[MMTK] Vectorfield and normal modes

[Konrad Hinsen]

On 05.05.2007, at 17:40, Ramon Crehuet wrote:

> > 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)

...

> 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 different?

You write "mode*i" in the last line; I don't know what i is. Other  
than that, the scales should be the same. However, the interpolation  
effect is quite important. On a grid with spacing 0.1, most grid  
points will have the value zero for a C-alpha model (where the  
closest inter-atom distance is about 0.4 nm). As a result, I'd expect  
the interpolated values to be smaller than the input values.

> 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?

Yes, but at the price of getting meaningless interpolations (very  
close to zero) already at short distances from the atom positions.

Konrad.
--
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
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--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
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