Figure 3

Box size effect on lipid diffusion. Diffusion coefficient for POPC lipid extracted from 1.2–1.5 μs simulation of a planar membrane in different boxes of size \({L}_{x}={L}_{y}=L\) and \({L}_{z}=240\) Å (cyan circles). For each system the last part of the trajectory (800 ns) was divided into independent blocks of 100 ns. The diffusion coefficient D was obtained for each block from a linear fit of the MSD using a time window of 20-40 ns for the fit. The averages and standard errors were computed over the independent blocks. The continuous line represents a fit of the data performed according to the theory proposed in ref.⁵⁵. The fit was done using the bulk fluid viscosity set in LBMD, and the characteristic size of a lipid molecule \(R=0.5\) nm. We also assumed the value of the interleaflet friction to be equal to what was obtained for the same CG model by Lyman et al.⁴⁴ (\(b=2.87\cdot 1{0}^{5}\) P cm⁻¹). The membrane-surface viscosity we derived from the fit is \({\eta }_{m}=5.09\cdot 1{0}^{-8}\) P cm. In the figure we also report the data from ref.⁴⁴ based on STRD simulations of the POPC lipid planar membrane with inter-membrane separation of \(200\) Å (black circles). Inset: Log-linear plot of the diffusion coefficients.