[gmx-users] g_covar

[Ruben Martinez Buey]

Hi all,
I think I got it!
I get only the backbone in the Structure file with editconf.
to joining the two individual trajectories I only used the backbone as
well.
And now it works, but why not before if you choose only backbone when it
ask to you
wich group do you want for the fit?
Thanks a lot
cheers,
Ruben



Ruben Martinez Buey wrote:

> Hi all,
> i´m trying to do a covariance analysis on a combined trajectory. When
> I join the two individual trajectories I only use the backbone.
> When I try to do the covariance analysis, using only the backbone for
> the fit and for the covar analysis (i.e. the same atoms than in the
> trajectoy),
> I get the next error listed below.
>
> WARNING: masses will be determined based on residue and atom names,
>          this can deviate from the real mass of the atom type
> Opening library file /usr/local/gromacs/share/top/atommass.dat
> Opening library file /usr/local/gromacs/share/top/aminoacids.dat
>
> Choose a group for the least squares fit
> Group     0 (    Backbone) has  1002 elements
> There is one group in the index
>
> Choose a group for the covariance analysis
> Group     0 (    Backbone) has  1002 elements
> There is one group in the index
>
> 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.
>
>
> Warning: can not make broken molecules whole without a run input file,
>
>          don't worry, mdrun doesn't write broken molecules
>
> Constructing covariance matrix (3006x3006)...
> Reading frame       0 time    0.000   Fatal error: Numerical Recipes:
> Too many iterations in routine JACOBI
>
> Any help would be very appreciated!
> Thanks in advance,
> with best wishes,
> Ruben
>
>
>
>
> --
> ___________________________________________
>
> Rubén Martínez-Buey. PhD student
> Protein Function and Structure Dept. Lab. 352
> Centro de Investigaciones Biológicas (CIB-CSIC)
> C/ Velázquez, 144,  28006  MADRID (SPAIN)
> Tlf: +34-91-561 18 00 ext. 4380
> Fax: +34-91-562 75 18
>
>

--
___________________________________________

Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144,  28006  MADRID (SPAIN)
Tlf: +34-91-561 18 00 ext. 4380
Fax: +34-91-562 75 18


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