[MMTK] Two proteins in a universe

[konrad.hinsen@laposte.net]

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.
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Konrad Hinsen
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E-Mail: konrad.hinsen at cea.fr
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