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 etcuntil 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. Davide
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