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

[Mark Abraham]

Una Bjarnadottir wrote:
> 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.

The matrix you are diagonalizing is probably too big. Reduce the 
dimensionality of your problem - either system size or number of frames 
(I can't be bothered working out which of them it should be... that's 
your job :-) )

Mark