[MMTK] Normal Modes

vanitha@cs.wisc.edu vanitha at cs.wisc.edu
Fri Mar 24 17:48:06 CET 2006

I am using an all-atom force field to do my minimization. And I need to
add the normal mode vector to the gradient of the energy (w.r.t. cartesian
co-rodinates of all atoms). I'd have vectors of differing lengths if I
apply the normal mode calulation to just the C-Alpha model. I have to
think about whether I can minimize the C-alpha model to begin with!

> 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.
> --
> ---------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------

More information about the mmtk mailing list