[gmx-users] a qiestion about using g_cluster

Marcus Kubitzki mkubitz at gwdg.de
Wed Aug 29 21:30:35 CEST 2007

Hi Li,

> I think g_cluster will do a removing of translation and rotation 
> displacement automatically. I am not quite sure whether it will do such 
> part on the group of atoms I pick in the index file? If so is there any 
> way I can specify which region to do the removement or if I can simply 
> turn off the removement?
By default, g_cluster performs a least squares fit before clustering.
The fitting *and* the clustering is done on the one group you specify.
With g_cluster -nofit fitting can be switched off.

> I am asking this becuase what I really want to 
> do is to fit all the snapshots by their cores and then clusterize the 
> loop comformations. Even if I can just switch off the fitting, it will 
> be good enough since I can use other routines to fit first.
Fitting the trj first to the core and using g_cluster with -nofit on the
core-fitted trj should work.


Marcus Kubitzki
Max Planck Institute for Biophysical Chemistry
Computational Biomolecular Dynamics Group
Am Fassberg 11
D-37077 Göttingen
phone: ++49-551-2012312
fax: ++49-551-2012302
Email: mkubitz[at]gwdg.de
www: http://www.mpibpc.mpg.de/groups/de_groot/

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