[MMTK] Segmentation fault, normal modes calculation

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu Jan 11 13:46:48 UTC 2007

On Jan 11, 2007, at 12:00, Konrad Hinsen wrote:

> My suggestion for handling your big protein is to switch to a  
> different algorithm, which requires only two changes:

Make that "SparseMatrixSubspaceNormalModes" instead of  
"FiniteDifferenceSubspaceNormalModes". The latter uses numerical  
derivatives, which won't work with DeformationForceField because the  
latter always yields zero forces. However, it is a short-range force  
field, so using a sparse matrix representation should keep memory  
requirements much smaller.

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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 2745 bytes
Desc: not available
Url : http://starship.python.net/pipermail/mmtk/attachments/20070111/36defd4d/attachment.bin 

More information about the mmtk mailing list