[MMTK] question about implementing ccbb

Konrad Hinsen hinsen at cnrs-orleans.fr
Wed Mar 21 08:27:16 UTC 2007


On 20.03.2007, at 21:55, Qing Yuan wrote:

> I learned about mmtk not very long ago, and wanted to use to implement
> the Continous Configuration Boltzmann Biased Method for generating
> inital structure for large polymer molecules. I am not sure what is
> the best approach. Could someone offer me some advice ?

I don't know much about the method, other than that it is a Monte- 
Carlo approach. I suggest the following steps to get started:

1) Make sure you can calculate the potential energies of your  
polymers in MMTK. You will probably have to define force field  
parameters, maybe even new force field terms.

2) Write Python functions that perform the conformational changes  
used in the method (which I don't know), unless of course those  
functions already exist (i.e. changes of Cartesian coordinates of  
groups of atoms or of individual internal coordinates).

3) Implement the Monte-Carlo integrator in Python.

4) Make sure it works...

5) ... and only then check performance. If you are not happy with  
performance, look into rewriting the conformational changes in Pyrex  
first.

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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