<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'>
Using g_dist I got the distance between the atom pair for which i need rdf. Made a histogram, using the default bin width used in gromacs. Then divide by 4*Pi*r^2 to normalize (where r is the distance between the pair). I expect my values to agree with that from g_rdf. While the graphs are exactly alike, the values from g_rdf are greater by a small factor.<BR>
Have I missed out something in my calculation?<BR>
I would appreciate any help.<BR>
Regards<BR>
John<BR><BR><BR>
<BLOCKQUOTE>
<HR>
From: omovie_johnnie@hotmail.com<BR>To: gmx-users@gromacs.org<BR>Date: Fri, 21 Dec 2007 09:40:19 -0500<BR>Subject: [gmx-users] problem with result from g_rdf<BR><BR>
<META content="Microsoft SafeHTML" name=Generator>
<STYLE>
.ExternalClass .EC_hmmessage P
{padding:0px;}
.ExternalClass EC_body.hmmessage
{font-size:10pt;font-family:Tahoma;}
</STYLE>
<P class=EC_EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; COLOR: #444444; FONT-FAMILY: Verdana">Dear all,<BR> <BR>When I use g_rdf to find the rdf between the alpha C-atoms in my simulation, I get the usually expected result.<BR>However, when I use g_rdf to get the rdf between just the central alpha C-atoms of the two peptides (my simulation is 2 peptide in a box of water, each peptide has 3 residues), I get some really weird result: </SPAN></P>
<P class=EC_EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; COLOR: #444444; FONT-FAMILY: Verdana">I get several plots that start off from a peak and gradually die off at the cut-off radius.<BR>I would appreciate any help.<BR>Regards<BR>John</SPAN></P><BR>
<HR>
Get the power of Windows + Web with the new Windows Live. <A href="http://www.windowslive.com/?ocid=TXT_TAGHM_Wave2_powerofwindows_122007" target=_blank>Get it now!</A> </BLOCKQUOTE><br /><hr />Make distant family not so distant with Windows Vista® + Windows Live™. <a href='http://www.microsoft.com/windows/digitallife/keepintouch.mspx?ocid=TXT_TAGLM_CPC_VideoChat_distantfamily_012008' target='_new'>Start now!</a></body>
</html>