@SRMaiti Thank you so much for all these your help. I looked at the link that you mentioned and trying to calculate with consideration of center of mass :) hope it would work!

@DGKang Yes although in your case, I think you are trying to calculate from particle A to particle B, so it would be slightly different I think.

I think a good test of your code would be to run an actual molecular dynamics simulation in a software like gromacs or NAMD and then use their tools to get the RDF. Then compare it to the one that you got from python. Their tools have been tested a lot, so it would probably give the right result.