Hi Nikhil, Try extracting the frame just before and just after the jump and view them in pymol/vmd/rasmol/... to check for a possible cause.
Cheers, Tsjerk On Fri, Sep 25, 2009 at 5:50 AM, nikhil damle <[email protected]> wrote: > Yes. I am correcting the trajectory for periodicity > > Regards, > Nikhil > > ________________________________ > From: Justin A. Lemkul <[email protected]> > To: Discussion list for GROMACS users <[email protected]> > Sent: Wednesday, 23 September, 2009 3:48:47 PM > Subject: Re: [gmx-users] Probelm of g_rms > > > > nikhil damle wrote: >> Hi all, >> >> I am facing the problem while calculating backbone RMSD over 30 ns. >> upto ~6-7 ns g_rms gives correct RMSDs and later all RMSD values are >> unexpectedly and unusually high (within 20 ps RMSD value shoots up by ~8A). >> But when i calculate RMSD using g_confrms programme, it gives me expected >> and usual RMSD. I tried running g_rms separately for that particular time >> range which was giving me high values only to get same result once again. Is >> there problem with g_rms or i am calculating wrongly ? >> > > Are you correcting the trajectory for periodicity? > > -Justin > >> Regards, >> Nikhil >> >> ------------------------------------------------------------------------ >> Connect more, do more and share more with Yahoo! India Mail. Learn more >> <http://in.rd.yahoo.com/tagline_galaxy_3/*http://in.overview.mail.yahoo.com/>. >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.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 > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.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 > > ________________________________ > Connect more, do more and share more with Yahoo! India Mail. Learn more. > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.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 > -- 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://lists.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
