<html><body><div style="color:#000; background-color:#fff; font-family:bookman old style, new york, times, serif;font-size:14pt"><div><span>Dear Prof.</span></div><div><br><span></span></div><div><span>Thank you very much from your reply.</span></div><div><br><span></span></div><div><span>Best Regards</span></div><div><span>Sara</span></div><div><br></div> <div style="font-family: bookman old style, new york, times, serif; font-size: 14pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Dallas Warren <Dallas.Warren@monash.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, February 2, 2012 2:49 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> RE:
[gmx-users] g_rdf<br> </font> </div> <br>
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<div class="yiv931210356MsoNormal"><span style="font-size:11.0pt;color:#1F497D;">d(r) = (N/V)*g(r)</span></div>
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<div class="yiv931210356MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Catch ya,<br>
<br>
Dr. Dallas Warren</span></div>
<div class="yiv931210356MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Medicinal Chemistry and Drug Action</span></div>
<div class="yiv931210356MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;color:#1F497D;">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu</span></div>
<div class="yiv931210356MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">+61 3 9903 9304<br>
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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;">
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<div class="yiv931210356MsoNormal"><b><span style="font-size:10.0pt;">From:</span></b><span style="font-size:10.0pt;"> 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</span></div>
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<div class="yiv931210356MsoNormal" style="background:white;"><span style="font-size:14.0pt;color:black;">Dear Prof.</span></div>
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<div class="yiv931210356MsoNormal" style="background:white;"><span style="font-size:14.0pt;color:black;">Thank you very much from your reply.</span></div>
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<div class="yiv931210356MsoNormal" style="background:white;"><span style="font-size:14.0pt;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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<div class="yiv931210356MsoNormal" style="background:white;"><b><span style="font-size:10.0pt;color:black;">From:</span></b><span style="font-size:10.0pt;color:black;"> Dallas Warren <<a rel="nofollow" ymailto="mailto:Dallas.Warren@monash.edu" target="_blank" href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>><br>
<b>To:</b> Discussion list for GROMACS users <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>
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<b>Sent:</b> Wednesday, February 1, 2012 2:12 AM<br>
<b>Subject:</b> RE: [gmx-users] g_rdf</span><span style="color:black;"></span></div>
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<div class="yiv931210356MsoNormal" 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;"></span></div>
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<div class="yiv931210356MsoNormal" style="background:white;"><span style="font-size:10.0pt;color:#1F497D;">Catch ya,<br>
<br>
Dr. Dallas Warren</span><span style="color:black;"></span></div>
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<div class="yiv931210356MsoNormal" style="background:white;"><span style="font-size:10.0pt;color:#1F497D;">Medicinal Chemistry and Drug Action</span><span style="color:black;"></span></div>
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<div class="yiv931210356MsoNormal" 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 rel="nofollow" ymailto="mailto:dallas.warren@monash.edu" target="_blank" href="mailto:dallas.warren@monash.edu">dallas.warren@monash.edu</a></span><span style="color:black;"></span></div>
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<div class="yiv931210356MsoNormal" 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;"></span></div>
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<div class="yiv931210356MsoNormal" style="background:white;"><b><span style="font-size:10.0pt;color:black;">From:</span></b><span style="font-size:10.0pt;color:black;">
<a rel="nofollow" ymailto="mailto:gmx-users-bounces@gromacs.org" target="_blank" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [<a rel="nofollow" ymailto="mailto:gmx-users-bounces@gromacs.org" target="_blank" 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 rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<b>Subject:</b> [gmx-users] g_rdf</span><span style="color:black;"></span></div>
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<div class="yiv931210356MsoNormal" style="background:white;"><span style="font-size:14.0pt;color:black;">Dear Prof.</span><span style="color:black;"></span></div>
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<div class="yiv931210356MsoNormal" 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;"></span></div>
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<div class="yiv931210356MsoNormal" 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;"></span></div>
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<div class="yiv931210356MsoNormal" 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;"></span></div>
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<div class="yiv931210356MsoNormal" style="background:white;"><span style="font-size:14.0pt;color:black;">Please help me.</span><span style="color:black;"></span></div>
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<div class="yiv931210356MsoNormal" style="background:white;"><span style="font-size:14.0pt;color:black;">Best Regards</span><span style="color:black;"></span></div>
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<div class="yiv931210356MsoNormal" style="background:white;"><span style="font-size:14.0pt;color:black;">Sara</span><span style="color:black;"></span></div>
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