Figure 2.

Different periodic boundary conditions (PBCs) used in bilayer simulations. (A) Standard P1 PBCs commonly used in MD simulations of lipid bilayers. When a lipid exits the unit box from one side it reappears on the opposite side in the same leaflet, prohibiting free exchange of lipids between leaflets. (B) Modified P2₁ PBCs where the primary simulation cell is rotated and translated to allow free passage of lipids between leaflets. When a lipid exits the unit box from one side it reappears in the opposite leaflet via an orthogonal face allowing sampling of both leaflet environments. Schematics on the left in (A,B) were adapted with permission from Ref. [63] (2002, Elsevier) and illustrate the lipid headgroups on the two leaflets.