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 the particles in the group? I'm asking b/c my
particular covar.dat file is of dimmensions 1934427 X 3 , for a group of
about 100 atoms and a traj of 1 NS. Just trying to make sense out of it
. . .
Thanks,
Arneh
Tsjerk Wassenaar wrote:
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 PROTECTED]> wrote:
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
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 covariance matrix), you have to divide each element m_ij
by sqrt(m_ii)*sqrt(m_jj).
Cheers,
Tsjerk
On 8/31/07, Arneh Babakhani <[EMAIL PROTECTED]> 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, as
specifed
in the Karplus paper (Proteins: Vol 11:205-217, 1991), where each entry
of
the matrix is defined as the correlation between the i-th and j-th atom:
c_ij = <delta r_i> <delta r_j>
where delta r is the deviation of i from its average position, averaged
over the ensemble.
Or, is there a way to use g_covar and suppress the diagonalization step,
so as to obtain only the translation correlation matrix??? (I couldn't
find anything to this effect in the manual).
Much thanks,
Arneh
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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