[gmx-users] NMA on Calphas only / Matrix inversion routine in Gromacs ?

Marc Baaden baaden at smplinux.de
Thu Jun 16 16:18:17 CEST 2005


we are trying to implement the method to reduce the Hessian that was
indicated by Berk (see below). It requires a matrix inversion, and I
now wonder whether Gromacs provides a suitable routine for this (we
are using the CVS version).

I could find several routines in the code (invert_mat, m_inv, m_inv_gen ..),
but without a clear picture how they are used, whether they do the right
thing or not, and which one to choose.

Thanks in advance,

gmx3 at hotmail.com said:
>> You first need to reduce the Hessian and then diagonalize the C-alpha only
>> Hessian.

>> definitions: Interesting particle coordinates: x Uninsteresting particle
>> coordinates y full hessian in terms of (x, y): H

>> Split H into four blocks:

>>      Hxx    Hxy H =
>>      Hyx    Hyy

>> 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
>>  multiplications.

  Marc Baaden

 BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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