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)
--
========================================
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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