[gmx-users] Re: how to define an index file

Justin A. Lemkul jalemkul at vt.edu
Tue May 18 22:58:01 CEST 2010

Vitaly Chaban wrote:
>     I am trying to create an index file to get interaction energies between
>     hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my
>     system.
>     To do this how should I define my index groups. Should I include all 125
>     molecuels in index file? now I have only the first 20 atoms (first
>     molecule)..
> To get the total interaction energy among your hexanes, all atoms of 
> all C6H14's should be listed in the NDX file, e.g. 125 * 20...

The underlying issue with this approach is that there are then in excess of 
125*125 energy terms written to the .edr file, which will quickly make this file 
very (perhaps prohibitively) large.  Let the OP be warned...


> Good luck.
> Dr. Vitaly Chaban


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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