[gmx-users] Orientation of DMSO

[Dinesh Pinisetty]

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.
  >
  >
  >
  >
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