Hi everyone,

I have 5 PBI polymer chains in an MD simulation box filled with water. I want to check whether polymer aggregation occurs using RDF analysis. Could someone guide me on how to properly calculate the PBI–PBI RDF? Specifically, how should I define/select the atoms in the PBI chains for the RDF calculation (e.g., which atoms or groups are most appropriate to capture aggregation behavior)?

Thanks in advance for your help.

Hakkim