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 -- Marcus Kubitzki Max Planck Institute for Biophysical Chemistry Computational Biomolecular Dynamics Group Am Fassberg 11 D-37077 Göttingen Germany phone: ++49-551-2012312 fax: ++49-551-2012302 Email: mkubitz[at]gwdg.de www: http://www.mpibpc.mpg.de/groups/de_groot/ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
