Sevink G J A, Fraaije J G E M
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
Soft Matter. 2014 Jul 28;10(28):5129-46. doi: 10.1039/c4sm00297k.
We rigorously derived effective potentials for solvent-free DPD simulation of lipid bilayers. The derivation relies on an earlier developed hybrid particle/field method and is based on the idea that the solvent is always in local equilibrium on a coarse-grained time scale, given the instantaneous templates set by the self-assembly structure. By relating the parameters in the effective implicit-solvent potentials directly to the lipid-solvent interactions and membrane properties for the explicit solvent DPD model, we constitute an efficient and general procedure for reformulating any DPD membrane model in an implicit-solvent form. Here, we determined these membrane properties for two existing DPD models, via an analysis of membrane fluctuation spectra. Equivalent single-processor implicit- and explicit-solvent calculations show the trade-mark of implicit solvent simulation: a 20-fold reduction of the total simulation time for a system containing 92% solvent. This increased efficiency enabled us to realistically simulate the spontaneous formation of a ∼20 nm diameter vesicle on a single processor overnight. We believe that this work will contribute to an enhanced computational study of large vesicles and thus a better understanding of experimental liposome dynamics.
我们严格推导了用于脂质双层无溶剂耗散粒子动力学（DPD）模拟的有效势。该推导依赖于早期开发的混合粒子/场方法，其基于这样一种观点：鉴于由自组装结构设定的瞬时模板，溶剂在粗粒度时间尺度上始终处于局部平衡状态。通过将有效隐式溶剂势中的参数直接与显式溶剂DPD模型中的脂质 - 溶剂相互作用和膜性质相关联，我们构建了一种高效且通用的程序，用于将任何DPD膜模型重新表述为隐式溶剂形式。在此，我们通过分析膜波动光谱确定了两个现有DPD模型的这些膜性质。等效的单处理器隐式和显式溶剂计算显示了隐式溶剂模拟的特点：对于一个含有92%溶剂的系统，总模拟时间减少了20倍。这种提高的效率使我们能够在单处理器上通宵逼真地模拟直径约20 nm的囊泡的自发形成。我们相信这项工作将有助于加强对大囊泡的计算研究，从而更好地理解实验性脂质体动力学。
