<html><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><META name="Author" content="Novell GroupWise WebAccess"></head><body style='font-family: Tahoma, sans-serif; font-size: 13px; '>Hello<br><br>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:<br><br>Select a group: 1<br>Selected 1: 'Protein'<br>Reading frame 20000 time 500.000 <br>Allocated 171637200 bytes for frames<br>Read 20847 frames from trajectory MutTailA00000.xtc<br>Computing 20847x20847 RMS deviation matrix<br># RMSD calculations left: 0 <br><br>The RMSD ranges from 0.0994814 to 2.5311 nm<br>Average RMSD is 0.160043<br>Number of structures for matrix 20847<br>Energy of the matrix is 8507.75 nm<br>WARNING: rmsd minimum 0 is below lowest rmsd value 0.0994814<br>Linking structures **<br>Sorting and renumbering clusters<br><br>Found 20846 clusters<br><br>Writing middle structure for each cluster to clusters.pdb<br>Counted 20845 transitions in total, max 0 between two specific clusters<br><br>-------------------------------------------------------<br>Program g_cluster, VERSION 4.5.1<br>Source code file: matio.c, line: 943<br><br>Fatal error:<br>hi (0.000000) <= lo (0.000000)<br><br>The command-line options i used were:<br><br>g_cluster -f MutTailA00000.xtc -dist -sz -tr -clid -cl -tu ns -method linkage -s topol.pdb<br><br>Please help<br><br>TIA<br><span style="text-decoration: underline;"></span><PRE>_____________________________________________________________________
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