My system has 20 polymer chains, like A-A-A-A-A-A. I want to calculate the RDF between pairs: atom A and atom A. Now I want to know when lammps calculates RDF for A:A, does it only consider the atom A from the different chains, or also include A in the same chain.
The compute rdf command does not pay any attention
to molecule IDs. However, if you have defined the
special_bonds command to turn off nearby pairwise
interactions in the same chain, e.g. 1-2 and 1-3 interactions,
then those will not appear in the neighbor list, and hence
will not be included in the RDF calculation. However,
monomers far away on the same chain will be in the RDF.
If you don't want this, the only current option would be
to dump snapshots with molecule IDs and post-process
the modified RDF you want.