Mark,
You are right. I've run gmxdump on the eigenvectors and I can see nan
coordinates in 3 consecutive frames (13589 to 13591):
eigenvectors.trr frame 13589:
natoms= 4600 step= 13588 time=-3.2829557e-06 lambda= 0
box (3x3):
box[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
box[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
box[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
x (4600x3):
x[ 0]={ nan, nan, nan}
x[ 1]={ nan, nan, nan}
x[ 2]={ nan, nan, nan}
x[ 3]={ nan, nan, nan}
x[ 4]={ nan, nan, nan}
x[ 5]={ nan, nan, nan}
I've just re-run g_covar the the same input and i got identical eigenvectors
(checked with gmxcheck and diff). I'll have to check my input to g_covar...
Thanks,
Rui Rodrigues
________________________________________
De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] Em Nome De
Mark Abraham [mark.abra...@anu.edu.au]
Enviado: quinta-feira, 26 de Julho de 2012 16:48
Para: Discussion list for GROMACS users
Assunto: Re: [gmx-users] nan in g_anaeig -over
On 27/07/2012 12:31 AM, Joaquim Rui de Castro Rodrigues wrote:
> Dear all,
>
> I am getting a nan while calculating the overlap between covariance matrices
> (in this case, using the same vectors for -v and -v2):
> g_anaeig455 -v atp/eigenvectors.trr -v2 atp/eigenvectors.trr -over
> overlap_atp-atp
>
> I tried different gromacs versions, different -last values, and also setting
> the -eig and -eig2 flags, with the same results.
> Any idea what could be wrong here?
> Please find below the content of the .xvg file and the ouput from g_anaeig.
>
> Thanks for your time,
> Rui Rodrigues
>
>
>
> Here is the content of overlap_atp-atp.xvg:
(...)
>
> Here is the complete ouput from g_anaeig:
(...)
Something's wrong with your eigenvectors. Look at the other output files
and/or gmxdump the eigenvector files.
Mark
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