[gmx-users] non isotropic kinetic energy

herz alexander.herz at mytum.de
Tue Sep 15 12:57:59 CEST 2009

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?


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