Fukuda Ikuo, Nakamura Haruki
Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima, Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan.
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan.
Biophys Rev. 2023 Jan 11;14(6):1315-1340. doi: 10.1007/s12551-022-01029-2. eCollection 2022 Dec.
In molecular simulations, it is essential to properly calculate the electrostatic interactions of particles in the physical system of interest. Here we consider a method called the non-Ewald method, which does not rely on the standard Ewald method with periodic boundary conditions, but instead relies on the cutoff-based techniques. We focus on the physicochemical and mathematical conceptual aspects of the method in order to gain a deeper understanding of the simulation methodology. In particular, we take into account the reaction field (RF) method, the isotropic periodic sum (IPS) method, and the zero-multipole summation method (ZMM). These cutoff-based methods are based on different physical ideas and are completely distinguishable in their underlying concepts. The RF and IPS methods are "additive" methods that incorporate information outside the cutoff region, via dielectric medium and isotropic boundary condition, respectively. In contrast, the ZMM is a "subtraction" method that tries to remove the artificial effects, generated near the boundary, from the cutoff sphere. Nonetheless, we find physical and/or mathematical similarities between these methods. In particular, the modified RF method can be derived by the principle of neutralization utilized in the ZMM, and we also found a direct relationship between IPS and ZMM.
在分子模拟中,正确计算感兴趣的物理系统中粒子的静电相互作用至关重要。在此,我们考虑一种称为非埃瓦尔德方法的方法,该方法不依赖于具有周期性边界条件的标准埃瓦尔德方法,而是依赖于基于截断的技术。我们专注于该方法的物理化学和数学概念方面,以便更深入地理解模拟方法。特别是,我们考虑了反应场(RF)方法、各向同性周期求和(IPS)方法和零多极求和方法(ZMM)。这些基于截断的方法基于不同的物理思想,并且在其基本概念上完全不同。RF和IPS方法是“加法”方法,分别通过介电介质和各向同性边界条件纳入截断区域之外的信息。相比之下,ZMM是一种“减法”方法,试图从截断球中消除在边界附近产生的人为效应。尽管如此,我们发现这些方法之间存在物理和/或数学上的相似性。特别是,改进的RF方法可以通过ZMM中使用的中和原理推导出来,并且我们还发现了IPS和ZMM之间的直接关系。