<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><div><br></div><div><br></div>I tried without -dt or -e, still the same problem exists in either case.<div><br></div><div>Thanks,</div><div><br></div><div>Yao<br><br>--- On <b>Wed, 9/29/10, David van der Spoel <i><spoel@xray.bmc.uu.se></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 <spoel@xray.bmc.uu.se><br>Subject: Re: [gmx-users] g_hbond segmentation fault<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><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.
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