[MMTK] undefined functions in effectiveMassAndForceConstant

ra.biehl ra.biehl at fz-juelich.de
Tue May 10 16:37:49 UTC 2011


Hi Konrad

using the example
Fast normal modes for large proteins using an elastic network model
 and trying
modes[7].effectiveMassAndForceConstant()
gives an error
AttributeError: 'VibrationalMode' object has no attribute
'massWeightedProjection'
in MMTK 2.7.1 but 2.7.4 looks the same.

There seem to be 2 undefined functions in NormalModes/Core.py  module
Mode line 85

    def effectiveMassAndForceConstant(self):
        m = self.massWeightedProjection(self)/self.projection(self)
        k = m*(2.*N.pi*self.frequency)**2
        return m, k

massWeightedProjection and projection

should this be the factor "f" from

 def scaledToMassWeightedNorm(self, norm):
        f = norm/self.massWeightedNorm()
        return ParticleVector(self.universe, f*self.array)

f is temperature independent and around the average mass of protein
atoms (around 7)


Best Ralf




--

Dr. Ralf Biehl
Jülich Centre for Neutron Science (JCNS-1) &
Institute for Complex Systems (ICS-1)
Forschungszentrum Jülich
52425 Jülich
Germany

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Email:  ra.biehl at fz-juelich.de
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