[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):



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)


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list