[MMTK] Vectorfield and normal modes

Ramon Crehuet rcrehuet at gmail.com
Sat May 5 15:40:14 UTC 2007

2007/5/5, Konrad Hinsen <hinsen at cnrs-orleans.fr>:
> On 04.05.2007, at 18:43, Ramon Crehuet wrote:
> > 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)
> A VectorField is defined on a regular grid. When the VectorField
> object is created, its values at the grid points are calculated as a
> weighted combination of the atomic vectors. When a value is requested
> at another point, it is calculated through linear interpolation. In
> general this does not yield exactly the same values at the positions
> of the atoms.

Surely I understand this, but both operations give results quite different
(the VMD images are quite different). Maybe the scale of mode and field is

> 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)
> I don't see any way to obtain exactly the same values and still get
> reasonable values at other points. If you need to retrieve the exact
> values for each input atom, then you should use an interpolation
> algorithm that is not grid based. You could for example assign to
> each atom the average value of its three nearest C-alpha neighbours,
> weighted by the distance from each C-alpha. This can be implemented
> efficiently by using the nonbonded list object from the force field
> module, with a cutoff of about 5 Ang. This is a bit tricky to use;
> see Tests/energy_tests.py for an example.

I don't need an exact result, I was just comparing the results for my
understanding of the operations. Anyway, reducing the grid space should make
the field value tend to the mode value, isn't it?

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