GROMOS++Software for the Analysis of Biomolecular Simulation Trajectories

A.P. Eichenberger; J.R. Allison; J. Dolenc; D.P. Geerke; B.A.C. Horta; K Meier; B.C. Oostenbrink; N. Schmid; D Steiner; D. Wang; W.F. van Gunsteren

doi:10.1021/ct2003622

GROMOS++Software for the Analysis of Biomolecular Simulation Trajectories

A.P. Eichenberger, J.R. Allison, J. Dolenc, D.P. Geerke, B.A.C. Horta, K Meier, B.C. Oostenbrink, N. Schmid, D Steiner, D. Wang, W.F. van Gunsteren

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

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. © 2011 American Chemical Society.

Original language	English
Pages (from-to)	3379-3390
Number of pages	13
Journal	Journal of Chemical Theory and Computation
Volume	7
DOIs	https://doi.org/10.1021/ct2003622
Publication status	Published - 2011

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title = "GROMOS++Software for the Analysis of Biomolecular Simulation Trajectories",

abstract = "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. {\textcopyright} 2011 American Chemical Society.",

author = "A.P. Eichenberger and J.R. Allison and J. Dolenc and D.P. Geerke and B.A.C. Horta and K Meier and B.C. Oostenbrink and N. Schmid and D Steiner and D. Wang and {van Gunsteren}, W.F.",

year = "2011",

doi = "10.1021/ct2003622",

language = "English",

volume = "7",

pages = "3379--3390",

journal = "Journal of Chemical Theory and Computation",

issn = "1549-9618",

publisher = "American Chemical Society",

}

TY - JOUR

T1 - GROMOS++Software for the Analysis of Biomolecular Simulation Trajectories

AU - Eichenberger, A.P.

AU - Allison, J.R.

AU - Dolenc, J.

AU - Geerke, D.P.

AU - Horta, B.A.C.

AU - Meier, K

AU - Oostenbrink, B.C.

AU - Schmid, N.

AU - Steiner, D

AU - Wang, D.

AU - van Gunsteren, W.F.

PY - 2011

Y1 - 2011

N2 - 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. © 2011 American Chemical Society.

AB - 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. © 2011 American Chemical Society.

U2 - 10.1021/ct2003622

DO - 10.1021/ct2003622

M3 - Article

SN - 1549-9618

VL - 7

SP - 3379

EP - 3390

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

ER -

GROMOS++Software for the Analysis of Biomolecular Simulation Trajectories

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