I'm struggling to understand a paper in which someone has presented radial distribution functions (RDFs) for a system that contains multiple Na, Cl, and water atoms/molecules. I don't know exactly how the RDFs have been calculated--there must be some standard method.
I'm a newbie to molecular dynamics and have run my own simulations. I would like to compare my RDFs to the ones in the paper. However, I am not sure that I understand RDFs. One reason I'm worried is that I keep receiving an error when I try to plot my own RDFs using the software, VMD. The error is something like "cannot measure RDF." It is either a bug in VMD or a conceptual misunderstanding on my part. I don't know exactly how VMD calculates an RDF.
Let's say we have an RDF from Na to Cl in my system that contains multiple Na and Cl. Is it correct that an RDF is based on an average of what ALL Cl atoms are doing in relation to ALL Na atoms? Or do I have to somehow define pairs of Na and Cl (I don't have these--they're all far apart in my system) and create RDFs for each pair?
I'm not sure whether "Chemistry" is the right StackExchange section for this question. If it isn't and anyone has any advice on a more appropriate section, I'd be very grateful. Thank you.