[gmx-users] calculation of pair wise interaction energy of residues

[SHAHEE ISLAM]

thank so much for your reply. Is there any loop which i can use to
calculate all the residue pair wise interaction energy. So all the data can
be handled.


On Tue, Apr 16, 2019 at 2:29 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You have to compute all the pairwise interactions if you want to compare
> all the pairwise interactions.
>
> But I'm deeply skeptical that you can learn anything from this anyway. The
> potential energy of typical force fields is not constructed to be
> decomposable, and such an analysis neglects the entropic component of the
> free energy anyway.
>
> Mark
>
> On Tue, 16 Apr 2019 at 07:52, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
>
> > hi,
> > Is it possible to calculate pair wise interaction energy of each residue.
> > My protein consist of 129 residue. Because if i mention each residue as a
> > group in mdp file then i will get a huge number of data. Which is very
> > difficult to handle.
> > Can anyone please suggest me how i can do this.
> > Thanking you
> > Shahee
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