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

Enemark Soeren chees at nus.edu.sg
Wed Oct 21 07:28:39 CEST 2009

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

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?






-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091021/31a92441/attachment.html>

More information about the gromacs.org_gmx-users mailing list