[gmx-users] on calculation of the atomic covariance

[Justin A. Lemkul]

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
> Graduate Student,
> 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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