[MMTK] hi

子茗 810918909 at qq.com
Mon Nov 5 12:56:46 UTC 2012


Hi friends:
 I want to use MMTK to do some work about normal mode analysis,accurately I want get the hessian matrix of the energy function.however I'm a freshman so there are many thing I can not figure out.
 first I input some code like these:
 from MMTK import *
>>> universe.protein=Protein('bala1')
 >>> minimizer=ConjugateGradientMinimizer(universe,actions=[StandardLogOutput(50)])
>>> minimizer(convergence=1.e-3,steps=10000)
 >>> energyandhess=universe.energyAndForceConstants()
>>> 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?
  
 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?
 thaks!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://starship.python.net/pipermail/mmtk/attachments/20121105/0be9549f/attachment.html>


More information about the mmtk mailing list