[gmx-users] Segmentation Fault using g_cluster

[Mark Abraham]

On 28/03/2012 1:00 PM, Davide Mercadante wrote:
> Dear Gromacs Users,
>
> I am trying to run g_cluster to find an average structure for my 
> system and after giving the following command line:
>
> g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n --g
>
> g_cluster started without problems and continued calculating the 
> matrix etc...until I got this:
>
> Last frame       5000 time 50000.004
> Allocated 645448320 bytes for frames
> Read 5001 frames from trajectory allnj10_XM10.xtc
> Computing 5001x5001 RMS deviation matrix
> # RMSD calculations left: 0
>
> The RMSD ranges from 0.0816802 to 0.301369 nm
> Average RMSD is 0.208468
> Number of structures for matrix 5001
> Energy of the matrix is 364.532 nm
> WARNING: rmsd minimum 0 is below lowest rmsd value 0.0816802
> Linking structures **************
> Sorting and renumbering clusters
>
> Found 1425 clusters
>
> Writing middle structure for each cluster to pdb_ligplot_XM.pdb
> Segmentation fault: 11
>
> Can you please help me to understand where the problem comes from and 
> how I can solve it?
> Any help is greatly appreciated.

I don't think this should happen. You haven't stated your GROMACS 
version. If you can reproduce this with 4.5.5., please open an issue 
here http://redmine.gromacs.org/ and upload your files and instructions 
on how to reproduce the problem.

Mark
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