# [gmx-users] Re: Covariance file format

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jul 1 08:30:35 CEST 2013

```where N is the number of atoms and n is the number of frames :p

T.

On Mon, Jul 1, 2013 at 8:29 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> 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>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.
>
>

--
Tsjerk A. Wassenaar, Ph.D.

```