<P>Hello,</P>
<P> As suggested I tried using g_order with an .ndx file for only DMSO molecules. I did get an output file which did not have anything in it. </P><FONT size=2>
<P># This file was created by g_order which is part of G R O M A C S:</P>
<P># GROningen MAchine for Chemical Simulation # All this happened at: Thu Mar 29 17:00:05 2007#</P>
<P>@ title "Order tensor diagonal elements"</P>
<P>@ xaxis label "Atom"</P>
<P>@ yaxis label "S"</P>
<P>@TYPE xy</P>
<P></FONT>I did not get any data, what I desire to achieve is to get an orientation profile for DMSO molecules. Can anyone please suggest me how to achieve it.</P>
<P>Sincerely,</P>
<P>Dinesh.</P>
<P> </P>
<P><BR><BR> </P>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">----- Original Message -----<BR>From: "Carl Caleman" <CALLE@XRAY.BMC.UU.SE><BR>To: "Discussion list for GROMACS users" <GMX-USERS@GROMACS.ORG><BR>Subject: Re: [gmx-users] Orientation of DMSO<BR>Date: Thu, 29 Mar 2007 00:32:31 +0200<BR><BR><BR>Hi,<BR><BR>I believe you should generate an index file (make_ndx) with the <BR>atoms you are interested in and run g_order.<BR><BR>Good luck,<BR><BR>/Carl<BR><BR><BR>Dinesh Pinisetty wrote:<BR>> Hello Everyone,<BR>><BR>> I have a 50ns simulation which involves DMSO molecules. <BR>> How do I find the orientation of DMSO molecules for the whole <BR>> simulation. I know that water orientation can be found by using <BR>> the command g_h2order. I tried using g_h2order for DMSO molecules <BR>> orientation but I was not sure if that is right. I will greatful <BR>> if anyone could suggest me the right command to be used.<BR>><BR>> Sincerely,<BR>><BR>> Dinesh.<BR>><BR>><BR>><BR>> ------------------------------------------------------------------------<BR>><BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the www <BR>> interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the www <BR>interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR>