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Hi,<br>
<br>
Could you file a bugzilla and attach the trr and tpr files please?
If you do I'll try to sort it out today or at least this week.<br>
<br>
Erik<br>
<br>
Yao Yao skrev 2010-09-29 08.22:
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I tried without -dt or -e, still the same problem exists
in either case.
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<div>Thanks,</div>
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<div>Yao<br>
<br>
--- On <b>Wed, 9/29/10, David van der Spoel <i><a class="moz-txt-link-rfc2396E" href="mailto:spoel@xray.bmc.uu.se"><spoel@xray.bmc.uu.se></a></i></b>
wrote:<br>
<blockquote style="border-left: 2px solid rgb(16, 16,
255); margin-left: 5px; padding-left: 5px;"><br>
From: David van der Spoel <a class="moz-txt-link-rfc2396E" href="mailto:spoel@xray.bmc.uu.se"><spoel@xray.bmc.uu.se></a><br>
Subject: Re: [gmx-users] g_hbond segmentation fault<br>
To: "Discussion list for GROMACS users"
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
Date: Wednesday, September 29, 2010, 6:11 AM<br>
<br>
<div class="plainMail">On 2010-09-29 08.02, Yao Yao
wrote:<br>
> Hi Gmxers,<br>
><br>
> I used the command line,<br>
><br>
> g_hbond -f tst.trr -s tst.tpr -ac test -e 500
-dt 1<br>
><br>
> and I got the message like,<br>
><br>
try without the -dt 1<br>
<br>
> ----------------------------------<br>
> Found 1048 different hydrogen bonds in
trajectory<br>
> Found 2292 different atom-pairs within hydrogen
bonding distance<br>
> Merging hbonds with Acceptor and Donor swapped<br>
> 2/10915 *Segmentation fault*<br>
> __________________________________<br>
><br>
> Anyone knows what could be the reason for this
Segmentation Fault ?<br>
><br>
> A couple of Q's I am also curious,<br>
><br>
> why do we need to swap Acceptors and Acceptors
when merging hbonds?<br>
><br>
> Does gromacs suggest that the number of
different hydrogen bonds in<br>
> trajectory<br>
> should be the same as that of different
atom-pairs within hydrogen<br>
> bonding distance?<br>
><br>
> Thanks,<br>
><br>
> Yao<br>
><br>
><br>
><br>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala
University.<br>
Box 596, 75124 Uppsala, Sweden. Phone:
+46184714205.<br>
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<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>
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