Parallel molecular dynamics simulation of a protein

被引：16

作者：

Komeiji, Y ^{[1
]}

Haraguchi, M

Nagashima, U

机构：

[1] Natl Inst Adv Ind Sci & Technol, AIST, Tsukuba, Ibaraki 3058562, Japan

[2] BestSyst Inc, Tsukuba, Ibaraki 3050047, Japan

来源：

PARALLEL COMPUTING | 2001年 / 27卷 / 08期

关键词：

molecular dynamics; protein; MPI; PEACH; GRAPE;

D O I：

10.1016/S0167-8191(01)00079-5

中图分类号：

TP301 [理论、方法];

学科分类号：

081202 ;

摘要：

Program for energetic analysis of biochemical molecules (PEACH) is a software package for molecular dynamics (MD) simulation of biological molecules. The subroutines for the nonbonded interactions were modified to allow parallel computation by using the MPI library. The parallel efficiencies of the modified subroutines were close to 90% or better when using 32 processors of an IBM SP computer. The total performance was comparable to that of the special-purpose computer MD-GRAPE with 8 LSI chips. (C) 2001 Elsevier Science B,V. All rights reserved.

引用

页码：977 / 987

页数：11

共 19 条

[11]

Komeiji Y, 1997, J COMPUT CHEM, V18, P1546, DOI 10.1002/(SICI)1096-987X(199709)18:12<1546::AID-JCC11>3.0.CO

[12]

2-I

[13] Change in conformation by DNA-peptide association:: Molecular dynamics of the Hin-recombinase-hixL complex [J].

Komeiji, Y ;

Uebayasi, M .

BIOPHYSICAL JOURNAL, 1999, 77 (01) :123-138

[14] Ewald summation and multiple time step methods for molecular dynamics simulation of biological molecules [J].

Komeiji, Y .

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 2000, 530 (03) :237-243

[15] Molecular dynamics simulation of the Hin-recombinase - DNA complex [J].

Komeiji, Y ;

Uebayasi, M .

MOLECULAR SIMULATION, 1999, 21 (5-6) :303-324

[16]

*MPI, 1995, MESS PASS INT STAND

[17] Molecular dynamics simulation of trp-repressor/operator complex:: analysis of hydrogen bond patterns of protein-DNA interaction [J].

Suenaga, A ;

Yatsu, C ;

Komeiji, Y ;

Uebayasi, M ;

Meguro, T ;

Yamato, I .

JOURNAL OF MOLECULAR STRUCTURE, 2000, 526 :209-218

[18] REVERSIBLE MULTIPLE TIME SCALE MOLECULAR-DYNAMICS [J].

TUCKERMAN, M ;

BERNE, BJ ;

MARTYNA, GJ .

JOURNAL OF CHEMICAL PHYSICS, 1992, 97 (03) :1990-2001

[19] STRUCTURE OF FORM-III CRYSTALS OF BOVINE PANCREATIC TRYPSIN-INHIBITOR [J].

WLODAWER, A ;

NACHMAN, J ;

GILLILAND, GL ;

GALLAGHER, W ;

WOODWARD, C .

JOURNAL OF MOLECULAR BIOLOGY, 1987, 198 (03) :469-480

← 1 2 →