GROMOS plus plus Software for the Analysis of Biomolecular Simulation Trajectories

被引：186

作者：

Eichenberger, Andreas P. ^{[1
]}

Allison, Jane R. ^{[1
]}

Dolenc, Jozica ^{[1
,4
]}

Geerke, Daan P. ^{[3
]}

Horta, Bruno A. C. ^{[1
]}

Meier, Katharina ^{[1
]}

Oostenbrink, Chris ^{[2
]}

Schmid, Nathan ^{[1
]}

Steiner, Denise ^{[1
]}

Wang, Dongqi ^{[1
]}

van Gunsteren, Wilfred F. ^{[1
]}

机构：

[1] ETH, Lab Phys Chem, Swiss Fed Inst Technol, Zurich, Switzerland

[2] Univ Nat Resources & Life Sci, Inst Mol Modeling & Simulat, Vienna, Austria

[3] Free Univ Amsterdam, Div Mol & Computat Toxicol, Amsterdam, Netherlands

[4] Univ Ljubljana, Fac Chem & Chem Technol, Ljubljana, Slovenia

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2011年 / 7卷 / 10期

基金：

瑞士国家科学基金会; 欧洲研究理事会;

关键词：

MOLECULAR-DYNAMICS SIMULATIONS; FORCE-FIELD; SECONDARY STRUCTURE; PARAMETER SET; FREE-ENERGY; PROTEINS; SOLVATION; CHARMM; DISTRIBUTIONS; HEPTAPEPTIDE;

D O I：

10.1021/ct2003622

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：

GROMOS++ is a set of C++ programs for pre- and postprocessing of molecular dynamics simulation trajectories and as such is part of the GROningen MOlecular Simulation software for (bio)molecular simulation. It contains more than 70 programs that can be used to prepare data for the production of molecular simulation trajectories and to analyze these. These programs are reviewed and the various structural, dynamic, and thermodynamic quantities that can be analyzed using time series, correlation functions, and distributions are described together with technical aspects of their implementation in GROMOS. A few examples of the use of GROMOS++ for the analysis of MD trajectories are given. A full list of all GROMOS++ programs, together with an indication of their capabilities, is given in the Appendix.

引用

页码：3379 / 3390

页数：12

共 60 条

[41]

Ponder JW, 2003, ADV PROTEIN CHEM, V66, P27

[42]

Riniker S., 2011, J PHYS CHEM UNPUB

[43] On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase [J].

Riniker, Sereina ;

Kunz, Anna-Pitschna E. ;

van Gunsteren, Wilfred F. .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2011, 7 (05) :1469-1475

[44] NUMERICAL-INTEGRATION OF CARTESIAN EQUATIONS OF MOTION OF A SYSTEM WITH CONSTRAINTS - MOLECULAR-DYNAMICS OF N-ALKANES [J].

RYCKAERT, JP ;

CICCOTTI, G ;

BERENDSEN, HJC .

JOURNAL OF COMPUTATIONAL PHYSICS, 1977, 23 (03) :327-341

[45] Protein-folding dynamics: Overview of molecular simulation techniques [J].

Scheraga, Harold A. ;

Khalili, Mey ;

Liwo, Adam .

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, 2007, 58 (57-83) :57-83

[46] ESTIMATION OF ABSOLUTE AND RELATIVE ENTROPIES OF MACROMOLECULES USING THE COVARIANCE-MATRIX [J].

SCHLITTER, J .

CHEMICAL PHYSICS LETTERS, 1993, 215 (06) :617-621

[47]

SCHMID N, 2011, COMPUT PHYS CO UNPUB

[48] Biomolecular structure refinement using the GROMOS simulation software [J].

Schmid, Nathan ;

Allison, Jane R. ;

Dolenc, Jozica ;

Eichenberger, Andreas P. ;

Kunz, Anna-Pitschna E. ;

van Gunsteren, Wilfred F. .

JOURNAL OF BIOMOLECULAR NMR, 2011, 51 (03) :265-281

[49] Definition and testing of the GROMOS force-field versions 54A7 and 54B7 [J].

Schmid, Nathan ;

Eichenberger, Andreas P. ;

Choutko, Alexandra ;

Riniker, Sereina ;

Winger, Moritz ;

Mark, Alan E. ;

van Gunsteren, Wilfred F. .

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2011, 40 (07) :843-856

[50] An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase [J].

Schuler, LD ;

Daura, X ;

Van Gunsteren, WF .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2001, 22 (11) :1205-1218

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