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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>If you have aggregation and a small box size, then the rdf will
not be able to asymptote to one.<o:p></o:p></span></p>
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color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Drug Delivery, Disposition and Dynamics</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>
</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>,
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>
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<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>Antonia V.<br>
<b>Sent:</b> Thursday, 11 March 2010 2:18 AM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] rdf problem<o:p></o:p></span></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;
font-family:"Verdana","sans-serif"'>Dear all,<br>
<br>
I am simulating a binary system of two non mixing components (5CB and water
using version 4-0-3; the whole equilibrated trajectory is about 300ns). <br>
I want to calculate the rdf of the centers of mass of 5CB using the command <br>
g_rdf -f traj300.xtc -rdf mol_com -o rdf_com_300.xvg -noxvgr.<br>
The problem is that the rdf I am getting does not approach one at long
distances. Is there a way to correct that? <br>
I have the same problem, with all rdfs, and also when I compute the rdfs for a
lipid bilayer (DPPC-water)... I think it has to do with the way that the
normalization is done, <br>
because the ones that are calculated for a one component system (i.e. bulk 5CB)
are normal (they do approach one). <br>
<br>
Thank you,<br>
Antonia<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>Hotmail:
Trusted email with Microsoft’s powerful SPAM protection. <a
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