I am trying to study rdf of my system. My script is something like this:

coor anal select type ION end -
xref @xsite yref @ysite zref @zsite -
firstu 51 nunit 1 begin ?start skip ?skip -
isdist 41 -
rsph 999.9 mgn 800 dr 0.2 -
dens 0.001

The trajectory file contains 500ns data. I also run the script for every 100ns data by assigning the "begin" and "stop" in the third line such as "firstu 51 nunit 1 begin 10000000 stop 20000000 skip ?skip -".
I thought the rdf using all 500ns should be the average of the five 100ns rdf. However, although the five 100ns rdf plots are similar, their average is very different from the 500ns one. I even see a peak not present in any of the 100ns plots appears in the 500ns plot (within r<1). I am quite confused. Can anyone give me some hint? isn't rdf the average of rdf from each frame?

thank you very much.
james