[gmx-users] on calculation of the atomic covariance

[Vigneshwar Ramakrishnan]

Dear All,

I tried using the xpm2ps -combine option to plot the two matrices in the
same plot.

"xpm2ps -f covara_cognate.xpm -f2 covara_G5C.xpm -diag none -combine halves
-cmin -0.5 -cmax 0.8"

However, I still get two legends and each of the matrices are scaled
differently. That is, the output range is NOT combined, as the -combine
option is supposed to do. I tried different options (add, sub, div ; with
and without the -cmin and -cmax options etc)

I am sure I am missing something here. May I please know if anybody got it
worked, and if so, can help me out?

Thanks very much,
Vignesh

On Thu, Nov 11, 2010 at 10:12 AM, Vigneshwar Ramakrishnan <
vmsrvignesh at gmail.com> wrote:

> 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
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> 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)
>



-- 
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)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101111/870ccc19/attachment.html>