Re: [gmx-users] Correlation Matrix Calculation

Hi Tsjerk, yes I did make a mistake in the group that I chose . . . should be C-alpha. Anyway, thanks for the help, appreciate it, Arneh > Hi Arneh, > > I think this has been covered on the mailing list before. But anyway, > the number indeed refers to the atom index number, running from 1-N. >

Re: [gmx-users] Correlation Matrix Calculation

Hi Arneh, I think this has been covered on the mailing list before. But anyway, the number indeed refers to the atom index number, running from 1-N. You mean that you have 1934427 X 3 elements in the covar.dat file? So that corresponds to sqrt( 1934427 X 3 ) / 3 = 803 atoms. I think you made a mis

Re: [gmx-users] Correlation Matrix Calculation

Thanks Tsjerk, One other question, regarding the covar.dat file (the covariance matrix that's outputted when using the -ascii flag): I dont' quite understand the format of it. In the manual, it states: "The order of the elements is: x1x1, x1y1, x1z1, x1x2, ..." Does "1" and "2" refer to th

Re: [gmx-users] Correlation Matrix Calculation

Hi Arneh, Yes. As you should be able to recall, the (linear, not "generalized") correlation is formally given as: cor(x,y) = cov(x,y) / ( sqrt(var(x))*sqrt(var(y)) ) The diagonal elements of the covariance matrix give the variances... Cheers, Tsjerk On 8/31/07, Arneh Babakhani <[EMAIL PROTECT

Re: [gmx-users] Correlation Matrix Calculation

Sorry for the confusion . I want the correlation. So I can just use g_covar to get the covar. matrix, and divide each term by what you stated, to get the correlation matrix? (if I follow you correctly). Thanks, > Hi Arneh, > > You're not clear on what you want. Is it a covariance matrix or a > c

Re: [gmx-users] Correlation Matrix Calculation

Yes, I have seen this, had trouble compiling it. Does it matter what version of gromacs you're trying to compile it with? > Hi, > > > On Friday, 31. August 2007 05:14, Arneh Babakhani wrote: >> Can anyone briefly recommend a procedure for calculating the correlation >> matrix (not the diagonalize

Re: [gmx-users] Correlation Matrix Calculation

Hi, On Friday, 31. August 2007 05:14, Arneh Babakhani wrote: > Can anyone briefly recommend a procedure for calculating the correlation > matrix (not the diagonalized covariance matrix, as done by g_covar) of a > specified group? > > In particular, I'm looking to calculate the covariance matrix,

Re: [gmx-users] Correlation Matrix Calculation

Hi Arneh, You're not clear on what you want. Is it a covariance matrix or a correlation matrix. Correlation and covariance are different things. g_covar lets you write out a covariance matrix using the option -ascii. In case you want the correlation matrix (though IIRC Karplus also used the covari

[gmx-users] Correlation Matrix Calculation

Can anyone briefly recommend a procedure for calculating the correlation matrix (not the diagonalized covariance matrix, as done by g_covar) of a specified group? In particular, I'm looking to calculate the covariance matrix, as specifed in the Karplus paper (Proteins: Vol 11:205-217, 1991), where