[MMTK] [Fwd: Re: Normal Modes]

vanitha@cs.wisc.edu vanitha at cs.wisc.edu
Fri Mar 24 18:50:18 CET 2006


---------------------------- Original Message ----------------------------
Subject: Re: Normal Modes
From:    vanitha at cs.wisc.edu
Date:    Fri, March 24, 2006 11:49 am
To:      "Konrad Hinsen" <konrad.hinsen at cea.fr>
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That sounds very interesting. I see AtomicVectorField(..) defined in
Field.py. Do you have any examples in MMTK that demonstrate it's use?

Thanks,

- Vanitha

> On Mar 24, 2006, at 17:48, vanitha at cs.wisc.edu wrote:
>
>> I am using an all-atom force field to do my minimization. And I
>> need to
>> add the normal mode vector to the gradient of the energy (w.r.t.
>> cartesian
>> co-rodinates of all atoms). I'd have vectors of differing lengths if I
>> apply the normal mode calulation to just the C-Alpha model. I have to
>> think about whether I can minimize the C-alpha model to begin with!
>
> There are ways to extend a C-alpha mode vector to an all-atom
> displacement vector by interpolation. For example, you can create an
> AtomicVectorField from the C-alpha displacements and set the
> displacements of the all-atom model to the values of that field at
> the atom positions. That yields a spatial interpolation of the
> displacement vectors. Of course I cannot judge if this is a
> physically reasonable approach in your application.
>
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire Léon Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: konrad.hinsen at cea.fr
> ---------------------------------------------------------------------
>
>
>
>






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