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
--
========================================
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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