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

Una Bjarnadottir una.bjarnadottir at ucd.ie
Thu May 31 16:47:44 CEST 2007

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.



On 5/29/07, Una Bjarnadottir <una.bjarnadottir at ucd.ie> 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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