In this chapter different ways of analyzing your trajectory are described. The names of the corresponding analysis programs are given. Specific information on the in- and output of these programs can be found in the tool documentation here. The output files are often produced as finished Grace/Xmgr graphs.

First, in sec. Using Groups, the group concept in analysis is explained. Selections explains a newer concept of dynamic selections, which is currently supported by a few tools. Then, the different analysis tools are presented.