A local instantaneous surface method for extracting membrane elastic moduli from simulation: Comparison with other strategies
A local instantaneous surface method for extracting membrane elastic moduli from simulation: Comparison with other strategies
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DOI：
10.1016/j.chemphys.2018.03.004
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发表时间：
2018-10-25
期刊：
影响因子：
2.3
通讯作者：
Harries, Daniel
中科院分区：
文献类型：
--
作者：
Allolio, Christoph;Haluts, Amir;Harries, Daniel
过去十年的进展使得从分子动力学模拟中提取脂类集合体的弹性常数成为可能。我们总结了现有的获取膜弹性模数的策略，并阐明了基本方法的差异。我们深入分析了这些策略，包括几个重要的优势和局限性。通过解决这些局限性，我们得到了一种新的空间局部方法：真实空间瞬时面法(RESIS)。这种方法的实现是免费的，适用于具有任意界面几何形状的高度动态系统。我们演示了该方法如何为任意大小的膜提供一致的结果。此外，我们描述了各种傅立叶空间方法的替代实现，并使用这些方法来比较不同可用的方法和公布的计算数据的结果。我们特别关注倾斜系数，在这里可以观察到傅立叶方法和基于实空间的方法之间的巨大差异，包括那些使用Resis推导的方法。这些差异很可能是由于根据相应的响应函数得出的模型模数和热力学模数之间的已知差异造成的。此外，我们还重新研究了角简并问题及其对构象系综的影响。最后，范特霍夫对倾斜和弯曲模数的分析表明，这两种模式都起到了熵弹簧的作用，而热焓有利于非零倾斜，这可能预示着较低温度下凝胶相的脂链自发倾斜。(C)2018爱思唯尔B.V.保留所有权利。
Advances over the past decade have made it possible to extract elastic constants of lipid assemblies from molecular dynamics simulations. We summarize existing strategies for obtaining membrane elastic moduli and clarify the differences in the underlying approaches. We analyze these strategies in depth, including several important advantages and limitations. By addressing these limitations, we obtain a newly formulated spatially local methodology for extracting bending and tilt moduli: The Real Space Instantaneous Surface Method (ReSIS). With its freely available implementation, this method is designed for highly dynamic systems with arbitrary interface geometries. We demonstrate how the method provides consistent results for membranes of arbitrary size. In addition, we describe alternative implementations of various Fourier-space methods, and use these to compare the results from the different available methods and from published computational data. We specifically focus on the tilt modulus, where very large differences between Fourier and real-space based methods are observed, including those derived using ReSIS. These discrepancies are likely due to the known difference between model moduli and thermodynamic moduli that are derived from the corresponding response functions. In addition, we reexamine the issue of angular degeneracy and its effect on conformational ensembles. Finally, a van't Hoff analysis of the tilt and bending moduli reveals that both modes act as entropic springs and that enthalpy favors nonzero tilt, perhaps heralding the spontaneous lipid chain tilt of the gel phase at lower temperatures. (C) 2018 Elsevier B.V. All rights reserved.