[gmx-users] on calculation of the atomic covariance

Vigneshwar Ramakrishnan vmsrvignesh at gmail.com
Wed Nov 10 14:26:56 CET 2010

Dear All,

I am trying to study the effect of single-point mutations on correlated
motions in a protein-DNA system.
I am able to calculate the atomic covariance matrix using the g_covar -xpma
option. However, when I try to compare the covariance matrices for the two
systems (to study the effect of the mutation), I find that the output is not
scaled identically. That is, in one of the systems the atomic covariance
varies between -0.04 and +0.5 whereas in the other it varies between -0.1
and +0.4. Now, this means that I cannot compare the two systems immediately
from the eps file output (obtained after xpm2ps).

Could anybody please tell me if there is a way to plot the output on
identical scales (say, -1 to +1, or any other scale) using GROMACS?

The other way, I understand is to use the ascii output of g_covar and use
the values to create the covariance plot using softwares like MATLAB which
can rescale the image colors. However, for this, one needs to calculate the
atomic covariance from the ascii output (which is x1x1,x1y1,x1z1 etc). From
the manual, I understand that the way to calculate atomic covariance is "for
each atom pair the sum of the xx, yy and zz covariances". Am I right if I
understand that this means:

atomic cov (X1) = x1x1 + y1y1 + z1z1
atomic cov (X2) = x2x2 + y2y2 + z2z2 ...

I greatly appreciate any help or pointers.

Thanks very much,

Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
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