Paper Citing NAMD - Abstract
Eichenberger, Andreas P.; Allison, Jane R.; Dolenc, Jozica; Geerke, Daan P.; Horta, Bruno A. C.; Meier, Katharina; Oostenbrink, Chris; Schmid, Nathan; Steiner, Denise; Wang, Dongqi; van Gunsteren, Wilfred F.
GROMOS plus plus Software for the Analysis of Biomolecular Simulation Trajectories
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3379-3390, OCT 2011
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.
