[gmx-users] Total energy for a group of molecule

[Justin Lemkul]

On 11/2/12 11:35 AM, Hanne Antila wrote:
> Dear experts,
>
> This question has been asked several times before but so far it
> remains unanswered.
>
> I would like to calculate the total energy (kinetic plus potential)
> for a group of molecules. In my case, I would like to look at certain
> water molecules. So far, I know that I can get the kinetic energy from
> g_traj, and some of the potential energy components by defining energy
> groups and using g_energy (Coul-SR, Coul-14, LJ-SR, LJ-14). It is
> unclear for me whether this is really all the components I need? Also,

I'll repeat one of the comments that has often been made before - of what use is 
this?  One can pick a given configuration of water and calculate its energy, but 
the relevance of these configurations, in isolation, is very debatable.  There 
will be no 1-4 terms for water molecules, since they only have 3 atoms.  In 
theory, one would also need bond and angle terms for these molecules to fully 
describe the internal energy, but if using a rigid model (likely), then these 
energies will not exist.

> is there some technical reason why one doesn't get the average group
> kinetic/potential/total energy directly from g_energy by defining
> energy groups?
>

The size of the .edr file would explode.  Since one can already get kinetic 
energy for a group using g_traj with a .trr file, there is no point to the 
redundancy.  I also recall reading about technical problems with doing this 
(especially in decomposing bonded terms and pairwise energies), but I can't 
point you directly to that post.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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