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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