[gmx-users] subspaces / cov. matrices overlap

Bert de Groot bgroot at gwdg.de
Tue Apr 2 09:19:54 CEST 2002

Jose D Faraldo-Gomez wrote:
> g_anaeig_d -v $trr -v2 $trr2 -over -last 402 (for 134 C-alphas)
> and I always get that the 402 eigenvectors in $trr2 overlap completely wiht
> the 402 eienvetors in $trr (the overlap increases linearly), independently
> of the choice of these sets.

yes, these coordinates span the same space! Usually we take -last 5 or -last 10.
This will produce a graph (overlap.xvg) that tells you how many vectors from
one set you need to (approximately) rebuild the 5 (or 10) dimensional essential
subspace of the other.


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

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