[gmx-users] make_ndx and rdf

[Justin A. Lemkul]

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 <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
> 
> -- ========================================
> 
> 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

========================================