[gmx-users] Extracting C-alpha component from all-atom Hessian matrix
zhoumadison at gmail.com
Thu Sep 21 21:52:24 CEST 2006
I have been working on extracting the C-alpha component from the
all-atom Hessian matrix, according to the
equation proposed initially by Berk, H'=Hxx-HxyHyy-1Hyx. It worked
quite nice in my hand and for
a test protein, there is almost no visual difference in the
confromational changes described by the eigenvectors
between two methods (all-atom normal mode or C-alpha only).
I am wondering whether there is a reference for this equation? Is it
based on Gram-Schmidt formula for deriving a
new set of vectors? There was a old paper by Brooks and Karplus (J.
Comp. Chem., 1995) gave a detailed description
of the normal mode analysis and prosposed a methods for extracting
dihedral angle normal modes. So is there any
difference between the method they proposed and equation mentioned above?
Thank you for the help.
[gmx-users] Normal Mode Analysis on Calphas only ?? *Berk Hess* gmx3 at
*Wed May 18 08:42:23 CEST 2005*
- Previous message: [gmx-users] Normal Mode Analysis on Calphas only
- Next message: [gmx-users] Normal Mode Analysis on Calphas only ??
- *Messages sorted by:* [ date
Here is the formula (thanks to Herman Berendsen).
I was slightly wrong. You first need to reduce the Hessian
and then diagonalize the C-alpha only Hessian.
Interesting particle coordinates: x
Uninsteresting particle coordinates y
full hessian in terms of (x, y): H
Split H into four blocks:
Then the hessian H' in the subspace of x coordinates, under the condition
that the y coordinates are in a minimum, is
H' = Hxx - Hxy Hyy^-1 Hyx
This is a simple transformation, requiring only one inversion and two matrix
FREE pop-up blocking with the new MSN Toolbar - get it now!
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users