Accurate and Efficient Estimation of Lennard-Jones Interactions for Coarse-Grained Particles via a Potential Matching Method

doi:10.1021/acs.jctc.2c00513

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	Accurate and Efficient Estimation of Lennard-Jones Interactions for Coarse-Grained Particles via a Potential Matching Method
	Zhang, Yuwei 1; Wang, Yunchu 2; Xia, Fei 3; Cao, Zexing 4,5; Xu, Xin 1
	2022-08-09
发表期刊	JOURNAL OF CHEMICAL THEORY AND COMPUTATION
ISSN	1549-9618
卷号	18 期号:8 页码:4879-4890
摘要	commonly used to describe the nonbonded interactions in bulk coarse-grained (CG) models, which contribute significantly to the stabilization of a local binding configuration or a self-assembly system. In many cases, systematic development of the LJ interaction parameters in a CG model requires a comprehensive sampling of the objective molecules at the all-atom (AA) level, which is therefore extremely time-consuming for large systems. Inspired by the concept of electrostatic potential (ESP), we define the LJ static potential (LJSP), by which the embedding potential energy surface can be constructed analytically. A semianalytic approach, namely, the LJSP matching method, is developed here to derive the CG parameters by minimizing the LJSP difference between the AA and the CG models, which provides a universal way to derive the CG LJ parameters from the AA models without doing presampling. The LJSP matching method is successful not only in deriving the LJ interaction energy landscape in the CG models for proteins, lipids, and DNA but also in reproducing the critical properties such as intermediate structures and enthalpy contributions as exemplified in simulating the self-assembly process of the dipalmitoylphosphatidylcholine (DPPC) lipids.
DOI	10.1021/acs.jctc.2c00513
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[21991130] ; National Natural Science Foundation of China[21773065] ; National Natural Science Foundation of China[21933009] ; Chinese Postdoctoral Science Foundation[2021M700808]
WOS研究方向	Chemistry ; Physics
WOS类目	Chemistry, Physical ; Physics, Atomic, Molecular & Chemical
WOS记录号	WOS:000830489800001
出版者	AMER CHEMICAL SOC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/61134
专题	中国科学院数学与系统科学研究院
通讯作者	Xia, Fei; Cao, Zexing; Xu, Xin
作者单位	1.Fudan Univ, Collaborat Innovat Ctr Chem Energy Mat, Dept Chem, Shanghai Key Lab Mol Catalysis & Innovat Mat,MOE K, Shanghai 200433, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Inst Computat Math & Sci Engn Comp, LSEC, Beijing 100190, Peoples R China 3.East China Normal Univ, NYU ECNU Ctr Computat Chem NYU Shanghai, Sch Chem & Mol Engn, Shanghai 200062, Peoples R China 4.Xiamen Univ, Coll Chem & Chem Engn, State Key Lab Phys Chem Solid Surfaces, Xiamen 361005, Peoples R China 5.Xiamen Univ, Coll Chem & Chem Engn, Fujian Prov Key Lab Theoret & Computat Chem, Xiamen 361005, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Yuwei,Wang, Yunchu,Xia, Fei,et al. Accurate and Efficient Estimation of Lennard-Jones Interactions for Coarse-Grained Particles via a Potential Matching Method[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2022,18(8):4879-4890.
APA	Zhang, Yuwei,Wang, Yunchu,Xia, Fei,Cao, Zexing,&Xu, Xin.(2022).Accurate and Efficient Estimation of Lennard-Jones Interactions for Coarse-Grained Particles via a Potential Matching Method.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,18(8),4879-4890.
MLA	Zhang, Yuwei,et al."Accurate and Efficient Estimation of Lennard-Jones Interactions for Coarse-Grained Particles via a Potential Matching Method".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 18.8(2022):4879-4890.