Improve initAfterFirstFrame() usability

Improve initAfterFirstFrame() usability

The initAnalysis() function was changed a long time ago to take the
analysis settings as a parameter, to make it easy to use those values in
initialization without storing them in local variables.
Do the same for initAfterFirstFrame(), now that there is a tool in
pipeline (gmx rdf) that would actually use this function and sees the
same issue there.

Change-Id: Ib10abb3790ac5472070edc76155cfa50cce96541