Suppr超能文献

广义 Yvon-Born-Green 理论的参考态:疏水水合的粗粒模型的应用。

Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration.

机构信息

Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

出版信息

J Chem Phys. 2010 Sep 28;133(12):124107. doi: 10.1063/1.3481574.

Abstract

Coarse-grained (CG) models provide a computationally efficient means for investigating phenomena that remain beyond the scope of atomically detailed models. Although CG models are often parametrized to reproduce the results of atomistic simulations, it is highly desirable to determine accurate CG models from experimental data. Recently, we have introduced a generalized Yvon-Born-Green (g-YBG) theory for directly (i.e., noniteratively) determining variationally optimized CG potentials from structural correlation functions. In principle, these correlation functions can be determined from experiment. In the present work, we introduce a reference state potential into the g-YBG framework. The reference state defines a fixed contribution to the CG potential. The remaining terms in the potential are then determined, such that the combined potential provides an optimal approximation to the many-body potential of mean force. By specifying a fixed contribution to the potential, the reference state significantly reduces the computational complexity and structural information necessary for determining the remaining potentials. We also validate the quantitative accuracy of the proposed method and numerically demonstrate that the reference state provides a convenient framework for transferring CG potentials from neat liquids to more complex systems. The resulting CG model provides a surprisingly accurate description of the two- and three-particle solvation structures of a hydrophobic solute in methanol. This work represents a significant step in developing the g-YBG theory as a useful computational framework for determining accurate CG models from limited experimental data.

摘要

粗粒化 (CG) 模型为研究原子细节模型无法涵盖的现象提供了一种计算效率高的方法。虽然 CG 模型通常是通过参数化来重现原子模拟的结果,但从实验数据中确定准确的 CG 模型是非常可取的。最近,我们引入了一种广义 Yvon-Born-Green (g-YBG) 理论,用于直接(即非迭代)从结构相关函数确定变分优化的 CG 势。原则上,这些相关函数可以从实验中确定。在本工作中,我们将参考状态势引入 g-YBG 框架中。参考状态定义了 CG 势的固定贡献。然后确定势的其余项,使得组合势提供对平均力多体势的最佳逼近。通过指定势的固定贡献,参考状态大大降低了确定剩余势所需的计算复杂性和结构信息。我们还验证了所提出方法的定量准确性,并数值证明了参考状态为将 CG 势从纯液体转移到更复杂系统提供了一个方便的框架。所得到的 CG 模型对疏水溶质在甲醇中的二聚体和三聚体溶剂化结构提供了惊人准确的描述。这项工作代表了将 g-YBG 理论发展为从有限的实验数据中确定准确 CG 模型的有用计算框架的重要一步。

相似文献

2
Investigation of coarse-grained mappings via an iterative generalized Yvon-Born-Green method.
J Phys Chem B. 2014 Jul 17;118(28):8295-312. doi: 10.1021/jp501694z. Epub 2014 Apr 16.
4
The role of many-body correlations in determining potentials for coarse-grained models of equilibrium structure.
J Phys Chem B. 2012 Jul 26;116(29):8621-35. doi: 10.1021/jp3002004. Epub 2012 Jun 1.
5
BOCS: Bottom-up Open-source Coarse-graining Software.
J Phys Chem B. 2018 Apr 5;122(13):3363-3377. doi: 10.1021/acs.jpcb.7b09993. Epub 2018 Jan 12.
8
Bottom-Up Coarse-Graining of Peptide Ensembles and Helix-Coil Transitions.
J Chem Theory Comput. 2015 Mar 10;11(3):1278-91. doi: 10.1021/ct5009922. Epub 2015 Feb 25.
9
Multiscale coarse graining of liquid-state systems.
J Chem Phys. 2005 Oct 1;123(13):134105. doi: 10.1063/1.2038787.
10
Multiscale coarse-graining and structural correlations: connections to liquid-state theory.
J Phys Chem B. 2007 Apr 26;111(16):4116-27. doi: 10.1021/jp068549t. Epub 2007 Mar 30.

引用本文的文献

2
Bottom-up Coarse-Graining: Principles and Perspectives.
J Chem Theory Comput. 2022 Oct 11;18(10):5759-5791. doi: 10.1021/acs.jctc.2c00643. Epub 2022 Sep 7.
5
A Review of Multiscale Computational Methods in Polymeric Materials.
Polymers (Basel). 2017 Jan 9;9(1):16. doi: 10.3390/polym9010016.
6
Recovering physical potentials from a model protein databank.
Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):19867-72. doi: 10.1073/pnas.1006428107. Epub 2010 Nov 1.

本文引用的文献

1
The MARTINI Coarse-Grained Force Field: Extension to Proteins.
J Chem Theory Comput. 2008 May;4(5):819-34. doi: 10.1021/ct700324x.
2
Recovering physical potentials from a model protein databank.
Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):19867-72. doi: 10.1073/pnas.1006428107. Epub 2010 Nov 1.
4
The multiscale coarse-graining method. V. Isothermal-isobaric ensemble.
J Chem Phys. 2010 Apr 28;132(16):164106. doi: 10.1063/1.3394862.
5
Coarse-grained potential models for phenyl-based molecules: II. Application to fullerenes.
J Phys Chem B. 2010 May 20;114(19):6394-400. doi: 10.1021/jp9117375.
7
Generalized Yvon-Born-Green theory for molecular systems.
Phys Rev Lett. 2009 Nov 6;103(19):198104. doi: 10.1103/PhysRevLett.103.198104.
8
A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids.
J Chem Theory Comput. 2009 Aug 11;5(8):2115-2124. doi: 10.1021/ct800441u.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验