Table 1.
Description of AA simulations.
| AA Simulations | Lipid compositiona) | Time | Ensemble | Replicas | Setup |
|---|---|---|---|---|---|
| Bulk TG | 216 TG | 100 ns | NPT | 6b) | PACKMOL |
| Bulk TG-vacuum | 216 TG | 200 ns | NVT | 6b) | From above sim. |
| POPC bilayer | 128 POPC | 200 ns | NPT | 1 | PACKMOL |
| POPC + TG bilayer | 128 POPC + 1 TG | 1 μs | NPT | 1 | PACKMOL |
| POPC + TG bilayer | 128 POPC + 1 TG | 300 ns | NPT + biased | 12c) | From above sim. |
| POPC + TG bilayer | 128 POPC + 1 TG | 2 μs | NPT + biased | 5 | From above sim. |
| POPC + TG bilayer | 124 POPC + 8 TG | 1 μs | NPT | 1 | PACKMOL |
| POPC + TG bilayer | 1984 POPC + 128 TG | 600 ns | NPT | 1 | From above sim. |
| POPC bilayer | 4050 POPC | 300 ns | NPT | 1 | CHARMM-GUI |
| POPC + DAG bilayer (referred to as DAG 10%) | 3200 POPC + 320 DAG | 1 μs | NPT | 1 | CHARMM-GUI |
| POPC + DAG bilayer (referred to as DAG 20%) | 3200 POPC + 640 DAG | 1 μs | NPT | 1 | CHARMM-GUI |
| POPC + DAG bilayer (referred to as DAG 30%) | 3200 POPC + 960 DAG | 1 μs | NPT | 1 | CHARMM-GUI |
| DAG 30% membrane deformation and then NPAT | 3200 POPC + 960 DAG | 20 ns + 1 μs | NPγT and then NPAT | 1 | From above sim. |
| DOPC bilayer | 128 DOPC | 200 ns | NPT | 1 | CHARMM-GUI |
a)
The total number of lipid molecules of each type in a system.
b)
With varying LJ cutoff distances
c)
12 windows