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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">d(r) = (N/V)*g(r)<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>
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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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><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@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<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>mohammad agha<br>
<b>Sent:</b> Thursday, 2 February 2012 3:48 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] g_rdf<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black">Dear Prof.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black">Thank you very much from your reply.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black">Is your mean that "density=(N/V)*g(r)", where N is the number of total atoms in box not in the shell and V is the volume of box
not in the shell?<br>
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Best Regards<br>
Sara<br>
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<o:p></o:p></span></p>
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<br>
<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black"> Dallas Warren <<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>><br>
<b>To:</b> Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>
<br>
<b>Sent:</b> Wednesday, February 1, 2012 2:12 AM<br>
<b>Subject:</b> RE: [gmx-users] g_rdf</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;color:#1F497D">An RDF is normalised to the density for the entire box, so you should simply be using that.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:#1F497D">Medicinal Chemistry and Drug Action</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:#1F497D">Monash Institute of Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu">dallas.warren@monash.edu</a></span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:#1F497D">+61 3 9903 9304<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;color:#1F497D">
</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><b><span style="font-size:10.0pt;color:black">From:</span></b><span style="font-size:10.0pt;color:black">
<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [<a href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>mohammad agha<br>
<b>Sent:</b> Tuesday, 31 January 2012 7:26 PM<br>
<b>To:</b> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<b>Subject:</b> [gmx-users] g_rdf</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;color:black">Dear Prof.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;color:black">I am confused about generation a radial density graph (density vs distance from center of mass), I know that I should use g_rdf. Then I count the number of atoms in the
shells around the COM of special group by " trjorder -com -nshell -r " , next I use from this formula for compute the density:</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;color:black">density = (dN/4*pi*dr*r^2)*g(r), where dN, dr, r and g(r) are the number of atoms in each shell, wide of shell, radius of COM of special group, and averaged RDF in each
shell, respectively.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;color:black">While the plot of g(r) is consistent with published previous results but density has not consistence with them, I think that I am wrong in compute the density.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;color:black">Please help me.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;color:black">Best Regards</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;color:black">Sara</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span style="color:black"><br>
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