[MMTK] native-centric potential

[Konrad Hinsen]

On 08.11.2007, at 14:42, Sanzo Miyazawa wrote:

> I am interested in simulations of proteins
> consisting of Calpha atom only
> with a native-centric potential, such as
> the Go-type potential, with/without a Langevin force.
>
> Is it easy to make a simulation program, for example,
> by modifying a program for Calpha normal mode analyses?

You could use all the machinery for constructing the protein etc.  
exactly as in the examples for C-alpha normal mode analysis. You  
could also use the Langevin integrator that comes as an example with  
MMTK.

What you would have to add is the Go-type potential. I have never  
used such potentials, so I do not know how one would best go about  
implementing them.

Good luck,
   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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