[gmx-users] Re: Covariance file format

[Tsjerk Wassenaar]

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>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:;>
> > >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.