Figure 5.

Converting a continuum patch to a CG simulation. (A) Scheme demonstrating how a 30× 30 nm² continuum patch is converted into a CG simulation using the Createsims module. (B, C) Inner leaflet lipid densities from the continuum simulation, a single CG lipid placement, and an average of 1000 CG lipid placements shown for a patch with two RAS-RBDCRD and one RAS-only (B) and one RAS-only and one RAS-RBDCRD (C). Note that continuum macro model densities are in lipids per μm² while the CG setup are counts and averaged counts per cell. (D) Fraction of inner leaflet PIP2 (left) or POPC (right) lipids that are within 5 nm of the RAS farnesyl lipid anchor. The darker color lines show simulations started with the MuMMI continuum-to-CG build routine, while the lighter color lines are the same continuum patches build with a modified routine that randomizes the location of the lipids in each leaflet. Simulations from eight continuum patches are shown, all with one protein, four with RAS-only, and four with RAS-RBDCRD, and starting from different protein conformational states.