Large scale FMO-MP2 calculations on a massively parallel-vector computer

被引：103

作者：

Mochizuki, Yuji ^{[1
,2
,3
]}

Yamashita, Katsumi ^{[4
]}

Murase, Tadashi ^{[4
]}

Nakano, Tatsuya ^{[2
,3
,5
]}

Fukuzawa, Kaori ^{[6
]}

Takematsu, Kazutomo ^{[7
]}

Watanabe, Hirofumi ^{[2
,8
]}

Tanaka, Shigenori ^{[2
,7
,8
]}

机构：

[1] Rikkyo Univ, Fac Sci, Dept Chem, Toshima Ku, Tokyo 1718501, Japan

[2] Japan Sci & Technol Agcy, CREST Project, Kawaguchi, Saitama 3320012, Japan

[3] Univ Tokyo, Inst Ind Sci, Meguro Ku, Tokyo 1538505, Japan

[4] NEC Soft Ltd, Valway Technol Ctr, Koto Ku, Tokyo 1368627, Japan

[5] Natl Inst Hlth Sci, Div Med Safety Sci, Setagaya Ku, Tokyo 1588501, Japan

[6] Mizuho Informat & Res Inst Inc, Chiyoda Ku, Tokyo 1018442, Japan

[7] Kobe Univ, Fac Human Dev, Dept Human Environm Sci, Nada Ku, Kobe, Hyogo 6578501, Japan

[8] Kobe Univ, Grad Sch Human Dev & Environm, Nada Ku, Kobe, Hyogo 6578501, Japan

来源：

CHEMICAL PHYSICS LETTERS | 2008年 / 457卷 / 4-6期

基金：

日本科学技术振兴机构;

关键词：

D O I：

10.1016/j.cplett.2008.03.090

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 fragment molecular orbital (FMO) calculations have been successfully applied to a variety of realistic biochemical problems, by using our original ABINIT-MP program. In these applications, the inclusion of electron correlation through the second-order Moller-Plesset perturbation (MP2) was demonstrated to be essential to obtain qualitatively correct descriptions. Recently, the FMO calculations in ABINIT-MP were tuned for a massively parallel-vector processing. A series of FMO-MP2/6-31G calculations were performed on the Earth Simulator by which up to 4096 vector processors are available. The largest FMO-MP2 computation was carried out for an influenza hemagglutinin antigen-antibody system consisting of 921 residues, which was completed within one hour with 4096 processors. (c) 2008 Elsevier B. V. All rights reserved.

引用

页码：396 / 403

页数：8

共 37 条

[1] PRINCIPLES FOR A DIRECT SCF APPROACH TO LCAO-MO ABINITIO CALCULATIONS [J].

ALMLOF, J ;

FAEGRI, K ;

KORSELL, K .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1982, 3 (03) :385-399

[2] VISCANA: Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening [J].

Amari, S ;

Aizawa, M ;

Zhang, JW ;

Fukuzawa, K ;

Mochizuki, Y ;

Iwasawa, Y ;

Nakata, K ;

Chuman, H ;

Nakano, T .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2006, 46 (01) :221-230

[3]

AMARI S, UNPUB J CHEM INF MOD

[4]

[Anonymous], 1996, Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory

[5] Second order Moller-Plesset perturbation theory based upon the fragment molecular orbital method [J].

Fedorov, DG ;

Kitaura, K .

JOURNAL OF CHEMICAL PHYSICS, 2004, 121 (06) :2483-2490

[6] A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO) [J].

Fedorov, DG ;

Olson, RM ;

Kitaura, K ;

Gordon, MS ;

Koseki, S .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2004, 25 (06) :872-880

[7] Extending the power of quantum chemistry to large systems with the fragment molecular orbital method [J].

Fedorov, Dmitri G. ;

Kitaura, Kazuo .

JOURNAL OF PHYSICAL CHEMISTRY A, 2007, 111 (30) :6904-6914

[8] Pair interaction energy decomposition analysis [J].

Fedorov, Dmitri G. ;

Kitaura, Kazuo .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2007, 28 (01) :222-237

[9]

Fleury D, 2000, PROTEINS, V40, P572

[10] Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method (vol 110, pg 24276, 2006) [J].

Fukuzawa, Kaori ;

Mochizuki, Yuji ;

Tanaka, Shigenori ;

Kitaura, Kazuo ;

Nakano, Tatsuya .

JOURNAL OF PHYSICAL CHEMISTRY B, 2006, 110 (47) :24276-24276

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