[MMTK] Normal Modes

Konrad Hinsen konrad.hinsen at cea.fr
Fri Mar 24 17:16:07 CET 2006

On Mar 24, 2006, at 17:03, vanitha at cs.wisc.edu wrote:

> I ran the normal mode calculation on a protein (hetero dimer) with 400
> residues. It's past 24 hours and it's still running. I'm working on a
> Pentium 4 with Linux. Is this expected?

Assuming you are doing an all-atom calculation, you have almost 6000  
atoms, i.e. you are diagonalizing a 18000x18000 matrix that takes 2.5  
GB of memory. Assuming that your machine doesn't have that much  
physical RAM, it is swapping like crazy and will likely take many  
days for the computation. And even if you do have enough RAM, 24  
hours doesn't seem excessive for that size.

Do you really need an all-atom calculation? With a C-alpha model, it  
takes just a few minutes to handle a 400 residue protein. If you do  
need all atoms, why? That would be a guide towards choosing a method  
for getting just the lowest modes efficiently.

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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