[gmx-users] Fwd: gmx-users Digest, Vol 79, Issue 102

Silvia Crivelli SNCrivelli at ucdavis.edu
Sun Nov 14 19:56:35 CET 2010

We have a visualization tool that allows us to visualize the changes  
in the energy during energy minimization.
The areas with more intense color are those where the atoms contribute  
the most to the total energy value.
I just wrote a plug-in to use Gromacs for energy minimizations (or MD  
simulations) and I need the per-atom energies
to use our tool's energy visualization feature.

Thanks again,

> Message: 3
> Date: Sun, 14 Nov 2010 06:31:56 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] how to calculate per-atom energies
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CDEE7AC.9020305 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> On 14/11/2010 5:58 AM, Silvia Crivelli wrote:
>> Hello,
>> When I run energy minimization, I'd like to obtain the energy per  
>> atom
>> in addition to the (potential) energy value for the entire protein.
>> Is there a way to do this?
> You can get the nonbonded energy per energy group, which you could
> define to be a single atom, but you are limited to 256 of such groups,
> and to not using PME. Otherwise, there are approaches involving a  
> lot of
> hacking about with .top or .tpr files and using mdrun -rerun that  
> could
> do this for both nonbonded and bonded.
> However, a more important issue before doing such work is to be sure
> about what you expect such a decomposition to tell you. A high or low
> energy for a given atom doesn't necessarily mean anything, and even if
> it did, the force field wasn't necessarily parametrized to produce
> reliable per-atom energies (though it probably does do so).
> Mark
> ------------------------------

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