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 <jalem...@vt.edu>
To: Molecular Dynamics <moleculardynam...@yahoo.com>; Discussion list for
GROMACS users <gmx-users@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
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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