FE-NES Workflow Diagram

┌─────────────────────┐
│ System Preparation  │
├─────────────────────┤
│ • Prepare complex   │
│ • Set up box        │
│ • Solvate system    │
└──────────┬──────────┘
           │
           ▼
┌─────────────────────┐
│ Equilibration MD    │
├─────────────────────┤
│ • Energy minimize   │
│ • NVT equilibration │
│ • NPT equilibration │
│ • Production MD     │
└──────────┬──────────┘
           │
           ▼
┌─────────────────────┐
│ Edge Map            │
│ Construction        │
├─────────────────────┤
│ • Generate edge map │
└──────────┬──────────┘
           │
           ▼
┌─────────────────────┐
│ Nonequilibrium      │
│ Switching (NES)     │
├─────────────────────┤
│ • Vary λ from 0→1   │
│ • Record work values│
│ • Multiple switches │
└──────────┬──────────┘
           │
           ▼
┌─────────────────────┐
│ RBFE Prediction     │
├─────────────────────┤
│ • Calculate ΔΔG     │
│ • Analyze results   │
│ • Error estimation  │
│ • Calculate ΔΔG     │
└─────────────────────┘

Key Points:

  1. System Preparation: Set up the molecular system with the initial structure and define the alchemical transformation between ligands.

  2. Equilibration MD: Bring the system to equilibrium through successive MD simulations under different ensembles.

  3. Edge Map Construction: Define the alchemical transformation pathway and identify critical interactions that change during the process.

  4. Nonequilibrium Switching: Perform rapid, nonequilibrium MD simulations where the alchemical parameter λ is varied, generating work trajectories.

  5. RBFE Prediction: Use the Jarzynski equation to convert work values from NES simulations into relative binding free energy (ΔG).