oguz gurbulak wrote:
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
OK, you didn't say that. You said you tried the mailing list, manual, and the
wiki was unavailable. The "help" prompt is the best option. If you don't state
everything you tried, I'm going to go with the remaining option(s) :)
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.
For example, water oxygens (assuming SOL is group 2, as you said)
2 & a OW
Water hydrogens
2 & a H*
All carbon atoms in group 1
1 & a C*
-Justin
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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--
========================================
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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