[gmx-users] non isotropic kinetic energy

herz alexander.herz at mytum.de
Tue Sep 15 12:00:23 CEST 2009

> Have you tested the equipartitioning per atom? This must be correct.
We have done per atom (here of course only ekin is available). Here the
average ekin parallel to the interface deviates from the ekin
perpendicular to the interface (this is the data in the zip file of the
old mail).

You could use quaternions to do water as rigid body or eule angles or
some other scheme of your choide, there are many.
Generally, the EOM of any rigid body can be completely described using
this view (COM motion+rotation around COM), afaik.
So we analyzed the rotation around COM and the translational velocity of
the COM of each water molecule
(in addition to the per atom calcs). Here the rotational energy is not
equidistributed (translational is) for interfacial systems.
The com motion+rotation describtion is a physically valid describtion of
this kind of system.
If the constraints are not equivalent then this would be a real problem.

Unless of course, there is some error in my reasoning :)
> To make water move as a rigid body one would probably need to
> determine the force and torque on the center of mass and use that to
> integrate the equations of motion. A quaternion description of rigid
> water would do this I presume. Did you analyze the EkRot around the
> center of mass of the molecule?
> Whether or not a quaternion is equivalent to a constrained atomic
> system I do not know, but Berk's answer below seems to indicate it is
> not.


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