molecular-dynamics
Autonomous molecular dynamics simulation pipeline inspired by DynaMate (2026). Designs, executes, and analyzes complete MD workflows for protein and protein-ligand systems. Covers structure retrieval, system preparation, minimization, equilibration, production, and trajectory analysis (RMSD, RMSF, hydrogen bonds, binding free energy). Uses OpenMM as the primary engine with AmberTools for preparation. Self-correcting — detects and fixes common simulation failures. Use when users ask for MD simulations, protein stability analysis, binding free energy calculations, or "跑个分子动力学模拟". Requires OpenMM and optionally AmberTools.
Installation and usage
Autonomous molecular dynamics simulation pipeline inspired by DynaMate (2026). Designs, executes, and analyzes complete MD workflows for protein and protein-ligand systems. Covers structure retrieval, system preparation, minimization, equilibration, production, and trajectory analysis (RMSD, RMSF, hydrogen bonds, binding free energy). Uses OpenMM as the primary engine with AmberTools for preparation. Self-correcting — detects and fixes common simulation failures. Use when users ask for MD simulations, protein stability analysis, binding free energy calculations, or "跑个分子动力学模拟". Requires OpenMM and optionally AmberTools.
インストール後、ターミナルで以下のコマンドを実行してこのスキルを使用できます：
skills use molecular-dynamics