[gmx-users] on calculation of the atomic covariance

[Tsjerk Wassenaar]

Hi Vignesh,

If your covariances show different ranges, isn't that a difference
between your systems, wild-type and mutated? Then again, there's also
noise in the covariances (noise in the fluctuations, ergo noise in the
noise ;)). The rest might be comparable, making scaling based on the
extremes seem like a bad idea. You might be better of calculating
correlations, rather than covariances. There's a modified g_covar in
the contributions section of the gromacs site for calculating those.

Cheers,

Tsjerk

On Thu, Nov 11, 2010 at 3:53 AM, Vigneshwar Ramakrishnan
<vmsrvignesh at gmail.com> wrote:
> 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
>>>
>>> ========================================
>>> --
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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)
>
>
>
> --
> 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)
>
> --
> 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
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands