[MMTK] Normal Modes results question

Matias Saavedra matias_saavedra at yahoo.com
Wed Jan 11 06:19:29 CET 2006


Hi Konrad,

I would like to know a few things about the results of
a normal modes analysis:

1) the method fluctuations() applied to modes objects
gives what? the result is the average of the atomic
displacements between all modes?

2) What is the difference between the norm() and the
length() method? I can see that the length method
gives the length of the displacement vectors of each
atom for a given mode... but i can't relate this
concept with the norm. The norm is a sort of average
between the lengths of the displacement vectors of
each atom for a given mode? The length really contains
the atomic displacements?

3) which is the data i have to collect in order to
obtain the magnitude of the atomic displacements in
each mode?

4) It is possible to designate the desplacements to
the residues in stead of the atoms? (for example to
know which residue moves the most in a given mode)

Thanks a lot,

Matias



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