TABLE 1.
Summary of simulations
| Simulation name | System components | Peptide/lipid ratio | Box size (Å3) | Number of simulations | Simulation time (ns) |
|---|---|---|---|---|---|
| 1mac-sa | 1 M1.1, 256 DPPC (random*), 3200 waters | 1:256 | 100 × 100 × 100 | 9 | 200 or 300 |
| 16mac-bil | 16 M1.1, 256 DPPC (bilayer*), ∼5500 CG waters | 1:16 | 90 × 90 × 160 | 5 | 200 |
| 16mac-bil-1μs | 16 M1.1, 256 DPPC (bilayer*), ∼5500 CG waters | 1:16 | 90 × 90 × 160 | 3 | 1000 |
| 100mac-ves | 100 M1.1, 877 POPC (vesicle*), ∼55,000 CG waters | 1:9 | 210 × 210 × 210 | 1 | 1250 |
| 100WALP-ves | 100 WALP23, 877 POPC (vesicle*), ∼55,000 CG waters | 1.9 | 210 × 210 × 210 | 1 | 1250 |
| Control-ves | 877 POPC (vesicle*), ∼60,000 CG waters | — | 210 × 210 × 210 | 1 | 400 |
*
Three classes of simulations were performed: self-assembly (sa) simulations in which the lipid molecules were initially placed at random within the simulation box, bilayer (bil) simulations in which the lipids were initially in a (planar) lipid bilayer, and vesicle (ves) simulations in which the lipids were in a vesicle.