[gmx-users] on calculation of the atomic covariance

[Vigneshwar Ramakrishnan]

Dear Tsjerk,

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.

Thanks very much for all your help and pointers.

Sincerely,
Vignesh

On Thu, Nov 11, 2010 at 4:49 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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!
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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
> --
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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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