[gmx-users] on calculation of the atomic covariance

[Vigneshwar Ramakrishnan]

Thanks very much, Justin. Somehow this thread did not come up during my
search.

Really appreciate your help.

Sincerely,
Vignesh

On Wed, Nov 10, 2010 at 10:23 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
> 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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-- 
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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