<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Thank you for the prompt reply.! Indeed, I am using Gromacs version 4.5.5 compiled in double-precision and I am running the analysis on a MacBook PRO.</div><div><br></div><div>I tried to open an issue at <a href="http://redmine/gromacs.org">http://redmine/gromacs.org</a> but it asks me for login name and passwd which I don't think I have as I never subscribed as developer. I may be wrong though..do I need to register? </div><div>I suppose that if this is not an explainable issue at the moment there is no solution to it?</div><div><br></div><div>Thank you again for the reply. It has been much appreciated.</div><div><br></div><div>Davide</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br><span style="font-weight:bold">Reply-To: </span> Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><span style="font-weight:bold">Date: </span> Wed, 28 Mar 2012 13:29:40 +1100<br><span style="font-weight:bold">To: </span> Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [gmx-users] Segmentation Fault using g_cluster<br></div><div><br></div><div>
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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>
</div></div>
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