Hi all and thanks Tsjerk for your reply
I found out I used the wrong group in the index file when running g_rmsf
But now when I run:
g_covar -f md.trr -s xaver.pdb -ascii covar.dat -ref
I get some memory error:
*** glibc detected *** g_covar: malloc(): memory corruption: 0x09b03660 ***
But g_covar runs fine using other -ref files like md.tpr but does not accept
the xaver.pdb file. My md.trr file is 541M does that has to do with anything.
All helpful comments are highly appreciated.
Best regards, Una
Hi Una,
Do the xaver.pdb and the md.trr correspond in terms of atom numbers?
The JACOBI error has to do with the fitting. The 'broken molecule'
thing is a warning, issued because you give a .pdb file which does not
contain information regarding connectivity, which coulod otherwise be
used to make broken molecules whole. But you shouldn't have broken
molecules if you didn't run trjconv on the trajectory with certain the
-pbc options.
Cheers,
Tsjerk
On 5/29/07, Una Bjarnadottir <[EMAIL PROTECTED]> wrote:
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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