[MMTK] a few questions about normal mode calc

khinsen at cea.fr khinsen at cea.fr
Wed Jul 13 11:27:51 CEST 2005


On 13.07.2005, at 03:34, OMAR NABEEL ALY DEMERDASH wrote:

> 1.)  When I try to run the attached script, I get the following error
> message:
>
> Traceback (most recent call last):
>   File "<input>", line 1, in ?
>   File "/Users/omar/Desktop/fastnm_write_pdb2.py", line 13, in ?
>     from MMTK.ForceFields import DeformationForceField
>   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/
> python2.4/site-packages/MMTK/ForceFields/__init__.py", line 23, in ?
>     'force_fields')).readlines()
> IOError: [Errno 13] Permission denied: '/Library/Frameworks/
> Python.framework/Versions/2.4/lib/python2.4/site-packages/MMTK/
> ForceFields/force_fields'

Apparently you are using MacOS and the precompiled binary modules from  
the Web site. Please download and install it again, that should fix  
that problem, which is due to a missing read permission on a particular  
file.

You can also fix the problem by changing the permissions on the file

/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/MMTK/ForceFields/force_fields

to allow everyone read access.

> 2.)  What would be the simplest way to write the eigenvectors to
> individual files?

That depends on what you want to do with them later on. You can write

	modes[i].array

to a binary or text file, that will get you just the eigenvector  
components, but their interpretation out of context is a risky  
business.

> 3.)  On page 114 of the MMTK instruction manual, it states that since
> the normal mode vectors are not mass-weighted, they are not orthogonal
> to each other.  Aren't the eigenvectors of a symmetric matrix such as
> the Hessian always orthogonal in a Cartesian basis?

Yes, but after diagonalization, MMTK undoes the mass weighting in order  
to have normal mode vectors that can be interpreted directly as  
coordinate displacements. After that operation, the vectors are no  
longer orthonormal as they are no longer the eigenvectors of a matrix.  
Note that there are some changes in MMTK 2.5 in this respect.

Konrad.
--
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Konrad Hinsen
Laboratoire Leon 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: khinsen at cea.fr
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