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
收藏
页码：473 / 479
页数：7
相关论文
共 31 条
  • [11] A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO)
    Fedorov, DG
    Olson, RM
    Kitaura, K
    Gordon, MS
    Koseki, S
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2004, 25 (06) : 872 - 880
  • [12] The Distributed Data Interface in GAMESS
    Fletcher, GD
    Schmidt, MW
    Bode, BM
    Gordon, MS
    [J]. COMPUTER PHYSICS COMMUNICATIONS, 2000, 128 (1-2) : 190 - 200
  • [13] Foresman J.B., 1996, EXPLORING CHEM ELECT
  • [14] Helgaker T., 2002, Molecular Electronic-Structure Theory
  • [15] Hu C.-H., 1998, ENCY COMPUTATIONAL C
  • [16] Definition of molecular orbitals in fragment molecular orbital method
    Inadomi, Y
    Nakano, T
    Kitaura, K
    Nagashima, U
    [J]. CHEMICAL PHYSICS LETTERS, 2002, 364 (1-2) : 139 - 143
  • [17] Jeffrey GA., 1997, An Introduction to Hydrogen Bonding
  • [18] 2ND-ORDER MOLLER-PLESSET PERTURBATION-THEORY AS A CONFIGURATION AND ORBITAL GENERATOR IN MULTICONFIGURATION SELF-CONSISTENT FIELD CALCULATIONS
    JENSEN, HJA
    JORGENSEN, P
    AGREN, H
    OLSEN, J
    [J]. JOURNAL OF CHEMICAL PHYSICS, 1988, 88 (06) : 3834 - 3839
  • [19] Pair interaction molecular orbital method: an approximate computational method for molecular interactions
    Kitaura, K
    Sawai, T
    Asada, T
    Nakano, T
    Uebayasi, M
    [J]. CHEMICAL PHYSICS LETTERS, 1999, 312 (2-4) : 319 - 324
  • [20] Fragment molecular orbital method: analytical energy gradients
    Kitaura, K
    Sugiki, SI
    Nakano, T
    Komeiji, Y
    Uebayasi, M
    [J]. CHEMICAL PHYSICS LETTERS, 2001, 336 (1-2) : 163 - 170
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