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Erik Marklund skrev 2010-12-18 16.36:
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Erik Marklund skrev 2010-12-18 16.23:
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leila karami skrev 2010-12-18 16.18:
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cite="mid:AANLkTimPwWBUEq5+y6e-tfBDxPCtA76gmQMGmFfNaS1Y@mail.gmail.com"
type="cite">Dear Erik<br>
<br>
excuse me, I sent .xtc and .tpr file your e-mail.<br
clear="all">
<font color="#888888"><br>
</font><br clear="all">
<br>
-- <br>
<pre style="font-family: arial,helvetica,sans-serif;">Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group</pre>
<br>
</blockquote>
I can reproduce the segfault. It doesn't happen without -hbn.
I'll have a crack at fixing it. I won't promise to have it done
before christmas, but I'll try.<br>
</blockquote>
Fixed it. There's a call to clearPshift in do_merge which causes a
segfault if g_hbond is run without -geminate. Here's what you do:<br>
<br>
In gmx_hbond.c, enclose the call in an if-statement:<br>
<br>
if (hb->per->pHist)<br>
{<br>
clearPshift(&(hb->per->pHist[a1][a2]));<br>
}<br>
<br>
I'll push this to the master and release branches some time today.<br>
<br>
Thanks for reporting this.<br>
<br>
Regards,<br>
<br>
Erik<br>
</blockquote>
As it turns out, I (or possibly someone else) had already fixed this
issue in the master and release branches. Hence the solution is
again to update your gromacs installation.<br>
<br>
Erik<br>
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<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
</pre>
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