[gmx-users] non isotropic kinetic energy

Berk Hess gmx3 at hotmail.com
Tue Sep 15 14:00:17 CEST 2009

Yes, we can agree that they are rigid bodies.

I would say that you should get equipartitioning of rotational
degrees of freedom.
g_traj can compute rotational kinetic energies.
For you whole system you would have to make each water
an index group, select each water in g_traj and add all number up.


> Date: Tue, 15 Sep 2009 12:57:59 +0200
> From: alexander.herz at mytum.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] non isotropic kinetic energy
> Berk Hess schrieb:
> > Equipartitioning only works per degree of freedom, not per atom.
> >
> > It works for translation and rotation of a water molecule,
> > but that requires a transformation from atomic to COM trans and rot
> > coordinates.
> Agreed. As said, we have performed this transfomation using another self
> made tool.
> Still, after this transformation rotational energy is not equidistributed.
> Can we agree that using constraints or a rigid body approach (so maybe
> using quaternions) should
> give the same physics (so the same equipartition rules should apply to
> both systems)?
> Or if we cannot agree on this, what kind of physical objects are
> constraint waters if not rigid bodies?
> Alex
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