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通过分布式多极展开对静电势进行粗粒化。

Coarse-graining the electrostatic potential via distributed multipole expansions.

作者信息

Gramada Apostol, Bourne Philip E

机构信息

University of California San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.

出版信息

Comput Phys Commun. 2011 Jul 1;182(7):1455-1462. doi: 10.1016/j.cpc.2011.03.014.

Abstract

Multipole expansions offer a natural path to coarse-graining the electrostatic potential. However, the validity of the expansion is restricted to regions outside a spherical enclosure of the distribution of charge and, therefore, not suitable for most applications that demand accurate representation at arbitrary positions around the molecule. We propose and demonstrate a distributed multipole expansion approach that resolves this limitation. We also provide a practical algorithm for the computational implementation of this approach. The method allows the partitioning of the charge distribution into subsystems so that the multipole expansion of each component of the partition, and therefore of their superposition, is valid outside an enclosing surface of the molecule of arbitrary shape. The complexity of the resulting coarse-grained model of electrostatic potential is dictated by the area of the molecular surface and therefore, for a typical three-dimensional molecule, it scale as N(2/3) with N, the number of charges in the system. This makes the method especially useful for coarse-grained studies of biological systems consisting of many large macromolecules provided that the configuration of the individual molecules can be approximated as fixed.

摘要

多极展开为粗粒化静电势提供了一条自然途径。然而,展开的有效性仅限于电荷分布的球形包络之外的区域,因此,不适用于大多数需要在分子周围任意位置进行精确表示的应用。我们提出并证明了一种分布式多极展开方法,该方法解决了这一限制。我们还为该方法的计算实现提供了一种实用算法。该方法允许将电荷分布划分为子系统,使得分区的每个组件的多极展开,以及它们的叠加,在任意形状分子的封闭表面之外都是有效的。由此产生的静电势粗粒化模型的复杂性由分子表面的面积决定,因此,对于典型的三维分子,它与系统中的电荷数N成N(2/3)比例。这使得该方法对于由许多大型大分子组成的生物系统的粗粒化研究特别有用,前提是单个分子的构型可以近似为固定的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bd0/3090642/a0991c015745/nihms285874f1.jpg

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