The Gromacs manual has the following regarding exclusions:

"If a run input file is supplied (-s) and -rdf is set to atom, exclusions defined in that file are taken into account when calculating the RDF. The option -cut is meant as an alternative way to avoid intramolecular peaks in the RDF plot."

The -cut option isn't appropriate for my case as I have intermolecular peaks (which I want to keep) in the same intramolecular pair distances that I want to exclude. How exactly can I add RDF "exclusions" to my input file after? Or, are there other ways to filter out intramolecular pairs from my RDF curve? The command I am using:

gmx rdf -f file1.xtc file2.tpr -n index.ndx -o rdf.xvg -cn coord.xvg -b t_initial -e t_final -bin 0.01 -rmax 1 -ref base_atom_index -sel distributed_atom_index