Alterlab 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. Part of the AlterLab Academic Skills suite.
To enable researchers to conduct and analyze molecular dynamics simulations for structural biology, drug binding, and biophysics research.
Funktionen
- Set up protein/small molecule systems
- Define force fields and water models
- Run energy minimization
- Perform NVT and NPT equilibration
- Execute production MD simulations
- Analyze trajectories (RMSD, RMSF, contacts)
- Estimate free energy surfaces
Anwendungsfälle
- Analyze protein stability and conformational changes
- Simulate drug binding modes and residence times
- Study protein-protein interactions and binding energetics
- Investigate membrane protein dynamics
Nicht-Ziele
- Performing ab initio quantum mechanical calculations
- Directly controlling hardware for simulations
- Providing a graphical user interface for simulation setup
Code Execution
- info:ValidationInput parameters for functions are documented in docstrings, but explicit schema validation libraries like Zod or Pydantic are not used for runtime parameter constraint checking.
Execution
- info:Pinned dependenciesInstallation instructions suggest Conda or Pip, which can pin versions, but explicit lockfiles for reproducibility are not bundled with the skill itself.
Installation
npx skills add AlterLab-IEU/AlterLab-Academic-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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