Dresden 2017 – scientific programme

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BP: Fachverband Biologische Physik

BP 1: Computational Biophysics (Joint Session BP/DY)

BP 1.3: Talk

Monday, March 20, 2017, 10:15–10:30, ZEU 250

Correction of Finite-Size Effects on Diffusion in Lipid Membrane Simulations — •Martin Vögele and Gerhard Hummer — Max-Planck-Institut für Biophysik, Frankfurt am Main

Calculating diffusion coefficients from the mean squared displacement is a common task in evaluating molecular dynamics simulations. However, periodic boundary conditions introduce artifacts caused by the self-interaction with the periodic image. In cubic simulation boxes, the diffusion coefficient converges for large sizes. However, this is not the case if the system size is increased asymmetrically. [1]

We specifically test the effect of box geometry on the diffusion in lipid membranes which are usually simulated in very flat periodic boxes. There we find a logarithmic (and therefore unbounded) increase with growing box width. We discuss consequences of the apparent inability to determine a well-defined lipid diffusion coefficient from simulation and present possible methods to rationalize difficulties in comparing simulation results to each other and to experiment.

[1] M. Vögele and G. Hummer, J. Phys. Chem. B, 2016, 120 (33)