[MMTK] Two proteins in a universe

konrad.hinsen@laposte.net konrad.hinsen at laposte.net
Fri Feb 24 11:34:51 CET 2006

On Feb 23, 2006, at 19:33, vanitha at cs.wisc.edu wrote:

> Thanks. If Protein 1 has N atoms, and Protein 2 has M atoms, the
> configuration vector will then be a 3(N+M) X 1 vector. Can I safely  
> assume
> that the first 3N X 1 entries will correspond to Protein 1 and the  
> last 3M
> X 1 entries will correspond to Protein 2 provided Protein 1 was  
> added to
> the universe before Protein 2.

No. I do not recommend to make any assumption about the internal atom  
indices. Even if what you assume may be true today, I don't promise  
it will be true in the next release.

If you want to do operations on configurations that affect only the  
atoms of a particular protein, you can use masks:

	mask_protein1 = protein1.booleanMask()
	new_conf = conf + mask_protein1 * (delta_t*velocities)

You can also use the boolean mask to obtain the atom indices  
corresponding to some object, for working at the level of arrays.

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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