Molecular Dynamics Simulation Pipeline

Autonomous molecular dynamics simulation from structure to analysis. Inspired by DynaMate's three-module architecture: Experiment Planner → Simulation Performer → Result Analyzer.

When to Use

• "帮我跑个 MD 模拟" or "molecular dynamics simulation for X"
• "计算 X 和 Y 的结合自由能" or "binding free energy"
• "这个蛋白稳定吗" or "protein stability analysis"
• "蛋白-配体相互作用模拟"
• User provides a PDB ID, UniProt ID, or protein structure file

Prerequisites Check

Before starting any simulation, verify the environment:

bash: python3 << 'PYEOF'
import sys