[gmx-users] nan in g_anaeig -over

Joaquim Rui de Castro Rodrigues joaquim.rodrigues at ipleiria.pt
Fri Jul 27 17:55:36 CEST 2012

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...

Rui Rodrigues

De: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] Em Nome De Mark Abraham [Mark.Abraham at 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.

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