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
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