Molecular dynamics of water transport through membranes: Water from solvent to solute

An application of Molecular Dynamics computer simulation (MD) to the process of transport of water through a lipid bilayer membrane is described. The permeation process is far too slow to be modeled by straightforward MD. In stead the inverse of the permeability coefficient is expressed as an integral over a local permeation resistance, which itself is inversely proportional both to the local density and the local diffusion constant. These quantities are recovered from MD simulations. The local density relates to a free energy profile, which is constructed by a combination of density determination, of the mean force on constrained molecules, and particle insertion. Thus a slow process can be accurately predicted from relatively short MD simulations.