Fragment molecular orbital method: application to molecular dynamics simulation, 'ab initio FMO-MD'

被引：94

作者：

Komeiji, Y

Nakano, T

Fukuzawa, K

Ueno, Y

Inadomi, Y

Nemoto, T

Uebaysai, M

Fedorov, DG

Kitaura, K

机构：

[1] AIST, Natl Inst Adv Ind Sci & Technol, Tsukuba, Ibaraki 3058568, Japan

[2] Natl Inst Hlth Sci, Setagaya Ku, Tokyo 1508501, Japan

[3] Fuji Res Inst Corp, Chiyoda Ku, Tokyo 1350064, Japan

来源：

CHEMICAL PHYSICS LETTERS | 2003年 / 372卷 / 3-4期

关键词：

D O I：

10.1016/S0009-2614(03)00430-5

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：

A quantum molecular simulation method applicable to biological molecules is proposed. Ab initio fragment molecular orbital method-based molecular dynamics (FMO-MD) combines molecular dynamics simulation with the ab initio fragment molecular orbital method. Here, FMO computes the force acting on each atom's nucleus while MD computes the nuclei's time-dependent evolutions. FMO-MD successfully simulated a small polypeptide, demonstrating the method's applicability to biological molecules. (C) 2003 Elsevier Science B.V. All rights reserved.

引用

页码：342 / 347

页数：6

共 19 条

[1] Ab initio MD simulations of a prototype of methyl chloride hydrolysis with explicit consideration of three water molecules: a comparison of MD trajectories with the IRC path
Aida, M
Yamataka, H
Dupuis, M
[J]. THEORETICAL CHEMISTRY ACCOUNTS, 1999, 102 (1-6) : 262 - 271
[2] *AIST, PEACH VER 3 8
[3] RATTLE - A VELOCITY VERSION OF THE SHAKE ALGORITHM FOR MOLECULAR-DYNAMICS CALCULATIONS
ANDERSEN, HC
[J]. JOURNAL OF COMPUTATIONAL PHYSICS, 1983, 52 (01) : 24 - 34
[4] UNIFIED APPROACH FOR MOLECULAR-DYNAMICS AND DENSITY-FUNCTIONAL THEORY
CAR, R
PARRINELLO, M
[J]. PHYSICAL REVIEW LETTERS, 1985, 55 (22) : 2471 - 2474
[5] Haile J. M., 1992, MOL DYNAMICS SIMULAT
[6] 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
[7] 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
[8] Fragment molecular orbital method: an approximate computational method for large molecules
Kitaura, K
Ikeo, E
Asada, T
Nakano, T
Uebayasi, M
[J]. CHEMICAL PHYSICS LETTERS, 1999, 313 (3-4) : 701 - 706
[9] Parallel molecular dynamics simulation of a protein
Komeiji, Y
Haraguchi, M
Nagashima, U
[J]. PARALLEL COMPUTING, 2001, 27 (08) : 977 - 987
[10] Komeiji Y, 1997, J COMPUT CHEM, V18, P1546, DOI 10.1002/(SICI)1096-987X(199709)18:12<1546::AID-JCC11>3.0.CO

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