[gmx-users] g_covar error in Gromacs 5

[Justin Lemkul]

On 9/29/15 1:00 PM, Rebeca García Fandiño wrote:
> 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?
>

Yes, one that was fixed after 5.0.4.  When encountering potential bugs, always 
try upgrading to the latest version in your series (at least 5.0.6, if not 5.1) 
and try again.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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