[MMTK] hi

Konrad Hinsen research at khinsen.fastmail.net
Mon Nov 5 14:36:53 UTC 2012


子茗 writes:

 > >>> hess=energyAndhess[1].array
 > now I get the hessian matrix using the all-atom forcefield,next,how can I put this
 > matrix into a file for later use?

You don't say what your "later use" is. Assuming that you just want to load
the data again into another Python session, the simplest solution is to use

     save(hess, "hess.pickle")

You can save any Python object to a file in this way. However, the file format
is specific to Python, so you cannot easily read the data into other programs.

 > modes=NormalModes(universe)
 > from this command I can get the modes of the protein, the same question is how can I
 > save the frequency and eignvector of each mode to a file, and how can I visualize the
 > modes use VMD?

For saving to a file, use the same as above:

    save(modes, "modes.pickle")

For visualizing a single mode using VMD:

    modes[6].view()

assuming you have set the environment variable PDBVIEWER correctly as
explained in the MMTK manual.


You might want to study my tutorial on normal modes, which contains
many examples:

   http://dirac.cnrs-orleans.fr/plone/Members/hinsen/courses-and-lecture-notes/embo-course-on-biomolecular-simulations/embo-course-2010

Konrad.
-- 
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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: research AT khinsen DOT fastmail DOT net
http://dirac.cnrs-orleans.fr/~hinsen/
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