[MMTK] ask for help!

Ramon Crehuet rcrehuet at gmail.com
Mon Nov 5 08:37:30 UTC 2012

Dear 子茗,
The hessian matrix is the second derivative matrix of the energy. So you
have to decide which energy (i.e. force field) to use. Some require a
longer setup than others. And they have different strengths and weaknesses.
There are examples in the MMTK web page on how to setup a calculation and
one on the normal modes with a coarse grained force field (Calpha). Normal
modes are the eigenvectors of the hessian, so that is a good place to start.
When asking a question to the list you have to be more specific in you
question. In fact, you have to implicitly show that you have gone through
the documentation and the examples and that you couldn't find an answer
there. If you have just started using MMTK (or any other software) you have
to learn how it works. Don't expect to solve your specific problem just
typing a few lines.
Hope this helped.
Ramon Crehuet

2012/11/4 子茗 <810918909 at qq.com>

> I am new to MMTK so I write it for help!
> I want to get the Hessian matrix for a given protein which comes from
> protein data bank. And now I just do not know what to imput to the commond
> window to get the matrix.
> so would you help me out? please tell me how to do,thanks!
> _______________________________________________
> mmtk maillist  -  mmtk at starship.python.net
> http://starship.python.net/mailman/listinfo/mmtk
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