Molecular Dynamics
技能 已验证 活跃Run 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.
功能
- 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
使用场景
- 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
非目标
- Performing ab initio quantum chemistry calculations
- Directly controlling hardware resources for simulation
- Interfacing with laboratory automation hardware
工作流
- 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
实践
- Simulation setup best practices
- Equilibration strategies
- Trajectory analysis techniques
先决条件
- Python 3.11+
- conda or pip package manager
- OpenMM, MDAnalysis, NumPy, Matplotlib installed
安装
npx skills add K-Dense-AI/claude-scientific-skills通过 npx 运行 Vercel skills CLI(skills.sh)— 需要本地安装 Node.js,以及至少一个兼容 skills 的智能体(Claude Code、Cursor、Codex 等)。前提是仓库遵循 agentskills.io 格式。
质量评分
已验证类似扩展
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