[gmx-users] make_ndx and rdf

oguz gurbulak gurbulakoguz at yahoo.com
Mon Oct 3 16:39:57 CEST 2011

Dear Justin,

Of course I tried  typing "help" at the make_ndx prompt but I couldn't generate a .ndx file for my purposes.  I strongly need expert help for using make_ndx tool. I'm trying to generate .ndx file for more than one week. Finally I decided to ask it to mailing list. So I will be appreciate for any help.

Thanks for your help.

From: Justin A. Lemkul <jalemkul at vt.edu>
To: Molecular Dynamics <moleculardynamics at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, October 3, 2011 5:17 PM
Subject: Re: [gmx-users] make_ndx and rdf

Molecular Dynamics wrote:
> Dear All,
> I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water using g_rdf but how can I generate an .ndx file that are suitable for these systems ? I searched mailing list and read manual but couldn't generate .ndx file using make_ndx tool. However, I tried to see the make_ndx examples in gromacs wiki page but couldn't reach the wiki page. Could you please help me about generating .ndx file  ?
> Carbon in group 1
> hydrogen in group 2
> oxygen in group 2
> group 2 is water
> I will be gratefull for your helps.

Have you tried typing "help" at the make_ndx prompt?  You'll get tons of information, including the commands needed to create the groups you want.


-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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