Figure 3. Removing lipid molecules that clash.

The user can optionally instruct LipidWrapper to delete lipid molecules with steric clashes. A number of strategies are used to reduce the number of pairwise distance comparisons that must be performed. For example, A) only lipid molecules that are near the edges of their respective triangles (shown in blue) are evaluated for clashes. B) Clashing lipids are removed one by one, starting with the lipid that clashes with the greatest number of its neighbors, until all steric clashes have been resolved. Holes in the bilayer invariably result.