TABLE 1.
Simulation parameters for the various stages
| Lipid equilibration | Peptide insertion | Peptide-lipid equilibration | Production run | |
|---|---|---|---|---|
| Temperature (K) | 323 | 323 | 323 | 323 |
| Pressure (atm) | 1 | 1 | 1 | 1 |
| vdW cutoff (nm) | 1.2 | 1.2 | 1.2 | 1.2 |
| Electrostatics | PME | PME | PME | PME |
| Length of the run (ns) | 5 | 0.05 | 1 | 10 |
| Position restraints | none | Lipid phosphorus atoms* | Peptide backbone | none |
| Position restraint force (kJ/mol/m2) | — | 1000 | 1000 | — |
| Hole making force (kJ/mol/m2) | — | 100 | — | — |
vdW, van der Waals.
*
During the peptide insertion stage, the lipid phosphorus atoms were position-restrained in the xy plane.