Re: [AMBER] How to print the total Potential Energy for an atom?

From: Matias Machado <>
Date: Fri, 05 Jul 2019 17:57:27 -0300 (UYT)

I remember a long, long time ago (and probably in a galaxy far, far away) there used to be two commands named "anal" and "carnal" (yeap! no comments plz), which somehow could split the energy components and contributions from a set of atoms, but were deprecated...

Maybe cpptraj commands "energy" or "esander" could be of some help... I ignore weather calculations are done accounting for remaining atoms in the system... read the manual for consideration on PBC and PME...



PS: pffff... I'm getting old... :-/

Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "David A Case" <>
Para: "AMBER Mailing List" <>
Enviados: Viernes, 5 de Julio 2019 11:57:03
Asunto: Re: [AMBER] How to print the total Potential Energy for an atom?

On Thu, Jul 04, 2019, Biplab Ghosh wrote:

>For some reason, I want to print the total potential energy (EP) at a given
>time (T) for all atoms present in the structure of the protein being
>simulated, i.e., EP(atom no., T).

The potential energy is not a sum of terms that can be assoicated with
each atom (nor even one that can be broken into terms for pairs of
atoms.) So what you want doesn't have any (simple?) solution.


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