[gmx-users] make_ndx and rdf

[Justin A. Lemkul]

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

-- 
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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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