[MMTK] Orthogonality of normal modes

Konrad Hinsen research at khinsen.fastmail.net
Thu Apr 12 15:41:53 UTC 2012


--On 12 avril 2012 13:13:04 +0200 Ramon Crehuet <rcrehuet at gmail.com> wrote:

> Hi,
> I have performed a normal mode calculation (Calpha) and I am not sure I
> understand how to scale the modes so that they are orthonormalized.

Which kind of mode do you use?

EnergeticModes: the mode vectors are orthogonal to each other, i.e.

   modes[i].dotProduct(modes[j])

is zero for i != j. For i==j, you get the thermal amplitude of the mode.

VibrationalModes: the mode vectors are in unweighted Cartesian coordinates, 
meaning they are not orthogonal. However, you have

   modes[i].massWeightedDotProduct(modes[j])

which should be zero for i == j.

For both kinds of modes, you can specify temperature=None to skip scaling 
by the thermal fluctuation amplitudes. Then you should see the norms being 
equal to one.

Konrad.




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