Hi Prasad, You also have to reckon that the RMSD is always positive, so the average RMSD will also always be positive. It's a chi-variate. Try some thought experiments with distances, average distances and distances to an average position.
Cheers, Tsjerk On Jan 10, 2008 8:09 PM, David van der Spoel <[EMAIL PROTECTED]> wrote: > Prasad Gajula wrote: > > Dear Dr. David, > > Thank you very for the reply. > > When i looked the energy minimized average structure it looks just fine. > > ?? > but you did not say energy minimized... check the rmsd between average > and minimized average structure as well. > > Maybe you want to do a clustering analysis instead? > > > > > >>> I calcualted the average structure from the simulation trajectory. > when > >>> I > >>> calculate the rmsd of the protein to this average sturture, it is > giving > >>> average rmsd of 0.16 nm. But, it is not clear for me why the average > >>> sturcture is never adapted rmsd near (or equal) to zero. I did not > >>> calculate the rmsd with respect to the starting structure either. > >>> Any clue? > >> the average structure is unphysical, it may have long bonds etc. > >> > > > > _______________________________________________ > > 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 > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > 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
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