[gmx-users] Eigenvalues not saved from gmx covar in GROMACS 5

[Tsjerk Wassenaar]

Hi Steven,

The eigenvalue is the variance of the projection over time. So in stead of
waiting for the bug fix, you can also calculate the projections and get the
eigenvalues from those.

Hope it helps,

Tsjerk
On Aug 7, 2014 10:32 PM, "Steven Morgan" <SMorgan at brooklyn.cuny.edu> wrote:

> I have installed v5 of GROMACS and am doing simulations on a peptide VPGVG
> repeated five times.  I am trying to calculate entropy and the eigenvalues
> of the covariance matrix to get eigenfrequencies.  When I issue the command
> gmx covar -f full.trr -s full.tpr -v -o -mwa (for eigenvalues), I get an
> empty eigenvalues.xvg.  In GROMACS v4.5.5 I used to get the eigenvalues
> outputted, for the same data sets, same command (g_covar).  It says it's
> writing the eigenvalues, but when I open the file there are no eigenvalues
> there, only the preamble for the xvg file, ending at @TYPE xy.  What am I
> doing wrong or is this a bug?
>
> Thank you,
> -Steven
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