I don't really understand what you are trying to do, but one thing
that popped to mind is that if your current system is current.gro you
can do this:
genbox -cp empty_file_with_box_dimensions_I_want.gro -cs current.gro
Basically you are "solvating" an empty box with replicas of your
system. If your system if larger than the box then only part of your
system will be included in the output.
Probably you can trjconv -translate your current.gro and repeat genbox
to get the output you desire (although I am not sure about that one).
I do this for example if I have some waters that are too close to the
protein in an erroneous setup (or recently as output from an
improperly completed make_hole mdrun of a collegue) then I strip out
the waters into a seperate file of exactly the same size and then use
then to resolvate via genbox.
Chris.
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