We provide compelling evidence that different treatments of electrostatic interactions in molecular dynamics simulations may dramatically affect dynamic properties of lipid bilayers. To this end, we consider a fully hydrated pure dipalmitoylphosphatidylcholine bilayer through 50-ns molecular dynamics simulations and study various dynamic properties of individual lipids in a membrane, including the velocity autocorrelation function, the lateral and rotational diffusion coefficients, and the autocorrelation function for the area per molecule. We compare the results based on the Particle-Mesh Ewald (PME) and reaction field (RF) techniques with those obtained by an approach where the electrostatic interactions are truncated at r cut = 1.8, 2.0, and 2.5 nm. We find that the overall performance of PME is very good; its results are consistent with the expected behavior. The RF method performs rather well, too, despite certain inherent problems and the fact that its results differ from those obtained by PME. Nevertheless, the largest differences are found for the truncation methods, for which all examined truncation methods lead to results distinctly different from those obtained by PME. The lateral diffusion coefficients obtained by PME and truncation at 1.8 nm, for example, differ by a factor of 10, while the PME results are consistent with experimental values. The observed deviations can be interpreted in terms of artificial ordering due to truncation and highlight the important role of electrostatic interactions in the dynamics of systems composed of lipids and other biologically relevant molecules such as proteins and DNA.

We present a promising coarse-graining strategy for linking micro-and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD) simulations, which are then used in coarse-grained dissipative particle dynamics (DPD) simulations. Here, the effective potentials were obtained by applying the Inverse Monte Carlo method [Lyubartsev & Laaksonen, Phys. Rev. E. 52, 3730 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. In our first application of the method, the effective potentials were used in DPD simulations of aqueous NaCl solutions. With the same computational effort we were able to simulate systems of one order of magnitude larger as compared to the MD simulations. The results from the MD and DPD simulations are found to be in excellent agreement.

Róg, T. (2006). Dynamics of water at membrane surfaces : effect of headgroup structure. Biointerphases, 1(3), 98-105. DOI: 10.1116/1.2354573 General rightsCopyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Atomistic molecular dynamics simulations of fully hydrated 1-palmitoyl-2-oleoylphosphatidylcholine ͑POPC͒, 1-palmitoyl-2-oleoyl-phosphatidylethanolamine ͑POPE͒, and 1-palmitoyl-2-oleoyl-phosphatidylglycerol ͑POPG͒ bilayers in the liquid-crystalline state were carried out to investigate the effect of different lipid headgroups on the dynamics of water at the bilayer surface in short 80 ps time scales. Results obtained in these studies show that the hydrogen bonding amine group of POPE and the glycerol group of POPG slow water motion more than the equivalent choline group of POPC. Therefore, it is surprising that the effect of a POPC bilayer surface on water dynamics is similar to that of POPE and POPG bilayers. That result is due to a much higher number of water molecules interacting with the choline group of POPC than hydrogen-bonded molecules interacting with amine or glycerol groups of POPE and POPG.

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