Abstract We suggest an improved version of the intermediate resolution implicit solvent model for lipids, LIME, that was previously developed for use with discontinuous molecular dynamics (DMD) simulations. LIME gets its geometrical and energy parameters between bonded and nonbonded pairs of coarse-grained (CG) sites from atomistic simulations. The improved model, LIME 2.0, uses multiple square wells rather than the single square well used in original LIME to obtain intermolecular interactions that more faithfully mimic those from atomistic simulations. The multi-state iterative Boltzmann inversion (MS-IBI) scheme is used to determine the interaction parameters. This means that a single set of interaction parameters between coarse-grained sites can be used to represent the lipid bilayers at different temperatures. The physical properties of CG DSPE lipid bilayer are calculated using CG simulations and compared to atomistic simulations results to verify the improved model. The phase transition temperature of the lipid bilayer is measured accurately and the lipid translocation phenomenon, “flip-flop” is observed through CG simulation. These results suggest that CG parameterization using multiple square-wells and the MS-IBI scheme is well suited to the study of lipid bilayers across a range of temperatures with DMD simulations.

中文翻译：

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使用多态迭代玻尔兹曼反演和不连续分子动力学模拟为 DSPE 开发粗粒度脂质模型 LIME 2.0


摘要 我们提出了脂质中间分辨率隐式溶剂模型 LIME 的改进版本，该模型之前是为不连续分子动力学 (DMD) 模拟而开发的。 LIME 从原子模拟中获取键合和非键合粗粒 (CG) 位点对之间的几何和能量参数。改进后的模型 LIME 2.0 使用多个方孔而不是原始 LIME 中使用的单方孔来获得更忠实地模拟原子模拟的分子间相互作用。多状态迭代玻尔兹曼反演（MS-IBI）方案用于确定相互作用参数。这意味着粗粒位点之间的一组相互作用参数可用于表示不同温度下的脂质双层。使用CG模拟计算CG DSPE脂质双层的物理性质，并与原子模拟结果进行比较，以验证改进的模型。精确测量脂质双层的相变温度，并通过CG模拟观察脂质易位现象“翻转”。这些结果表明，使用多个方孔的 CG 参数化和 MS-IBI 方案非常适合通过 DMD 模拟研究各种温度下的脂质双层。