# Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible?

From: Jose Borreguero <borreguero.gmail.com>
Date: Thu, 31 Oct 2013 11:45:43 -0400

I have been reading cpptraj (I'm new to it) and the issue is not clear to
me. If I manage to get a parm and trajectory file for only the two groups
of atoms that I'm interested in, and then run the trajectory in amber with
imin=5, then amber will output energies E=Ea+Eb+Eab, where:

Ea: "internal" energy of group A
Eb: "internal" energy of group B
Eab: interaction between A and B.

I am interested in Eab only. Thus, it would seem I have to get a parm +
trajectory for only atoms from group A in order to get Ea (and similarly
for group B), then do Eab=E-Ea-Eb?

-Jose

On Tue, Oct 29, 2013 at 5:24 PM, Brian Radak <radak004.umn.edu> wrote:

> Three methods come to mind:
>
> 1) use cpptraj to strip out all but the atoms you want
>
> 2) use parmed to make a new prmtop with the only the interactions you want
>
> 3) if the energy is only a function of a few distances, extract those and
> recompute it by hand
>
> All of those energies will likely be slightly different if you are using
> PME, since then the energy isn't strictly pairwise in the reciprocal sum.
>
> Regards,
> Brian
>
>
> On Tue, Oct 29, 2013 at 4:37 PM, Jose Borreguero <borreguero.gmail.com
> >wrote:
>
> > Dear Amber users,
> >
> > I was wondering whether it is possible to read and MD trajectory and
> > calculate the energy between two groups of atoms, for instance, between
> two
> > nearby amino acids. From the manual, it seems that imin=5 will read the
> > trajectory and output the energy of the whole system. Can one select the
> > atoms for which Amber should calculate the energy?
> >
> > -Jose
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
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