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 .
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , Zürich, Switzerland.
authors.forename: Andreas P
authors.initials: AP
authors.lastname: Eichenberger
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , Zürich, Switzerland.
authors.forename: Jane R
authors.initials: JR
authors.lastname: Allison
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , Zürich, Switzerland.|Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: Jožica
authors.initials: J
authors.lastname: Dolenc
authors.affiliation: Division of Molecular and Computational Toxicology, Free University Amsterdam, Amsterdam, The Netherlands.
authors.forename: Daan P
authors.initials: DP
authors.lastname: Geerke
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , Zürich, Switzerland.
authors.forename: Bruno A C
authors.initials: BA
authors.lastname: Horta
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , Zürich, Switzerland.
authors.forename: Katharina
authors.initials: K
authors.lastname: Meier
authors.affiliation: Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna, Austria.
authors.forename: Chris
authors.initials: C
authors.lastname: Oostenbrink
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , Zürich, Switzerland.
authors.forename: Nathan
authors.initials: N
authors.lastname: Schmid
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , Zürich, Switzerland.
authors.forename: Denise
authors.initials: D
authors.lastname: Steiner
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , Zürich, Switzerland.
authors.forename: Dongqi
authors.initials: D
authors.lastname: Wang
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , Zürich, Switzerland.
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Gunsteren