[gmx-users] g_cluster fatal error

Louis Lategan Du Preez lategandupreezl at ufs.ac.za
Wed Sep 15 08:49:00 CEST 2010


I am trying to cluster an extremely large trajectory (about 550 ns) with g_cluster and i get the following fatal error from g_cluster:

Select a group: 1
Selected 1: 'Protein'
Reading frame   20000 time  500.000   
Allocated 171637200 bytes for frames
Read 20847 frames from trajectory MutTailA00000.xtc
Computing 20847x20847 RMS deviation matrix
# RMSD calculations left: 0           

The RMSD ranges from 0.0994814 to 2.5311 nm
Average RMSD is 0.160043
Number of structures for matrix 20847
Energy of the matrix is 8507.75 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0994814
Linking structures **
Sorting and renumbering clusters

Found 20846 clusters

Writing middle structure for each cluster to clusters.pdb
Counted 20845 transitions in total, max 0 between two specific clusters

Program g_cluster, VERSION 4.5.1
Source code file: matio.c, line: 943

Fatal error:
hi (0.000000) <= lo (0.000000)

The command-line options i used were:

g_cluster -f MutTailA00000.xtc -dist -sz -tr -clid -cl -tu ns -method linkage -s topol.pdb

Please help



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