[gmx-users] Total energy for a group of molecule
jalemkul at vt.edu
Sat Nov 3 15:02:07 CET 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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