<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 12 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"Bookman Old Style";
panose-1:2 5 6 4 5 5 5 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">An RDF is normalised to the density for the entire box, so you should simply be using 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>
<div>
<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, 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>
</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:0cm 0cm 0cm 4.0pt">
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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> Tuesday, 31 January 2012 7:26 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] g_rdf<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<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>
</div>
<div>
<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>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";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:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";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.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";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.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black">Please help me.<o:p></o:p></span></p>
</div>
<div>
<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>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black">Best Regards<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:14.0pt;font-family:"Bookman Old Style","serif";color:black">Sara<o:p></o:p></span></p>
</div>
</div>
</div>
</div>
</body>
</html>