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Hi,<br><br>g_covar -xpm or -ascii gives you the complete covariance matrix.<br>This contains all the correlations.<br>I could be that DCCM gives the matrix normalized with the square root<br>of the product of the diagonal, which is the normalized correlation.<br>This would be a useful option which I might put into g_covar.<br>But you can do this yourself with a small script on the -ascii output.<br><br>Berk<br><br>> Date: Tue, 19 Jan 2010 13:23:30 +0100<br>> Subject: Re: [gmx-users] dynamic cross correlation map (DCCM)<br>> From: tsjerkw@gmail.com<br>> To: jalemkul@vt.edu; gmx-users@gromacs.org<br>> CC: <br>> <br>> Hi,<br>> <br>> Well I'd say that 'DCCM' refers to the matrix (map) of correlations<br>> and not to that of covariances. More specifically, it refers to<br>> correlations of positional fluctuations. PCA, on the other hand,<br>> refers to the extraction of components or axes which better describe<br>> the data than the original axes do, not specifying what kind of data,<br>> nor whether correlations or covariances be used for their<br>> determination. That's quite a distinction.<br>> g_covar gives the covariance matrix, not the correlation matrix. I<br>> believe there was a modified version in the contributions section<br>> which was able to compute correlations.<br>> <br>> Cheers,<br>> <br>> Tsjerk<br>> <br>> <br>> On Tue, Jan 19, 2010 at 12:50 PM, Justin A. Lemkul <jalemkul@vt.edu> wrote:<br>> ><br>> ><br>> > leila karami wrote:<br>> >><br>> >> Hi<br>> >> I want to obtain dynamic cross correlation map (DCCM). I used following<br>> >> command for obtaining covariance matrix.<br>> >> g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l<br>> >> covar.log -xpm covar.xpm.<br>> >> my system consists protein of 70 aminoacids. I want survey correlated and<br>> >> anti-correlated motion between residues.<br>> >> Is my manner true? If so, which of output files in above give me dynamic<br>> >> cross correlation map (DCCM)? otherwise, please guide me.<br>> >><br>> ><br>> > No one has ever been able to explain to me the difference between DCCM and<br>> > PCA, so I'd say you're correct at least in obtaining the covariance matrix,<br>> > which will give you information about correlated and anticorrelated motion.<br>> > "DCCM" seems to be a popular term with the AMBER crowd, but I don't know<br>> > that their manual even gives the equations used for such an analysis to<br>> > potentially differentiate it from PCA. I believe there are some tips in<br>> > their mail reflector, however.<br>> ><br>> > -Justin<br>> ><br>> > --<br>> > ========================================<br>> ><br>> > Justin A. Lemkul<br>> > Ph.D. Candidate<br>> > ICTAS Doctoral Scholar<br>> > MILES-IGERT Trainee<br>> > Department of Biochemistry<br>> > Virginia Tech<br>> > Blacksburg, VA<br>> > jalemkul[at]vt.edu | (540) 231-9080<br>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> ><br>> > ========================================<br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www interface<br>> > or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> <br>> <br>> <br>> -- <br>> Tsjerk A. Wassenaar, Ph.D.<br>> <br>> Computational Chemist<br>> Medicinal Chemist<br>> Neuropharmacologist<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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