[gmx-users] make_ndx and rdf

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 3 16:17:05 CEST 2011

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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