Hi Tangj Jioawei, Erik. This is due to periodic boundary conditions. Make sure your molecules stay together (clustered/nojump) before determining the rmsd. Use trjconv...
Tsjerk On 9/27/07, Erik Marklund <[EMAIL PROTECTED]> wrote: > My first guess, without knowing how you used g_rms, is that the larde rmsd > for certain subunits is due to inadequate roto-translational fit prior to > rmsd-calculation. Does that help? If not, please be more explicit about what > you aim to do and what you have done. > > /Erik > > > 27 sep 2007 kl. 11.29 skrev TANG JIAOWEI: > Dear all, > I am studying on a big protein with 16 subunits and when i used g_rmsd to > one subunit of the protein, the result seems strange that the structure of > the subunit changes much but it should not.. I searched the mailing list and > it may be caused by the periodic thing. Could you tell me how to remove the > periodic thing in detail before i use g_rmsd. > > Thank you > > Tang jiaowei > _______________________________________________ > 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 > > _______________________________________________ > Erik Marklund, PhD student > Laboratory of Molecular Biophysics, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys > > > _______________________________________________ > 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 > -- 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
