[gmx-users] Fatal error: Error: Too many iterations in routine JACOBI

[Una Bjarnadottir]

Dear users,

I'm using g_covar to analyse my trajectories and saw here on the list 
that the one should use the average structure as the reference structre 
in the -s option in g_covar.

I made my average structure with g_rmsf but when I ran g_covar

g_covar -f md.trr -s xaver.pdb -ascii covar.dat -ref

I got these comments and error:

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

Calculating the average structure ...
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000   Fatal error: Error: Too many 
iterations in routine JACOBI

Why does it say "broken molecule" when I have full trajectory and an 
average structure what am I doing wrong to cause the error?

Many thanks to all commets.

All my best, Una