[gmx-users] Dynamics cross correlation map
Hi Tsjerk, Thank you for your reply. May be I was not very clear with my previous post. I am not looking for covariance / atomic covariances map (ie., covar.xpm/covara.xpm) which are generated by g_covar tool in GROMACS. I am particularly trying to get correlation map (example: http://www.pnas.org/content/102/4/994/F2.large.jpg, http://www.pnas.org/content/99/26/16597/F3.small.gif). I hope there is a difference between covariance matrix and correlation matrix. The correlated motions between two atoms is calculated as the magnitude of the co-relation coefficient between the atoms. In case of a system it can be assessed by examining the magnitude of all pairwise cross-correlation coefficients. The cross-correlation coefficient, C(i,j) for each pair of atoms i and j is calculated as: C(i,j) = delta r(i) * delta r(j) / sqrt sqr(delta r(i) ) . sqrt sqr(delta r(j) ) , where delta r(i) is the displacement from mean position of the ith atom and symbol represents the time average. This function returns a matrix of all atom-wise cross-correlations whose elements, C(i,j), may be displayed in a graphical representation frequently termed a dynamical cross-correlation map, or DCCM. If C(i,j) = 1 the fluctuations of atoms i and j are completely correlated, if C(i,j) = -1 the fluctuations of atoms i and j are completely anticorrelated and if C(i,j) = 0 the fluctuations of i and j are not correlated. Now my query is there any tool like g_correlation (http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/GeneralizedCorrelations/index.html) by which I can get the cross-correlation matrix from covariance matrix or directly from trajectory file. Ref:1. Hünenberger PH, Mark AE, van Gunsteren WF; Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations; JMB 1995; 252:492-503 2. Oliver F. Lange, H. Grubmüller; Generalized Correlation for Biomolecular Dynamics; Proteins 2006; 62:1053-1061 Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- 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] Dynamics cross correlation map
Hi Sukesh, I once put a version of g_covar that can calculate the correlations in the user contributions. Check if it's there or reply to me privately if you can't find it (though I'm on the road till Friday). Good luck, Ran On Wed, 24 Mar 2010 11:46:42 +0530 sukesh chandra gain suk...@atc.tcs.com wrote: Hi Tsjerk, Thank you for your reply. May be I was not very clear with my previous post. I am not looking for covariance / atomic covariances map (ie., covar.xpm/covara.xpm) which are generated by g_covar tool in GROMACS. I am particularly trying to get correlation map (example: http://www.pnas.org/content/102/4/994/F2.large.jpg, http://www.pnas.org/content/99/26/16597/F3.small.gif). I hope there is a difference between covariance matrix and correlation matrix. The correlated motions between two atoms is calculated as the magnitude of the co-relation coefficient between the atoms. In case of a system it can be assessed by examining the magnitude of all pairwise cross-correlation coefficients. The cross-correlation coefficient, C(i,j) for each pair of atoms i and j is calculated as: C(i,j) = delta r(i) * delta r(j) / sqrt sqr(delta r(i) ) . sqrt sqr(delta r(j) ) , where delta r(i) is the displacement from mean position of the ith atom and symbol represents the time average. This function returns a matrix of all atom-wise cross-correlations whose elements, C(i,j), may be displayed in a graphical representation frequently termed a dynamical cross-correlation map, or DCCM. If C(i,j) = 1 the fluctuations of atoms i and j are completely correlated, if C(i,j) = -1 the fluctuations of atoms i and j are completely anticorrelated and if C(i,j) = 0 the fluctuations of i and j are not correlated. Now my query is there any tool like g_correlation (http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/GeneralizedCorrelations/index.html) by which I can get the cross-correlation matrix from covariance matrix or directly from trajectory file. Ref:1. Hünenberger PH, Mark AE, van Gunsteren WF; Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations; JMB 1995; 252:492-503 2. Oliver F. Lange, H. Grubmüller; Generalized Correlation for Biomolecular Dynamics; Proteins 2006; 62:1053-1061 Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- 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 -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Skype: ran.friedman -- -- 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] Dynamics cross correlation map
Hi Sukesh, Great. This makes things much clearer. So basically what you'd need to do is to divide each i,j-th element of the covariance matrix you obtained (covar.dat) by the sqrt of the ii-th and jj-th diagonal element. That will commonly turn a covariance matrix into a correlation matrix. But, that also happens to be what the modified version of g_covar provided by Ran does. I think it's still on the contributions page. Just one more thing, the generalized correlation of Lange and Grubmueller is a bit of a different thing. Might also be handy though. In stead of calculating the correlation as the normalized product moment, they have a similarity parameter that measures how close the actual distribution of measurements is to the one you'd get if the measurements were uncorrelated (mutually independent). This compensates for non-linear relationships between variables. Cheers, Tsjerk On Wed, Mar 24, 2010 at 7:16 AM, sukesh chandra gain suk...@atc.tcs.com wrote: Hi Tsjerk, Thank you for your reply. May be I was not very clear with my previous post. I am not looking for covariance / atomic covariances map (ie., covar.xpm/covara.xpm) which are generated by g_covar tool in GROMACS. I am particularly trying to get correlation map (example: http://www.pnas.org/content/102/4/994/F2.large.jpg, http://www.pnas.org/content/99/26/16597/F3.small.gif). I hope there is a difference between covariance matrix and correlation matrix. The correlated motions between two atoms is calculated as the magnitude of the co-relation coefficient between the atoms. In case of a system it can be assessed by examining the magnitude of all pairwise cross-correlation coefficients. The cross-correlation coefficient, C(i,j) for each pair of atoms i and j is calculated as: C(i,j) = delta r(i) * delta r(j) / sqrt sqr(delta r(i) ) . sqrt sqr(delta r(j) ) , where delta r(i) is the displacement from mean position of the ith atom and symbol represents the time average. This function returns a matrix of all atom-wise cross-correlations whose elements, C(i,j), may be displayed in a graphical representation frequently termed a dynamical cross-correlation map, or DCCM. If C(i,j) = 1 the fluctuations of atoms i and j are completely correlated, if C(i,j) = -1 the fluctuations of atoms i and j are completely anticorrelated and if C(i,j) = 0 the fluctuations of i and j are not correlated. Now my query is there any tool like g_correlation (http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/GeneralizedCorrelations/index.html) by which I can get the cross-correlation matrix from covariance matrix or directly from trajectory file. Ref:1. Hünenberger PH, Mark AE, van Gunsteren WF; Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations; JMB 1995; 252:492-503 2. Oliver F. Lange, H. Grubmüller; Generalized Correlation for Biomolecular Dynamics; Proteins 2006; 62:1053-1061 Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology 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/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] Dynamics cross correlation map
Dear All, Could you please tell how to get the Dynamic Cross Correlation map with Gromacs analysis tool or other tools. I want to know over a 20 ns simulation whether the motions of two residues or group of residues are correlated or anti correlated. For this I want to plot a dynamics cross correlation map in which I could get the precise information of group of atoms. I have done the following step and got the covariance matrix but don't know how to proceed further. g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l covar.log -xpm covar.xpm -ascii covar.dat Waiting for your input. Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- 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] Dynamics cross correlation map
Hi Sukesh, You've posted this question several times now, without changing the phrasing. Did it occur to you that maybe nobody felt equipped to or sufficiently triggered by your post to reply? What do you mean with a 'dynamics cross correlation map' for 'residues or groups of residues'? Being more explicit, also pointing to some references or giving some formulas, might help you get a response. But isn't your answer already in the image covar.xpm? Otherwise, maybe using the atomic covariances (-xpma) might do what you want. If not, your problem is not as trivial as you may think. Cheers, Tsjerk On Tue, Mar 23, 2010 at 11:44 AM, sukesh chandra gain suk...@atc.tcs.com wrote: Dear All, Could you please tell how to get the Dynamic Cross Correlation map with Gromacs analysis tool or other tools. I want to know over a 20 ns simulation whether the motions of two residues or group of residues are correlated or anti correlated. For this I want to plot a dynamics cross correlation map in which I could get the precise information of group of atoms. I have done the following step and got the covariance matrix but don't know how to proceed further. g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l covar.log -xpm covar.xpm -ascii covar.dat Waiting for your input. Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology 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/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
