Re: [gmx-users] cross correlations
Thanks a lot Sir for your help. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, Read them in as a vector of numbers and divide them into sqrt(len(vector)) rows to get yourself a nice square correlation matrix. Cheers, Tsjerk On Jun 24, 2011 3:28 PM, bipin singh bipinel...@gmail.com wrote: Hello, I have some doubts regarding the output file correl.dat as it contains 3 columns, but I am not able to get what are these column contains,I mean how to change it to the format in which I can directly plot the data to get DCCM map... For e.g in this form Res1 Res2 Correlation coefficient x yz On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar tsje...@gmail.com wrote: Of course you did.. --- *Regards,* Bipin Singh -- 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 -- 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 -- --- *Regards,* Bipin Singh -- 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] cross correlations
Hello, I have calculated the covariance matrix for C-alpha atoms(179 aa) only,but after plotting the correlation, I have observed that it is of 537X537,instead of179X179.Please suggest me how to get correlation between the C-alpha atoms only. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, Read them in as a vector of numbers and divide them into sqrt(len(vector)) rows to get yourself a nice square correlation matrix. Cheers, Tsjerk On Jun 24, 2011 3:28 PM, bipin singh bipinel...@gmail.com wrote: Hello, I have some doubts regarding the output file correl.dat as it contains 3 columns, but I am not able to get what are these column contains,I mean how to change it to the format in which I can directly plot the data to get DCCM map... For e.g in this form Res1 Res2 Correlation coefficient x yz On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar tsje...@gmail.com wrote: Of course you did.. --- *Regards,* Bipin Singh -- 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 -- 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 -- --- *Regards,* Bipin Singh -- 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] cross correlations
Hi Bipin, You have three coordinates per residue, hence a 3Nx3N matrix. Cheers, Tsjerk On Jun 25, 2011 4:40 PM, bipin singh bipinel...@gmail.com wrote: Hello, I have calculated the covariance matrix for C-alpha atoms(179 aa) only,but after plotting the correlation, I have observed that it is of 537X537,instead of179X179.Please suggest me how to get correlation between the C-alpha atoms only. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, Read... -- --- *Regards,* Bipin Singh -- 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 -- 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] cross correlations
Hello, I have some doubts regarding the output file correl.dat as it contains 3 columns, but I am not able to get what are these column contains,I mean how to change it to the format in which I can directly plot the data to get DCCM map... For e.g in this form Res1 Res2 Correlation coefficient x yz On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar tsje...@gmail.com wrote: Of course you did... Though mind the brackets :) C_ij = x_i * x_j / sqrt ( x_i ^2 * x_j^2 ) The point I want to make is that you can easily take the output from g_covar -ascii and turn it into a correlation matrix. In R (r-project.org) there is even a dedicated function for it: x - scan(covar.dat) x - matrix(x,sqrt(length(x))) y - cov2cor(x) write(y,correl.dat,ncolumns=3) Cheers, Tsjerk On Sun, Jun 19, 2011 at 12:37 PM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi, Thats actualy that i did here [1]. Extracting coordinate for every atom in interesting two group and computing C_ij = x_i * x_j / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j is vectors [1] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Sun, 19 Jun 2011 12:27:53 +0200, Tsjerk Wassenaar wrote: Hey, The method from Lange is quite a different thing. It includes non-linear correlations, which is interesting to look at for overall correlation between atoms. If the ultimate goal is to do PCA on it, then it will give you awkward components that will give you a hard time trying to interpret. There is another way, besides using an external tool. Extract the diagonal elements and take the square root of each. Then for each element [i,j] in the matrix, divide by the elements i and j of these square roots, and you'll have yourself a correlation matrix. Hope it helps, Tsjerk On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi. There is two possibilitys 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that compites general corelation coefficients 2. My utility that computes pearson correlation coefficients [2] [1] http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html [2] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but thats not what im looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu [1] Links: -- [1] mailto:kork...@wisc.edu -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing
Re: [gmx-users] cross correlations
Hi Bipin, Read them in as a vector of numbers and divide them into sqrt(len(vector)) rows to get yourself a nice square correlation matrix. Cheers, Tsjerk On Jun 24, 2011 3:28 PM, bipin singh bipinel...@gmail.com wrote: Hello, I have some doubts regarding the output file correl.dat as it contains 3 columns, but I am not able to get what are these column contains,I mean how to change it to the format in which I can directly plot the data to get DCCM map... For e.g in this form Res1 Res2 Correlation coefficient x yz On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar tsje...@gmail.com wrote: Of course you did.. --- *Regards,* Bipin Singh -- 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 -- 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] cross correlations
Hi. There is two possibilitys 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that compites general corelation coefficients 2. My utility that computes pearson correlation coefficients [2] [1] http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html [2] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but thats not what im looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu [1] Links: -- [1] mailto:kork...@wisc.edu -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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] cross correlations
Hey, The method from Lange is quite a different thing. It includes non-linear correlations, which is interesting to look at for overall correlation between atoms. If the ultimate goal is to do PCA on it, then it will give you awkward components that will give you a hard time trying to interpret. There is another way, besides using an external tool. Extract the diagonal elements and take the square root of each. Then for each element [i,j] in the matrix, divide by the elements i and j of these square roots, and you'll have yourself a correlation matrix. Hope it helps, Tsjerk On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi. There is two possibilitys 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that compites general corelation coefficients 2. My utility that computes pearson correlation coefficients [2] [1] http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html [2] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but thats not what im looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu [1] Links: -- [1] mailto:kork...@wisc.edu -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] cross correlations
Hi, Thats actualy that i did here [1]. Extracting coordinate for every atom in interesting two group and computing C_ij = x_i * x_j / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j is vectors [1] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Sun, 19 Jun 2011 12:27:53 +0200, Tsjerk Wassenaar wrote: Hey, The method from Lange is quite a different thing. It includes non-linear correlations, which is interesting to look at for overall correlation between atoms. If the ultimate goal is to do PCA on it, then it will give you awkward components that will give you a hard time trying to interpret. There is another way, besides using an external tool. Extract the diagonal elements and take the square root of each. Then for each element [i,j] in the matrix, divide by the elements i and j of these square roots, and you'll have yourself a correlation matrix. Hope it helps, Tsjerk On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi. There is two possibilitys 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that compites general corelation coefficients 2. My utility that computes pearson correlation coefficients [2] [1] http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html [2] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but thats not what im looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu [1] Links: -- [1] mailto:kork...@wisc.edu -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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] cross correlations
Of course you did... Though mind the brackets :) C_ij = x_i * x_j / sqrt ( x_i ^2 * x_j^2 ) The point I want to make is that you can easily take the output from g_covar -ascii and turn it into a correlation matrix. In R (r-project.org) there is even a dedicated function for it: x - scan(covar.dat) x - matrix(x,sqrt(length(x))) y - cov2cor(x) write(y,correl.dat,ncolumns=3) Cheers, Tsjerk On Sun, Jun 19, 2011 at 12:37 PM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi, Thats actualy that i did here [1]. Extracting coordinate for every atom in interesting two group and computing C_ij = x_i * x_j / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j is vectors [1] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Sun, 19 Jun 2011 12:27:53 +0200, Tsjerk Wassenaar wrote: Hey, The method from Lange is quite a different thing. It includes non-linear correlations, which is interesting to look at for overall correlation between atoms. If the ultimate goal is to do PCA on it, then it will give you awkward components that will give you a hard time trying to interpret. There is another way, besides using an external tool. Extract the diagonal elements and take the square root of each. Then for each element [i,j] in the matrix, divide by the elements i and j of these square roots, and you'll have yourself a correlation matrix. Hope it helps, Tsjerk On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi. There is two possibilitys 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that compites general corelation coefficients 2. My utility that computes pearson correlation coefficients [2] [1] http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html [2] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but thats not what im looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu [1] Links: -- [1] mailto:kork...@wisc.edu -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
[gmx-users] cross correlations
Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but that's not what i'm looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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
[gmx-users] cross-correlations as a function of interatomic distance
Hi gromacs users After using g_covar for obtaining dynamic cross correlation map, how is obtained cross-correlations as a function of interatomic distance? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] cross-correlations as a function of interatomic distance
On 16/03/2010 5:16 PM, shahab shariati wrote: Hi gromacs users After using g_covar for obtaining dynamic cross correlation map, how is obtained cross-correlations as a function of interatomic distance? Thank you so much for any help! I'm not even sure whether cross-correlations as a function of interatomic distance makes sense. Perhaps you need to explain further what you mean. Writing out the maths of it may make it clear to you what it is you need to do with the output from g_covar. Mark -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cross-correlations as a function of interatomic distance
Hi gromacs users After using g_covar for obtaining dynamic cross correlation map, how is obtained cross-correlations as a function of interatomic distance? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
