BOCS: Bottom-up Open-source Coarse-graining Software
BOCS: Bottom-up Open-source Coarse-graining Software
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DOI：
10.1021/acs.jpcb.7b09993
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发表时间：
2018-04-05
影响因子：
3.3
通讯作者：
Noid, W. G.
中科院分区：
文献类型：
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作者：
Dunn, Nicholas J. H.;Lebold, Kathryn M.;Noid, W. G.
我们将 BOCS 工具包作为一套开源软件工具提供，用于参数化自下而上的粗粒度 (CG) 模型，以准确再现高分辨率模型的结构和热力学特性。 BOCS 工具包通过提供多尺度粗粒度 (MS-CG) 力匹配方法和广义 Yvon-Born-Green (g-YBG) 方法的稳健实现来补充可用的软件包。 g-YBG 方法允许人们根据结构相关性来分析和计算 MS-CG 电位。此外，BOCS 工具包还实现了扩展的系综框架，用于优化自下而上势的可传递性，以及自洽压力匹配方法，用于精确建模均质系统的压力状态方程。我们通过对 CG 模型的可转移势进行参数化来说明这些功能，这些模型可以准确地模拟液体烷烃系统的结构、压力和可压缩性，并通过量化多体相关性在确定液体甲醇单点 CG 模型的计算对势方面的作用。
We present the BOCS toolkit as a suite of open source software tools for parametrizing bottom-up coarse-grained (CG) models to accurately reproduce structural and thermodynamic properties of high-resolution models. The BOCS toolkit complements available software packages by providing robust implementations of both the multiscale coarse-graining (MS-CG) force-matching method and also the generalized-Yvon-Born-Green (g-YBG) method. The g-YBG method allows one to analyze and to calculate MS-CG potentials in terms of structural correlations. Additionally, the BOCS toolkit implements an extended ensemble framework for optimizing the transferability of bottom-up potentials, as well as a self-consistent pressure-matching method for accurately modeling the pressure equation of state for homogeneous systems. We illustrate these capabilities by parametrizing transferable potentials for CG models that accurately model the structure, pressure, and compressibility of liquid alkane systems and by quantifying the role of many-body correlations in determining the calculated pair potential for a one-site CG model of liquid methanol.