[gmx-users] Regarding obtaining potential energy using energy groups

Najamuddin Memon najamuddinmemon63 at gmail.com
Sat Sep 14 20:39:40 CEST 2019

No you should take two groups at a time
Like A VS B then A vs C and so on before doing energy analysis you should
make index file that you have to call in command line with -n index.ndx

On Fri, Sep 13, 2019, 3:21 PM Nirali Desai <nirali.d.imsc14 at ahduni.edu.in>

> Dear all
> I have a system with 3 protein chains A B and C. I want to calculate the
> potential energy between different chains.
> I created energy groups by creating a new index file.
> If I calculate potential energy between  C as one group and (AB) as another
> group, will it contain the potential energy of interaction between A and B
> too?
> Your kind guidance in this matter is highly appreciated.
> Thanking you,
> Nirali Desai
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