[gmx-users] g_covar

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Thu Apr 24 17:08:00 CEST 2003

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
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,


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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