<div dir="ltr"><div class="gmail_quote">On Wed, Oct 21, 2009 at 07:28, Enemark Soeren <span dir="ltr"><<a href="mailto:chees@nus.edu.sg">chees@nus.edu.sg</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<p class="MsoNormal">Dear users,</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:</p>
<p style="margin-left: 20.25pt;"><span>1)<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span>between
the amine hydrogen atoms in glycine and the oxygen atom in water</p>
<p class="MsoNormal"><span>2)<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span>between
the carboxyl oxygen atoms in glycine and the oxygen atom in water <br></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?</p></div></div></blockquote><div>If you mean that when focusing your RDF calculations on either one of the three hydrogens results in three different RDFs then it means that each hydrogen feels water differently. I bet this difference is only for the first peak of g(r) and the other peaks overlap between the three RDFs. As for how reasonable this result, its not unlikely because glycine has atleast 2 different types of hydrogens (say, C-H vs. N-H), depending on the protonation state. You might want to provide more details on the system you are studying to get better answer.<br>
I am assuming that the RDFs are converged so that including more trajectory data and/or sampled molecules and/or changing bin size does not result in a drastic change to the curves.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US"><div><p class="MsoNormal"> 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?<br></p></div></div></blockquote><div>I am not sure how good it is to use the first peak of g(r) to analyze strengths, but you should also consider the width and area under peak. This peak is an average on all nearest neighbours, bonded or not, so it might not give you a good estimate of the hydrogen bond, for example.<br>
If you are unsure of your g(r) calc it just for water (that is - only oxygen-oxygen of water-water). At long distances (~10 Angstroms) it should fluctuate around 1.<br><br>Bests, Omer Markovitch. <br></div></div><br></div>