Dear Tsjerk, <div><br></div><div>Thanks very much. Yes, true, difference in the ranges of the covariances means there is difference between the two systems. I did try the modified g_covar in the contribution section but couldn't make it work first, but I realized it worked only for GROMACS ver 3.3.3. Now, I am able to calculate the correlation matrix. </div>
<div><br></div><div>Thanks very much for all your help and pointers.</div><div><br></div><div>Sincerely,</div><div>Vignesh<br><br><div class="gmail_quote">On Thu, Nov 11, 2010 at 4:49 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Vignesh,<br>
<br>
If your covariances show different ranges, isn't that a difference<br>
between your systems, wild-type and mutated? Then again, there's also<br>
noise in the covariances (noise in the fluctuations, ergo noise in the<br>
noise ;)). The rest might be comparable, making scaling based on the<br>
extremes seem like a bad idea. You might be better of calculating<br>
correlations, rather than covariances. There's a modified g_covar in<br>
the contributions section of the gromacs site for calculating those.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
On Thu, Nov 11, 2010 at 3:53 AM, Vigneshwar Ramakrishnan<br>
<div><div></div><div class="h5"><<a href="mailto:vmsrvignesh@gmail.com">vmsrvignesh@gmail.com</a>> wrote:<br>
> Dear All,<br>
> I tried using the xpm2ps -combine option to plot the two matrices in the<br>
> same plot.<br>
> "xpm2ps -f covara_cognate.xpm -f2 covara_G5C.xpm -diag none -combine halves<br>
> -cmin -0.5 -cmax 0.8"<br>
><br>
> However, I still get two legends and each of the matrices are scaled<br>
> differently. That is, the output range is NOT combined, as the -combine<br>
> option is supposed to do. I tried different options (add, sub, div ; with<br>
> and without the -cmin and -cmax options etc)<br>
> I am sure I am missing something here. May I please know if anybody got it<br>
> worked, and if so, can help me out?<br>
> Thanks very much,<br>
> Vignesh<br>
> On Thu, Nov 11, 2010 at 10:12 AM, Vigneshwar Ramakrishnan<br>
> <<a href="mailto:vmsrvignesh@gmail.com">vmsrvignesh@gmail.com</a>> wrote:<br>
>><br>
>> Thanks very much, Justin. Somehow this thread did not come up during my<br>
>> search.<br>
>> Really appreciate your help.<br>
>> Sincerely,<br>
>> Vignesh<br>
>><br>
>> On Wed, Nov 10, 2010 at 10:23 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
>> wrote:<br>
>>><br>
>>> There are two relevant threads on this same topic that will likely<br>
>>> provide some insight (particularly the second):<br>
>>><br>
>>> <a href="http://lists.gromacs.org/pipermail/gmx-users/2009-November/046846.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2009-November/046846.html</a><br>
>>> <a href="http://lists.gromacs.org/pipermail/gmx-users/2009-November/046854.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2009-November/046854.html</a><br>
>>><br>
>>> -Justin<br>
>>><br>
>>> Vigneshwar Ramakrishnan wrote:<br>
>>>><br>
>>>> Dear All,<br>
>>>> I am trying to study the effect of single-point mutations on correlated<br>
>>>> motions in a protein-DNA system. I am able to calculate the atomic<br>
>>>> covariance matrix using the g_covar -xpma option. However, when I try to<br>
>>>> compare the covariance matrices for the two systems (to study the effect of<br>
>>>> the mutation), I find that the output is not scaled identically. That is, in<br>
>>>> one of the systems the atomic covariance varies between -0.04 and +0.5<br>
>>>> whereas in the other it varies between -0.1 and +0.4. Now, this means that I<br>
>>>> cannot compare the two systems immediately from the eps file output<br>
>>>> (obtained after xpm2ps).<br>
>>>> Could anybody please tell me if there is a way to plot the output on<br>
>>>> identical scales (say, -1 to +1, or any other scale) using GROMACS?<br>
>>>> The other way, I understand is to use the ascii output of g_covar and<br>
>>>> use the values to create the covariance plot using softwares like MATLAB<br>
>>>> which can rescale the image colors. However, for this, one needs to<br>
>>>> calculate the atomic covariance from the ascii output (which is<br>
>>>> x1x1,x1y1,x1z1 etc). From the manual, I understand that the way to calculate<br>
>>>> atomic covariance is "for each atom pair the sum of the xx, yy and zz<br>
>>>> covariances". Am I right if I understand that this means:<br>
>>>> atomic cov (X1) = x1x1 + y1y1 + z1z1 atomic cov (X2) = x2x2 + y2y2 +<br>
>>>> z2z2 ...<br>
>>>> I greatly appreciate any help or pointers.<br>
>>>> Thanks very much, Sincerely, Vignesh<br>
>>>><br>
>>>><br>
>>>> --<br>
>>>> R.Vigneshwar<br>
>>>> Graduate Student,<br>
>>>> Dept. of Chemical & Biomolecular Engg,<br>
>>>> National University of Singapore,<br>
>>>> Singapore<br>
>>>><br>
>>>> "Strive for Excellence, Never be satisfied with the second Best!!"<br>
>>>><br>
>>>> I arise in the morning torn between a desire to improve the world and a<br>
>>>> desire to enjoy the world. This makes it hard to plan the day. (E.B. White)<br>
>>>><br>
>>><br>
>>> --<br>
>>> ========================================<br>
>>><br>
>>> Justin A. Lemkul<br>
>>> Ph.D. Candidate<br>
>>> ICTAS Doctoral Scholar<br>
>>> MILES-IGERT Trainee<br>
>>> Department of Biochemistry<br>
>>> Virginia Tech<br>
>>> Blacksburg, VA<br>
>>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
>>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>>><br>
>>> ========================================<br>
>>> --<br>
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>><br>
>><br>
>><br>
>> --<br>
>> R.Vigneshwar<br>
>> Graduate Student,<br>
>> Dept. of Chemical & Biomolecular Engg,<br>
>> National University of Singapore,<br>
>> Singapore<br>
>><br>
>> "Strive for Excellence, Never be satisfied with the second Best!!"<br>
>><br>
>> I arise in the morning torn between a desire to improve the world and a<br>
>> desire to enjoy the world. This makes it hard to plan the day. (E.B. White)<br>
><br>
><br>
><br>
> --<br>
> R.Vigneshwar<br>
> Graduate Student,<br>
> Dept. of Chemical & Biomolecular Engg,<br>
> National University of Singapore,<br>
> Singapore<br>
><br>
> "Strive for Excellence, Never be satisfied with the second Best!!"<br>
><br>
> I arise in the morning torn between a desire to improve the world and a<br>
> desire to enjoy the world. This makes it hard to plan the day. (E.B. White)<br>
><br>
</div></div>> --<br>
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><br>
<br>
<br>
<br>
--<br>
</div>Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<div><div></div><div class="h5">--<br>
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Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>R.Vigneshwar<br>Graduate Student,<br>Dept. of Chemical & Biomolecular Engg,<br>National University of Singapore,<br>Singapore<br><br>"Strive for Excellence, Never be satisfied with the second Best!!"<br>
<br>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)<br>
</div>