Figure 2.

Progress of the Simulations

(A) Progress of the 0.3 μs vesicle equilibration simulation, tracking the outer diameter (black line, left-hand axis) and sphericity (cyan, right-hand axis) as functions of time. The outer diameter is calculated as twice the average radius of all hydroxylated sphingomyelin headgroup phosphate (PPCH PO₄) particles from the lipid centroid of the system. Seven time points are marked in 50 ns intervals. The inset images of the equilibrating vesicle (at time points 1, 3, and 6) have lipids shown in gray and the central core in green.

(B and C) Progress of the virion model simulations was also monitored by tracking sphericity (B) and outer diameter (C). The vesicle (black, temperature adjusted from 323 to 295 K at 0.3 μs), the virion (295 K, dark green; 323 K, light green), the protein-restrained virion (red), and the Forssman glycolipid inclusive virion (295 K, dark blue; 323 K, light blue) are shown. See also Figures S4 and S5.