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On 28/03/2012 1:00 PM, Davide Mercadante wrote:
<blockquote cite="mid:CB98D822.9101%25dmer018@aucklanduni.ac.nz"
type="cite">
<div>Dear Gromacs Users,</div>
<div><br>
</div>
<div>I am trying to run g_cluster to find an average structure for
my system and after giving the following command line:</div>
<div><br>
</div>
<div>g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot<span
style="font-style: italic">_</span>XM.pdb -n –g</div>
<div><br>
</div>
<div>g_cluster started without problems and continued calculating
the matrix etc…until I got this:</div>
<div><br>
</div>
<div>
<div>Last frame 5000 time 50000.004 </div>
<div>Allocated 645448320 bytes for frames</div>
<div>Read 5001 frames from trajectory allnj10_XM10.xtc</div>
<div>Computing 5001x5001 RMS deviation matrix</div>
<div># RMSD calculations left: 0 </div>
<div><br>
</div>
<div>The RMSD ranges from 0.0816802 to 0.301369 nm</div>
<div>Average RMSD is 0.208468</div>
<div>Number of structures for matrix 5001</div>
<div>Energy of the matrix is 364.532 nm</div>
<div>WARNING: rmsd minimum 0 is below lowest rmsd value
0.0816802</div>
<div>Linking structures **************</div>
<div>Sorting and renumbering clusters</div>
<div><br>
</div>
<div>Found 1425 clusters</div>
<div><br>
</div>
<div>Writing middle structure for each cluster to
pdb_ligplot_XM.pdb</div>
<div>Segmentation fault: 11</div>
</div>
<div><br>
</div>
<div>Can you please help me to understand where the problem comes
from and how I can solve it? </div>
<div>Any help is greatly appreciated. <br>
</div>
</blockquote>
<br>
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 <a href="http://redmine.gromacs.org/">http://redmine.gromacs.org/</a>
and upload your files and instructions on how to reproduce the
problem.<br>
<br>
Mark<br>
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