[MMTK] Vectorfield and normal modes

Konrad Hinsen hinsen at cnrs-orleans.fr
Sat May 5 13:36:37 UTC 2007


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.

> 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.

Konrad.
--
---------------------------------------------------------------------
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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