Hello, 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.
# This file was created by g_order which is part of G R O M A C S: # GROningen MAchine for Chemical Simulation # All this happened at: Thu Mar 29 17:00:05 2007# @ title "Order tensor diagonal elements" @ xaxis label "Atom" @ yaxis label "S" @TYPE xy 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. Sincerely, Dinesh. ----- Original Message ----- From: "Carl Caleman" To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] Orientation of DMSO Date: Thu, 29 Mar 2007 00:32:31 +0200 Hi, I believe you should generate an index file (make_ndx) with the atoms you are interested in and run g_order. Good luck, /Carl Dinesh Pinisetty wrote: > Hello Everyone, > > I have a 50ns simulation which involves DMSO molecules. > How do I find the orientation of DMSO molecules for the whole > simulation. I know that water orientation can be found by using > the command g_h2order. I tried using g_h2order for DMSO molecules > orientation but I was not sure if that is right. I will greatful > if anyone could suggest me the right command to be used. > > Sincerely, > > Dinesh. > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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