Re: [gmx-users] Re: Covariance file format
where N is the number of atoms and n is the number of frames :p T. On Mon, Jul 1, 2013 at 8:29 AM, Tsjerk Wassenaar tsje...@gmail.com 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.comwrote: 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.comjavascript:; 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 listgmx-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.orgjavascript:; . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-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.orgjavascript:;. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ankita Naithani -- gmx-users mailing listgmx-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. -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: Covariance file format
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.comwrote: 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.comjavascript:; 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 listgmx-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.orgjavascript:; . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-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.orgjavascript:;. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ankita Naithani -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] Re: Covariance file format
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.comwrote: 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.comjavascript:; 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.orgjavascript:;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.orgjavascript:;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 listgmx-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.orgjavascript:; . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-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.orgjavascript:;. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ankita Naithani -- gmx-users mailing listgmx-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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
