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<p class=MsoNormal>Dear users,<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>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:<o:p></o:p></p>

<p class=MsoListParagraph style='margin-left:20.25pt;text-indent:-.25in;
mso-list:l0 level1 lfo1'><![if !supportLists]><span style='mso-list:Ignore'>1)<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><![endif]>between
the amine hydrogen atoms in glycine and the oxygen atom in water<o:p></o:p></p>

<p class=MsoListParagraph style='margin-left:20.25pt;text-indent:-.25in;
mso-list:l0 level1 lfo1'><![if !supportLists]><span style='mso-list:Ignore'>2)<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><![endif]>between
the carboxyl oxygen atoms in glycine and the oxygen atom in water<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>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?<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>Thanks,<o:p></o:p></p>

<p class=MsoNormal>Soren<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

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