[gmx-users] Segmentation Fault using g_cluster

Davide Mercadante dmer018 at aucklanduni.ac.nz
Wed Mar 28 04:00:50 CEST 2012

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
etcŠuntil 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.

Thank you.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120328/0dd199ff/attachment.html>

More information about the gromacs.org_gmx-users mailing list