[gmx-users] Re. normalized overlap

[Mark Abraham]

Hi,

Yes, I have done so for future releases.

Mark

On Wed, 21 Dec 2016 02:42 Lovas, Sandor <SandorLovas at creighton.edu> wrote:

> Hello Mark,
> Thanks for the clarification, I have checked the trr file with gmx dump
> and, indeed, the eigenvalues are are written in them as time, for
> example
>
> "gmx dump -f eigenvec_5.trr
> ...
> eigenvec_5.trr frame 2:
> natoms=       443  step=         1  time=1.5521152e+01  lambda=    0
> ..."
> and 1.5521152e+01 is the first eigenvalue in the eigenval_5.xvg file.
>
> I think the manual, however, needs to be clarified since it implies
> that you need to use the eig and eig2 inputs to get the normalized
> overlap:
>
> "When -v, -eig, -v2 and -eig2 are given, a single number for the
> overlap between the covariance matrices is generated. The formulas
> are:..."
> Thanks again,
> Sandor
>
>
>
> >Hi,
> >
> >GROMACS tools write the eigenvalue to the time field of trr files, so
> >both of your runs are presumably computing the same quantity from the
> >same input data (which you can check by comparing the .xvg files to
> >the output of gmx dump on the trr files). I will amend the docs of gmx
> >anaeig to note that the -eig and -eig2 options permit you to supply
> >eigenvalues, which will replace those read from the trr file. So, if
> >what you want is to do the analysis with eigenvalues all zero, then
> >make copies of your .xvg files and zero the values suitably.
>
> Mar
> --
> ______________________________________
> Dr. Sandor Lovas, Professor
> Department of Biomedical Sciences
> Creighton University
> 2500 California Plaza,
> Omaha, NE 68178, USA
>
> Phone: 402-280-5753
> Fax:   402-280-2690
>
>
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