Summary of the enhanced sampling free energy calculation performed
| System . | Enhanced sampling technique . | Production . |
|---|---|---|
| NavAb (expanded α-model)—Na+ | AWH | 200 ns × 6 walkers |
| NavAb (expanded π-model)—Na+ | AWH | 200 ns × 6 walkers |
| NavAb (expanded α-model)—lidocaine | AWH | 200 ns × 6 walkers |
| NavAb (resting α-model)—lidocaine | AWH | 200 ns × 6 walkers |
| NavAb (asymmetric α-model)—lidocaine | AWH | 200 ns × 6 walkers |
| NavAb (expanded π-model)—lidocaine | AWH | 200 ns × 6 walkers |
| NavAb expanded π-model (N214L)—Na+ | AWH | 139 ns × 6 walkers |
| NavAb (resting α-model)—lidocaine | Well-tempered metadynamics | 94 ns × 12 walkers |
| NavAb (asymmetric α-model)—lidocaine | Well-tempered metadynamics | 94 ns × 12 walkers |
| NavAb (expanded π-model)—lidocaine | Well-tempered metadynamics | 140 ns × 16 walkers |
| NavAb (expanded α-model)—lidocaine | Well-tempered metadynamics | 140 ns × 16 walkers |
| Pore opening starting from contracted π-model (PDB ID 5VB2 WT) without CTD | ABMD | 840 ps × 3 replicas |
| Pore opening starting from contracted α-model (PDB ID 5VB2) without CTD | ABMD | 840 ps × 3 replicas |
| Pore opening starting from contracted π-model (PDB ID 5VB2 N1211L) without CTD | ABMD | 840 ps × 3 replicas |
| System . | Enhanced sampling technique . | Production . |
|---|---|---|
| NavAb (expanded α-model)—Na+ | AWH | 200 ns × 6 walkers |
| NavAb (expanded π-model)—Na+ | AWH | 200 ns × 6 walkers |
| NavAb (expanded α-model)—lidocaine | AWH | 200 ns × 6 walkers |
| NavAb (resting α-model)—lidocaine | AWH | 200 ns × 6 walkers |
| NavAb (asymmetric α-model)—lidocaine | AWH | 200 ns × 6 walkers |
| NavAb (expanded π-model)—lidocaine | AWH | 200 ns × 6 walkers |
| NavAb expanded π-model (N214L)—Na+ | AWH | 139 ns × 6 walkers |
| NavAb (resting α-model)—lidocaine | Well-tempered metadynamics | 94 ns × 12 walkers |
| NavAb (asymmetric α-model)—lidocaine | Well-tempered metadynamics | 94 ns × 12 walkers |
| NavAb (expanded π-model)—lidocaine | Well-tempered metadynamics | 140 ns × 16 walkers |
| NavAb (expanded α-model)—lidocaine | Well-tempered metadynamics | 140 ns × 16 walkers |
| Pore opening starting from contracted π-model (PDB ID 5VB2 WT) without CTD | ABMD | 840 ps × 3 replicas |
| Pore opening starting from contracted α-model (PDB ID 5VB2) without CTD | ABMD | 840 ps × 3 replicas |
| Pore opening starting from contracted π-model (PDB ID 5VB2 N1211L) without CTD | ABMD | 840 ps × 3 replicas |