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On 28/03/2012 2:14 PM, Davide Mercadante wrote:
<blockquote cite="mid:CB98E837.9108%25dmer018@aucklanduni.ac.nz"
type="cite">
<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 moz-do-not-send="true"
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? <br>
</div>
</blockquote>
<br>
Yes, just sign up. We need to be able to contact you to let you know
the solution or get more information, so anonymous bug submission is
not very useful.<br>
<br>
<blockquote cite="mid:CB98E837.9108%25dmer018@aucklanduni.ac.nz"
type="cite">
<div>I suppose that if this is not an explainable issue at the
moment there is no solution to it?</div>
</blockquote>
<br>
The problem with plain segfaulting is that there's no way to tell
what caused the problem. GROMACS tries hard not to do this, but
clearly it's not perfect. There may be a code bug. There may be a
way for you to use the code better. We just don't know yet. There's
certainly room to improve the code.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:CB98E837.9108%25dmer018@aucklanduni.ac.nz"
type="cite">
<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;
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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
moz-do-not-send="true" 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 moz-do-not-send="true"
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 moz-do-not-send="true"
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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<div bgcolor="#FFFFFF" text="#000000"> 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 moz-do-not-send="true"
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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</blockquote>
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