Dear users,
I would like to compare interactions between molecules by using RDF. I have tried looking at glycine and water, and compare the following two interactions: 1) between the amine hydrogen atoms in glycine and the oxygen atom in water 2) between the carboxyl oxygen atoms in glycine and the oxygen atom in water However, my result in 1) depends on how many of the 3 hydrogen atoms I include in the calculations. Why is that? Does that mean that I cannot directly compare the strengths (RDF peak height) of the two interactions as they are not based on the same number of atoms? Does it also mean that I must always calculate RDFs by using 1 atom on each of the particles/groups that I am comparing? Thanks, Soren
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