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

Hanne Antila hanne.antila at aalto.fi
Mon Nov 5 10:56:40 CET 2012

2012/11/3 Justin Lemkul <jalemkul at vt.edu>:
> 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.

The reason I'm asking is that I'm trying to estimate the entropy of
water molecules near a DNA strand. I'm more or less following what has
been done in this article:

You are right, I don't need the internal terms. I mentioned the 1-4
terms to illustrate what one can get out by defining energy groups.

>> 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.

Yes, I suspected something like this. It would be convenient if there
would be some more freedom of choice for the energy terms, but I can
see why this might be laborious to execute.

> -Justin
> --
> ========================================
> 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
> ========================================

Thank you for the help!


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