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

Mark Abraham mark.j.abraham at gmail.com
Tue Apr 16 10:59:03 CEST 2019


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.


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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