On 15/11/2010 5:56 AM, Silvia Crivelli wrote:
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.
Such a tool is all very nice, but what is it good for? If you apply it
to EM on a TIP3P water box, then you'll see that every oxygen
contributes more to the total energy than every hydrogen, because they
have a VDW interaction. However that was known already...
Anyway, as I mentioned in my first email, there are approaches to do the
decomposition, but GROMACS is not engineered to make this easy, because
that would severely compromise performance. Even if that were not true,
making the decomposition would be vastly more work than it is worth.
Mark
Thanks again,
Silvia
Message: 3
Date: Sun, 14 Nov 2010 06:31:56 +1100
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] how to calculate per-atom energies
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4cdee7ac.9020...@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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