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

[Najamuddin Memon]

It depends on interaction of proteins i.e A interacts with B
A&B both interact with C
Only A or only B interacts with C
In 2nd option you can make one group (A&B) and 2nd group as C

On Sun, Sep 15, 2019, 12:28 AM Nashit Jalal 17250017 <
nashit.jalal at iitgn.ac.in> wrote:

> I think so that the question is to confirm whether finding potential energy
> making (AB) and C as 2 groups similar to the potential energy obtained by
> adding energies obtained by making A -C and B -C as groups
>
> -Nashit
>
> On Sun, Sep 15, 2019 at 12:10 AM Najamuddin Memon <
> najamuddinmemon63 at gmail.com> wrote:
>
> > 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
> > Regards
> > Najam
> >
> > On Fri, Sep 13, 2019, 3:21 PM Nirali Desai <
> nirali.d.imsc14 at ahduni.edu.in>
> > wrote:
> >
> > > 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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