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贝叶斯选择用于粗粒化液态水模型。

Bayesian selection for coarse-grained models of liquid water.

机构信息

Computational Science and Engineering Laboratory, ETH Zurich, Clausiusstrasse 33, Zurich, CH-8092, Switzerland.

Collegium Helveticum, University Zurich and ETH Zurich, Zurich, 8092, Switzerland.

出版信息

Sci Rep. 2019 Jan 14;9(1):99. doi: 10.1038/s41598-018-37471-0.

Abstract

The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG water models rely mostly on a-priori specified assumptions. How these assumptions affect the model accuracy, efficiency, and in particular transferability, has not been systematically investigated. Here we propose a data driven comparison and selection for CG water models through a Hierarchical Bayesian framework. We examine CG water models that differ in their level of coarse-graining, structure, and number of interaction sites. We find that the importance of electrostatic interactions for the physical system under consideration is a dominant criterion for the model selection. Multi-site models are favored, unless the effects of water in electrostatic screening are not relevant, in which case the single site model is preferred due to its computational savings. The charge distribution is found to play an important role in the multi-site model's accuracy while the flexibility of the bonds/angles may only slightly improve the models. Furthermore, we find significant variations in the computational cost of these models. We present a data informed rationale for the selection of CG water models and provide guidance for future water model designs.

摘要

在能够跨越生物相关时间尺度的原子模拟中,准确且计算高效的水分子表示对于研究而言是非常必要的,这催生了粗粒化(CG)建模的需求。尽管已经取得了许多进展,但 CG 水模型主要还是依赖于先验指定的假设。这些假设如何影响模型的准确性、效率,特别是可转移性,尚未得到系统的研究。在这里,我们通过分层贝叶斯框架提出了一种用于 CG 水模型的基于数据的比较和选择方法。我们研究了在粗粒化程度、结构和相互作用位点数量上有所不同的 CG 水模型。我们发现,对于所考虑的物理系统,静电相互作用的重要性是模型选择的主要标准。多站点模型是首选,除非静电屏蔽中水分子的作用不相关,在这种情况下,由于其计算节省,单站点模型更受欢迎。我们发现,在多站点模型的准确性中,电荷分布起着重要作用,而键/角度的灵活性可能只会略微提高模型的准确性。此外,我们还发现这些模型的计算成本存在显著差异。我们提出了一种基于数据的 CG 水模型选择的基本原理,并为未来的水模型设计提供了指导。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8d9/6331618/050b849e1b18/41598_2018_37471_Fig1_HTML.jpg

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