The GROMOS software for biomolecular simulation:: GROMOS05

被引：500

作者：

Christen, M ^{[1
]}

Hünenberger, PH ^{[1
]}

Bakowies, D ^{[1
]}

Baron, R ^{[1
]}

Bürgi, R ^{[1
]}

Geerke, DP ^{[1
]}

Heinz, TN ^{[1
]}

Kastenholz, MA ^{[1
]}

Kräutler, V ^{[1
]}

Oostenbrink, C ^{[1
]}

Peter, C ^{[1
]}

Trzesniak, D ^{[1
]}

Van Gunsteren, WF ^{[1
]}

机构：

[1] ETH Honggerberg, Swiss Fed Inst Technol, Chem Phys Lab, CH-8093 Zurich, Switzerland

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2005年 / 26卷 / 16期

关键词：

molecular dynamics simulation; programming; GROMOS; biomolecular simulation;

D O I：

10.1002/jcc.20303

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

We present the latest version of the Groningen Molecular Simulation program package, GROMOS05. It has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization. An overview of GROMOS05 is given, highlighting features not present in the last major release, GROMOS96. The organization of the program package is outlined and the included analysis package GROMOS++ is described. Finally, some applications illustrating the various available functionalities are presented. (c) 2005 Wiley Periodicals, Inc.

引用

页码：1719 / 1751

页数：33

共 204 条

[61] WIGNER SOLIDS AND DIFFUSION CONTROLLED REACTIONS IN A REGULAR ARRAY OF SPHERES
FELDERHOF, BU
[J]. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 1985, 130 (1-2) : 34 - 56
[62] LONG-RANGE FORCES IN MOLECULAR-DYNAMICS CALCULATIONS ON WATER
FINNEY, JL
[J]. JOURNAL OF COMPUTATIONAL PHYSICS, 1978, 28 (01) : 92 - 102
[63] On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
Fukunishi, H
Watanabe, O
Takada, S
[J]. JOURNAL OF CHEMICAL PHYSICS, 2002, 116 (20) : 9058 - 9067
[64] García AE, 2001, PROTEINS, V42, P345, DOI 10.1002/1097-0134(20010215)42:3<345::AID-PROT50>3.0.CO
[65] 2-H
[66] Gee PJ, 2002, HELV CHIM ACTA, V85, P618, DOI 10.1002/1522-2675(200202)85:2<618::AID-HLCA618>3.0.CO
[67] 2-Q
[68] An effective force field for molecular dynamics simulations of dimethyl sulfoxide and dimethyl sulfoxide-water mixtures
Geerke, DP
Oostenbrink, C
van der Vegt, NFA
van Gunsteren, WF
[J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2004, 108 (04) : 1436 - 1445
[69] GEYER CJ, 1991, COMPUTING SCIENCE AND STATISTICS, P156
[70] Do valine side chains have an influence on the folding behavior of β-substituted β-peptides?
Glättli, A
Seebach, D
van Gunsteren, WF
[J]. HELVETICA CHIMICA ACTA, 2004, 87 (10) : 2487 - 2506

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