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

[Vitaly Chaban]

>
> 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...

Good luck.

Dr. Vitaly Chaban
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