[gmx-users] how to calculate per-atom energies

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 13 20:31:56 CET 2010

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).


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