# [gmx-users] on calculation of the atomic covariance

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 10 15:23:25 CET 2010

```There are two relevant threads on this same topic that will likely provide some
insight (particularly the second):

http://lists.gromacs.org/pipermail/gmx-users/2009-November/046846.html
http://lists.gromacs.org/pipermail/gmx-users/2009-November/046854.html

-Justin

Vigneshwar Ramakrishnan wrote:
> 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,
> Sincerely,
> Vignesh
>
>
> --
> R.Vigneshwar
> Dept. of Chemical & Biomolecular Engg,
> National University of Singapore,
> 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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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

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