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

[1] AFFENTRANGER R, UNPUB BIOPHYS J
[2] Allen M. P., 1987, J COMPUTER SIMULATIO, DOI DOI 10.2307/2938686
[3] Molecular dynamics simulations with constrained roto-translational motions: Theoretical basis and statistical mechanical consistency
Amadei, A
Chillemi, G
Ceruso, MA
Grottesi, A
Di Nola, A
[J]. JOURNAL OF CHEMICAL PHYSICS, 2000, 112 (01) : 9 - 23
[4] MOLECULAR-DYNAMICS SIMULATIONS AT CONSTANT PRESSURE AND-OR TEMPERATURE
ANDERSEN, HC
[J]. JOURNAL OF CHEMICAL PHYSICS, 1980, 72 (04) : 2384 - 2393
[5] Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation
Antes, I
Thiel, W
van Gunsteren, WF
[J]. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2002, 31 (07): : 504 - 520
[6] Simulations of apo and holo-fatty acid binding protein: Structure and dynamics of protein, ligand and internal water
Bakowies, D
van Gunsteren, WF
[J]. JOURNAL OF MOLECULAR BIOLOGY, 2002, 315 (04) : 713 - 736
[7] REACTION FIELD, SCREENING, AND LONG-RANGE INTERACTIONS IN SIMULATIONS OF IONIC AND DIPOLAR SYSTEMS
BARKER, JA
[J]. MOLECULAR PHYSICS, 1994, 83 (06) : 1057 - 1064
[8] MONTE-CARLO STUDIES OF DIELECTRIC PROPERTIES OF WATER-LIKE MODELS
BARKER, JA
WATTS, RO
[J]. MOLECULAR PHYSICS, 1973, 26 (03) : 789 - 792
[9] Principles of carbopeptoid folding: a molecular dynamics simulation study
Baron, R
Bakowies, D
Van Gunsteren, WF
[J]. JOURNAL OF PEPTIDE SCIENCE, 2005, 11 (02) : 74 - 84
[10] Carbopeptoid folding: Effects of stereochemistry, chain length, and solvent
Baron, R
Bakowies, D
van Gunsteren, WF
[J]. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2004, 43 (31) : 4055 - 4059

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