[gmx-users] Re: Covariance file format

[Tsjerk Wassenaar]

Hi Ankita,

No, the file contains the 3Nx3N covariance matrix, row by row, split over
triplets, mass weighted if you did the analysis mass-weighted. But for
C-alpha only there is no difference between mass-weighted and
non-mass-weighted, except for global scaling.

Cheers,

Tsjerk



On Mon, Jul 1, 2013 at 8:46 AM, Ankita naithani <ankitanaithani at gmail.com>wrote:

> Hi Tsjerk,
>
> Coffee is always magical, I tell you. Just a sniff in the air and it makes
> things clear.
>
> So, 1/n sum is the mass weighted ness? And x1 to zn spans from 1 to 1992?
>
> By any chance we don't obtain a file I. Which the first column wud have
> alpha atom one second column would have 2nd aloha atom n third would have
> correlation between them?
>
>
>
> Kind regards,
>
> Ankita
>
> On Monday, July 1, 2013, Tsjerk Wassenaar wrote:
>
> > Hi Ankita,
> >
> > I should not answer questions before coffee!! Sorry.
> >
> > It's the covariance matrix! So it's
> >
> > 1/n sum x1x1   1/n sum x1y1   1/n sum x1z1
> > 1/n sum x1x2   1/n sum x1y2   1/n sum x1z2
> > ...
> > 1/n sum zNxN  1/n sum zNyN  1/n sum zNzN
> >
> > Silly me :|
> >
> > Tsjerk
> >
> >
> > On Mon, Jul 1, 2013 at 8:09 AM, Ankita naithani <
> ankitanaithani at gmail.com<javascript:;>
> > >wrote:
> >
> > > Hi Tsjerk,
> > > Thank you for your reply. So, these are the eigenvectors. By any
> chance,
> > > can we obtain the covariance matrix containing the information of
> residue
> > > fluctuations I.e. the covariance information. Actually, it was needed
> to
> > > obtain the dot plot delta ri dot delta rj so I don't think so I can use
> > the
> > > eigenvectors
> > >
> > >
> > > Kind regards
> > >
> > > Ankita
> > >
> > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote:
> > >
> > > > Hi Ankita,
> > > >
> > > > The fie contains the eigenvectors as
> > > >
> > > > x1 y1 z1
> > > > x2 y2 z2
> > > > ...
> > > > xN yN zN
> > > >
> > > > Hope it helps,
> > > >
> > > > Tsjerk
> > > >
> > > >
> > > > On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani <
> > > ankitanaithani at gmail.com <javascript:;><javascript:;>
> > > > >wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I wanted to know the exact format of covariance.dat file as
> generated
> > > by
> > > > > g_covar during covariance analysis. The file format mentioned in
> the
> > > > manual
> > > > > was not quite clear to understand. I need to use the matrix
> > > information n
> > > > > so needed to know how the data is stored. My matrix is for 1992
> > calpha
> > > > > atoms.
> > > > >
> > > > > It would be really helpful if someone could explain the file
> format.
> > > > >
> > > > > Kind regards,
> > > > >
> > > > > Ankita
> > > > >
> > > > >
> > > > > --
> > > > > Ankita Naithani
> > > > > --
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> > > >
> > > > --
> > > > Tsjerk A. Wassenaar, Ph.D.
> > > > --
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> > >
> > > --
> > > Ankita Naithani
> > > --
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> > --
> > Tsjerk A. Wassenaar, Ph.D.
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>
> --
> Ankita Naithani
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.