Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method

被引：34

作者：

Pruitt, Spencer R. ^{[1
]}

Nakata, Hiroya ^{[2
]}

Nagata, Takeshi ^{[3
]}

Mayes, Maricris ^{[4
]}

Alexeev, Yuri ^{[1
]}

Fletcher, Graham ^{[1
]}

Fedorov, Dmitri G. ^{[3
]}

Kitaura, Kazuo ^{[5
]}

Gordon, Mark S. ^{[6
,7
]}

机构：

[1] Argonne Natl Lab, Argonne Leadership Comp Facil, 9700 S Cass Ave, Lemont, IL 60439 USA

[2] Kyocera Corp, R&D Ctr Kagoshima, Dept Fundamental Technol Res, 1-4 Kokubu Yamashita Cho, Kirishima, Kagoshima 8994312, Japan

[3] Natl Inst Adv Ind Sci & Technol, Nanosyst Res Inst, 1-1-1 Umenzono, Tsukuba, Ibaraki 3058568, Japan

[4] Univ Massachusetts, Dept Chem & Biochem, 285 Old Westport Rd, Dartmouth, MA 02747 USA

[5] Kobe Univ, Grad Sch Syst Informat, Nada Ku, 1-1 Rokkodai Cho, Kobe, Hyogo 6578501, Japan

[6] Iowa State Univ, Dept Chem, 201 Spedding Hall, Ames, IA 50011 USA

[7] Iowa State Univ, Ames Lab, 201 Spedding Hall, Ames, IA 50011 USA

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2016年 / 12卷 / 04期

基金：

美国国家科学基金会;

关键词：

TRANSFERABLE INTERACTION MODELS; OPEN-SHELL SYSTEMS; AB-INITIO; FMO-MD; HARTREE-FOCK; ACCURATE CALCULATIONS; ANALYTIC GRADIENT; BASIS-SET; ENERGY; CLUSTERS;

D O I：

10.1021/acs.jctc.5b01208

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted second-order Moller-Plesset perturbation theory, as well as for both restricted and unrestricted Hartree-Fock and density functional theory. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262 144 CPU cores are also discussed.

引用

页码：1423 / 1435

页数：13

共 50 条

[41] Application of resolution of identity approximation of second-order Møller–Plesset perturbation theory to three-body fragment molecular orbital method
Michio Katouda
Theoretical Chemistry Accounts, 2011, 130 : 449 - 453
[42] Application of resolution of identity approximation of second-order Moller-Plesset perturbation theory to three-body fragment molecular orbital method
Katouda, Michio
THEORETICAL CHEMISTRY ACCOUNTS, 2011, 130 (2-3) : 449 - 453
[43] Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods
Steinmann, Casper
Fedorov, Dmitri G.
Jensen, Jan H.
JOURNAL OF PHYSICAL CHEMISTRY A, 2010, 114 (33): : 8705 - 8712
[44] Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method
Fujita, Takatoshi
Watanabe, Hirofumi
Tanaka, Shigenori
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 2009, 78 (10)
[45] Three-body nonadditive interactions in water
Szalewicz, Krzysztof
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2013, 246
[46] Definition of molecular orbitals in fragment molecular orbital method
Inadomi, Y
Nakano, T
Kitaura, K
Nagashima, U
CHEMICAL PHYSICS LETTERS, 2002, 364 (1-2) : 139 - 143
[47] Effects of three-body diamond abrasive polishing on silicon carbide surface based on molecular dynamics simulations
Bian, Zhetian
Gao, Tinghong
Gao, Yue
Wang, Bei
Liu, Yutao
Xie, Quan
Chen, Qian
Xiao, Qingquan
Liang, Yongchao
DIAMOND AND RELATED MATERIALS, 2022, 129
[48] Symplectic reduction, geometric phase, and internal dynamics in three-body molecular dynamics
Physics Letters. Section A: General, Atomic and Solid State Physics, 234 (04):
[49] Symplectic reduction, geometric phase, and internal dynamics in three-body molecular dynamics
Lin, FJ
PHYSICS LETTERS A, 1997, 234 (04) : 291 - 300
[50] Floating orbital molecular dynamics simulations
Perlt, Eva
Bruessel, Marc
Kirchner, Barbara
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2014, 16 (15) : 6997 - 7005

← 1 2 3 4 5 →