[gmx-users] g_rdf and number of atoms to include

[Enemark Soeren]

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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