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

From: Brian Radak <>
Date: Tue, 29 Oct 2013 17:24:52 -0400

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.


On Tue, Oct 29, 2013 at 4:37 PM, Jose Borreguero <>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
> _______________________________________________
> AMBER mailing list

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Received on Tue Oct 29 2013 - 14:30:02 PDT
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