Atomistic simulations of biologically realistic transmembrane potential gradients

We present all-atom molecular dynamics simulations of biologically realistic transmembrane potential gradients across a DMPC bilayer. These simulations are the first to model this gradient in all-atom detail, with the field generated solely by explicit ion dynamics. Unlike traditional bilayer simulations that have one bilayer per unit cell, we simulate a 170 mV potential gradient by using a unit cell consisting of three salt-water baths separated by two bilayers, with full three-dimensional periodicity. The study shows that current computational resources are powerful enough to generate a truly electrified interface, as we show the predicted effect of the field on the overall charge distribution. Additionally, starting from Poisson's equation, we show a new derivation of the double integral equation for calculating the potential profile in systems with this type of periodicity. (C) 2004 American Institute of Physics.