[gmx-users] normal mode analysis.

[Bert de Groot]

Nguyen Hoang Phuong wrote:
> 
> Dear All,
> 
> I used the GROMACS program to do normal mode analysis for my molecule in
> vacuum. After energy minimization, Fmax = 10^-6. However, the eigenvectors
> obtained from diagonalization of the Hessian at the lowest energy
> structure (at Fmax = 10^-6) are not othogonal with each other. For
> example, V1.V2 = 0.0006 where V1 and V2 are two eigenvectors. This number
> is considered to be large compared to zero. Does anyone have the same
> observation? Thanks.
> 

how did you calculate the inner products? AFAIK, g_anaeig does not write out
individual innner products. Are you sure that your value of 0.0006 is severe
compared to machine precision? (remember you're adding 3N numbers, each
with limited precision)


Besides, the eigenvectors should be orthogonal irrespective of the value 
of Fmax (you'll get negative eigenvalues when you're not close enough to 
a minimum though).

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________