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<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Ahh, now I understand - sorry, Omer!<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>In fact, I have compared all three single hydrogen RDFs and they
are identical and also relatively smooth. Since, however, with 3 times more
data points (all three hydrogen atoms taken together) I get a different RDF, would
that indicate that I do not have enough data after all? <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Are RDFs known to be slow to converge? I have about 1000 water
molecules and about 50+ glycine molecules, simulated for 10ns with 1ps sampling
intervals. That should give me 500,000,000 data points for the distribution,
right? Can I compare this number with the literature in which RDFs for, say,
water-water interactions are reported?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>One important point, which was not really clear to me before was
if, provided that I have enough data, the RDFs should be identical no matter
whether I use 1, 2, or 3 hydrogen atoms for generating the RDF. As far as I
understood, both yours and Omer’s responses indicate that the RDFs should
be identical. Did I get that correctly?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Best regards,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Soren<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Dallas B. Warren<br>
<b>Sent:</b> Thursday, October 22, 2009 6:56 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> RE: [gmx-users] g_rdf and number of atoms to include<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Omar’s response answered that question on why they are
different. In the first one you are grouping all three into one group,
second is just one of the hydrogen types. The fact that the rdf you get
is different indicates that all three hydrogens are not identical. Have
you compared the rdf for each hydrogen type individually? Another factor
may also be that in the first you have three times the number of data points,
which can smooth out the curves more.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
Department of Pharmaceutical Biology <br>
Pharmacy and Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@pharm.monash.edu.au<br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
</div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt'>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Enemark Soeren<br>
<b>Sent:</b> Wednesday, 21 October 2009 8:28 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> RE: [gmx-users] g_rdf and number of atoms to include<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Omer,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks for your input.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Let me reformulate my problem:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I have glycine molecules in the form of zwitterions:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> ….<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> 1ZGLY
N 1 0.560 0.337 0.388
-0.0759 -0.2488 -0.5471<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> 1ZGLY
H1 2 0.625 0.312
0.461 0.6035 0.5922 -0.4315<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> 1ZGLY
H2 3 0.601 0.311
0.299 0.1500 -0.3357 -1.5372<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> 1ZGLY
H3 4 0.553 0.433
0.388 0.5086 2.8817 -1.8023<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> 1ZGLY
CA 5 0.426 0.272
0.403 0.3095 0.1790 -0.0455<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> 1ZGLY
HA1 6 0.352 0.335 0.345
-0.9032 0.4782 0.1366<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> 1ZGLY
HA2 7 0.433 0.173
0.358 0.7875 0.5369 -3.0389<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> 1ZGLY
C 8 0.378 0.267
0.551 0.1816 -0.4672 0.1868<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> 1ZGLY
OC1 9 0.449 0.218 0.644
-0.2820 -0.4080 0.2048<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'> 1ZGLY OC2
10 0.263 0.320 0.559 -0.0662 -0.2935
-0.8010<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> ….<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Now, I am interested in the interaction between the amine group
hydrogen atoms (H1, H2, and H3) and the water oxygen atom. Thus, I define 2
group in an index file:<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span
style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>aH1H2H3 (which contains all H1, H2, and H3 atoms in the glycine
molecules in my system)<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span
style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>aOwat (which contains all oxygen atoms in the water molecules in
my system)<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>However, I also tried setting up a different index file with the
groups:<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span
style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>aH1 (which contains all H1 atoms in my system)<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span
style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>aOwat (like before)<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I find that these 2 index files do not produce the same RDFs.
Why is that?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Best regards,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Soren<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Omer Markovitch<br>
<b>Sent:</b> Wednesday, October 21, 2009 4:27 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] g_rdf and number of atoms to include<o:p></o:p></span></p>
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<p class=MsoNormal>On Wed, Oct 21, 2009 at 07:28, Enemark Soeren <<a
href="mailto:chees@nus.edu.sg">chees@nus.edu.sg</a>> wrote:<o:p></o:p></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear
users,<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='margin-left:20.25pt'>1)<span style='font-size:7.0pt'>
</span>between the amine hydrogen atoms in glycine and the oxygen atom in water<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>2)<span
style='font-size:7.0pt'> </span>between the
carboxyl oxygen atoms in glycine and the oxygen atom in water <o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>However,
my result in 1) depends on how many of the 3 hydrogen atoms I include in the
calculations. Why is that?<o:p></o:p></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'>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.<span style='color:#1F497D'><o:p></o:p></span></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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>
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<p class=MsoNormal>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. <o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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