[gmx-users] g_covar error in Gromacs 5

[Rebeca García Fandiño]

Hi,
I am trying to use g_covar like this:

echo 2 2 | g_covar 
-s prod_clus_1_exp.tpr -f prod_clus_exp_fit.xtc -n index_noH_exp.ndx -o 
eigenval_300K_exp.xvg -v eigenvect_300K_exp.trr 

In Gromacs 5.0.4 I get an error:

(...)

Choose a group for the least squares fit
Group     0 (         System) has  4437 elements
Group     1 (          Other) has   147 elements
Group     2 (            MOL) has   147 elements
Select a group: 2
Selected 2: 'MOL'

Choose a group for the covariance analysis
Group     0 (         System) has  4437 elements
Group     1 (          Other) has   147 elements
Group     2 (            MOL) has   147 elements
Select a group: 2
Selected 2: 'MOL'

Note: the fit and analysis group are identical,
      while the fit is mass weighted and the analysis is not.
      Making the fit non mass weighted.

Calculating the average structure ...
Reading frames from gro file 'frame t= 18.000', 4437 atoms.
Last frame          0 time   18.000

Back Off! I just backed up average.pdb to ./#average.pdb.4#
Constructing covariance matrix (441x441) ...
Reading frames from gro file 'frame t= 18.000', 4437 atoms.
Last frame          0 time   18.000
Read 1 frames

Trace of the covariance matrix: 0 (nm^2)

Diagonalizing ...

Sum of the eigenvalues: 0 (nm^2)
Violación de segmento


That
 means "Segmentation fault". The most strange is that using Gromacs 
4.6.2 this error does not appear, and the command executes properly. 
Could it be maybe a bug in Gromacs 5?

Thanks a lot for your help in advance.

Dr. Rebeca Garcia
Santiago de Compostela University (Spain)