[MMTK] Vectorfield and normal modes

Ramon Crehuet rcrehuet at gmail.com
Fri May 4 16:43:34 UTC 2007


Hi,
This is a continuation of a post by Vanitha:
http://starship.python.net/pipermail/mmtk/2006/001103.html
Where Konrad suggested the use of vector fields to generate the position of
all atoms from the Calpha normal modes.
Before trying that I experimented a little with AtomicVectorField and the
Calpha model for which I have calculated the modes. I expected these two
setConfiguration to correspond do the same but they don't:

origin = uni.copyConfiguration()
field = AtomicVectorField(uni, 0.1, mode)
uni.setConfiguration(origin+field.particleValues()*delta/mode.frequency)
uni.setConfiguration(origin+mode*i*delta/mode.frequency)

(mode is a normal mode)

So how can I get the same desplacements that originate from the mode using
the AtomicVectorField? (then I'll be able to apply it to the all atom model)
Thanks!
Ramon
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