[gmx-users] dynamic cross correlation map (DCCM)

[Berk Hess]

Hi,

g_covar -xpm or -ascii gives you the complete covariance matrix.
This contains all the correlations.
I could be that DCCM gives the matrix normalized with the square root
of the product of the diagonal, which is the normalized correlation.
This would be a useful option which I might put into g_covar.
But you can do this yourself with a small script on the -ascii output.

Berk

> Date: Tue, 19 Jan 2010 13:23:30 +0100
> Subject: Re: [gmx-users] dynamic cross correlation map (DCCM)
> From: tsjerkw at gmail.com
> To: jalemkul at vt.edu; gmx-users at gromacs.org
> CC: 
> 
> Hi,
> 
> Well I'd say that 'DCCM' refers to the matrix (map) of correlations
> and not to that of covariances. More specifically, it refers to
> correlations of positional fluctuations. PCA, on the other hand,
> refers to the extraction of components or axes which better describe
> the data than the original axes do, not specifying what kind of data,
> nor whether correlations or covariances be used for their
> determination. That's quite a distinction.
> g_covar gives the covariance matrix, not the correlation matrix. I
> believe there was a modified version in the contributions section
> which was able to compute correlations.
> 
> Cheers,
> 
> Tsjerk
> 
> 
> On Tue, Jan 19, 2010 at 12:50 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > leila karami wrote:
> >>
> >> Hi
> >>  I want to obtain dynamic cross correlation map (DCCM). I used following
> >> command for obtaining covariance matrix.
> >>  g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l
> >> covar.log -xpm covar.xpm.
> >>  my system consists protein of 70 aminoacids. I want survey correlated and
> >> anti-correlated motion between residues.
> >>  Is my manner true? If so, which of output files in above give me dynamic
> >> cross correlation map (DCCM)? otherwise, please guide me.
> >>
> >
> > No one has ever been able to explain to me the difference between DCCM and
> > PCA, so I'd say you're correct at least in obtaining the covariance matrix,
> > which will give you information about correlated and anticorrelated motion.
> >  "DCCM" seems to be a popular term with the AMBER crowd, but I don't know
> > that their manual even gives the equations used for such an analysis to
> > potentially differentiate it from PCA.  I believe there are some tips in
> > their mail reflector, however.
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> 
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> -- 
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 		 	   		  
_________________________________________________________________
New Windows 7: Find the right PC for you. Learn more.
http://windows.microsoft.com/shop
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100119/1e545425/attachment.html>