDAnalysis
- Compute and plot RMSD
- Compute and plot RMSF
- Analyze protein-ligand contacts
Praktiken
- Simulation setup best practices
- Equilibration strategies
- Trajectory analysis techniques
Voraussetzungen
- Python 3.11+
- conda or pip package manager
- OpenMM, MDAnalysis, NumPy, Matplotlib installed
Installation
npx skills add K-Dense-AI/claude-scientific-skillsFührt das Vercel skills CLI (skills.sh) via npx aus — benötigt Node.js lokal und mindestens einen installierten skills-kompatiblen Agent (Claude Code, Cursor, Codex, …). Setzt voraus, dass das Repo dem agentskills.io-Format folgt.
Qualitätspunktzahl
VerifiziertVertrauenssignale
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