# [gmx-users] Re: Covariance file format

Ankita naithani ankitanaithani at gmail.com
Mon Jul 1 08:46:50 CEST 2013

```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

```