Large scale MP2 calculations with fragment molecular orbital scheme

被引：175

作者：

Mochizuki, Y

Koikegami, S

Nakano, T

Amari, S

Kitaura, K

机构：

[1] Univ Tokyo, Ctr Collaborat Res, Inst Ind Sci, Meguro Ku, Tokyo 1538904, Japan

[2] Natl Inst Hlth Sci, Div Safety Informat Drug Food & Chem, Setagaya Ku, Tokyo 1588501, Japan

[3] Natl Inst Adv Ind Sci & Technol, Res Inst Computat Sci, Tsukuba, Ibaraki 3058568, Japan

来源：

CHEMICAL PHYSICS LETTERS | 2004年 / 396卷 / 4-6期

关键词：

D O I：

10.1016/j.cplett.2004.08.082

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：

We have recently developed a parallelized integral-direct algorithm for the second-order Moller-Plesset perturbation theory (MP2) and implemented it into the ABINIT-MP program of the fragment molecular orbital (FMO) scheme. A flexible parallelization is possible by combining the fragment indices (upper level) and the two-electron integral indices (lower level) on distributed computational resources, leading to an enhancement of in-core processings. In this Letter, we carry out a series of benchmark FMO-MP2 calculations of realistic proteins consisting of the tens of thousands of basis functions. The performance is shown to be high, indicating that the ABINIT-MP program is easily applicable to the realistic systems. (C) 2004 Elsevier B.V. All rights reserved.

引用

页码：473 / 479

页数：7

共 31 条

[1] THE COUPLED PAIR FUNCTIONAL (CPF) - A SIZE CONSISTENT MODIFICATION OF THE CI(SD) BASED ON AN ENERGY FUNCTIONAL
AHLRICHS, R
SCHARF, P
EHRHARDT, C
[J]. JOURNAL OF CHEMICAL PHYSICS, 1985, 82 (02) : 890 - 898
[2] Molecular recognition of cyclic urea HIV-1 protease inhibitors
Ala, PJ
DeLoskey, RJ
Huston, EE
Jadhav, PK
Lam, PYS
Eyermann, CJ
Hodge, CN
Schadt, MC
Lewandowski, FA
Weber, PC
McCabe, DD
Duke, JL
Chang, CH
[J]. JOURNAL OF BIOLOGICAL CHEMISTRY, 1998, 273 (20) : 12325 - 12331
[3] AMARI S, UNPUB
[4] BOHN HJ, 2000, VIRTUAL SCREENING BI
[5] REFINEMENT OF AN ENZYME COMPLEX WITH INHIBITOR BOUND AT PARTIAL OCCUPANCY - HEN EGG-WHITE LYSOZYME AND TRI-N-ACETYLCHITOTRIOSE AT 1-BULLET-75-ANGSTROM RESOLUTION
CHEETHAM, JC
ARTYMIUK, PJ
PHILLIPS, DC
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1992, 224 (03) : 613 - 628
[6] Dykstra CE, 2000, INT J QUANTUM CHEM, V78, P226, DOI 10.1002/(SICI)1097-461X(2000)78:4<226::AID-QUA4>3.0.CO
[7] 2-N
[8] On the accuracy of the 3-body fragment molecular orbital method (FMO) applied to density functional theory
Fedorov, DG
Kitaura, K
[J]. CHEMICAL PHYSICS LETTERS, 2004, 389 (1-3) : 129 - 134
[9] Second order Moller-Plesset perturbation theory based upon the fragment molecular orbital method
Fedorov, DG
Kitaura, K
[J]. JOURNAL OF CHEMICAL PHYSICS, 2004, 121 (06) : 2483 - 2490
[10] The importance of three-body terms in the fragment molecular orbital method
Fedorov, DG
Kitaura, K
[J]. JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (15) : 6832 - 6840

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