[gmx-users] ED analysis

[Bert de Groot]

vincenzo venditti wrote:
> 
> Hi Bert,
> I've used g_covar with default options and I've used the same tpr file 
> for g_covar and g_anaeig.

and also the same .xtc (or .trr) file?

> Perhaps have I to use the average.pdb file (obtained with -av option of 
> g_covar command) as reference structure for g_anaeig command?

no, g_covar stores the average (and reference) used during the covariance analysis in the
eigenvec.trr file, so this should automatically be correct.

If you can't find the mistake, please specify step by step what you've done.
(or send me (ie not the list) a minimal set of files with which the problem can be reproduced).

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________