Hi, On Sat, Jan 24, 2009 at 12:04 PM, nishtha pandey <[email protected]> wrote: > Hello everyone, > While trying to do the RMSD analysis of my trajectory > file I am facing the error " Too many iterations in routine JACOBI". I have > gone through the archives which suggests that such problem arises if there > is mismatch between the reference structure and trajectory. However in my > case the problem lies somewhere else because, using the same .tpr file and > .trr file I have done RMSD analysis earlier also and it worked fine.
The .tpr and the .trr files will correspond per definition, provided the former is used to generate the latter. This is not the case for the .xtc. My guess is you do have a mismatch. Did you specify xtc-grps? In that case you might want to extract a corresponding reference structure from your .tpr. Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
