Developing initial conditions for simulations of asymmetric membranes: a practical recommendation

Abstract

It has been proposed that the surface tension difference between leaflets (or differential stress) in asymmetric bilayers is generally non-vanishing. This implies that there is no unique approach to generate initial conditions for simulations of asymmetric bilayers in the absence of experimentally derived constraints. Current generation methods include individual area per lipid (APL)-based, leaflet surface area (SA) matching, and zero leaflet tension-based (0-DS). Here, we propose a bilayer-based approach that aims for achieving partial chemical equilibrium by inter-leaflet switching of selected lipids via P21 periodic boundary conditions.