How to pin down relative groups in minddist and pair-dist?

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Hi there, I have used both pair-dist, mindist, distance in trying to find out distance between two groups of atoms in two different species. But both of these species are moving throughout the trajectory.
So how to pin down and on what grounds to pin down one species relative to the other?

I have created the groups with just selecting specific atom only in a residue.
I think the specs for on which ground has to be defined at the stage of group creation in index file. Can someone please let me know if this group should be created with COG, COM?

Is it possible to use this method to find the degree of distribution/localization of a certain species relative to another?

Thank you

if I understood correct you would want to have the distribution of a molecular type respect to the other. Maybe gmx rdf (gmx rdf — GROMACS 2022.2 documentation) can be useful?
There you can decide if you want the distribution based on COG or COM with option [-seltype ] and [-selrpos ]