Hi Ankita, No, the file contains the 3Nx3N covariance matrix, row by row, split over triplets, mass weighted if you did the analysis mass-weighted. But for C-alpha only there is no difference between mass-weighted and non-mass-weighted, except for global scaling.
Cheers, Tsjerk On Mon, Jul 1, 2013 at 8:46 AM, Ankita naithani <ankitanaith...@gmail.com>wrote: > Hi Tsjerk, > > Coffee is always magical, I tell you. Just a sniff in the air and it makes > things clear. > > So, 1/n sum is the mass weighted ness? And x1 to zn spans from 1 to 1992? > > By any chance we don't obtain a file I. Which the first column wud have > alpha atom one second column would have 2nd aloha atom n third would have > correlation between them? > > > > Kind regards, > > Ankita > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > Hi Ankita, > > > > I should not answer questions before coffee!! Sorry. > > > > It's the covariance matrix! So it's > > > > 1/n sum x1x1 1/n sum x1y1 1/n sum x1z1 > > 1/n sum x1x2 1/n sum x1y2 1/n sum x1z2 > > ... > > 1/n sum zNxN 1/n sum zNyN 1/n sum zNzN > > > > Silly me :| > > > > Tsjerk > > > > > > On Mon, Jul 1, 2013 at 8:09 AM, Ankita naithani < > ankitanaith...@gmail.com<javascript:;> > > >wrote: > > > > > Hi Tsjerk, > > > Thank you for your reply. So, these are the eigenvectors. By any > chance, > > > can we obtain the covariance matrix containing the information of > residue > > > fluctuations I.e. the covariance information. Actually, it was needed > to > > > obtain the dot plot delta ri dot delta rj so I don't think so I can use > > the > > > eigenvectors > > > > > > > > > Kind regards > > > > > > Ankita > > > > > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > > > > > Hi Ankita, > > > > > > > > The fie contains the eigenvectors as > > > > > > > > x1 y1 z1 > > > > x2 y2 z2 > > > > ... > > > > xN yN zN > > > > > > > > Hope it helps, > > > > > > > > Tsjerk > > > > > > > > > > > > On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani < > > > ankitanaith...@gmail.com <javascript:;><javascript:;> > > > > >wrote: > > > > > > > > > Hi, > > > > > > > > > > I wanted to know the exact format of covariance.dat file as > generated > > > by > > > > > g_covar during covariance analysis. The file format mentioned in > the > > > > manual > > > > > was not quite clear to understand. I need to use the matrix > > > information n > > > > > so needed to know how the data is stored. My matrix is for 1992 > > calpha > > > > > atoms. > > > > > > > > > > It would be really helpful if someone could explain the file > format. > > > > > > > > > > Kind regards, > > > > > > > > > > Ankita > > > > > > > > > > > > > > > -- > > > > > Ankita Naithani > > > > > -- > > > > > gmx-users mailing list > > > > > gmx-users@gromacs.org<javascript:;><javascript:;> > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > > www interface or send it to gmx-users-requ...@gromacs.org > <javascript:;> > > <javascript:;> > > > > . > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > > -- > > > > Tsjerk A. Wassenaar, Ph.D. > > > > -- > > > > gmx-users mailing list > > > > gmx-users@gromacs.org<javascript:;><javascript:;> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > www interface or send it to gmx-users-requ...@gromacs.org > <javascript:;> > > <javascript:;>. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > -- > > > Ankita Naithani > > > -- > > > gmx-users mailing list gmx-users@gromacs.org <javascript:;> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org<javascript:;> > > . > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > gmx-users mailing list gmx-users@gromacs.org <javascript:;> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org<javascript:;>. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > Ankita Naithani > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists