<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br><div class="plainMail">Hi Gmxers,<br><br>Sorry, Eric and David, <br><br>I cannot transfer my trr file to report a bug because of its huge size.<br>It is just a regular protein with 70 Angstrom cubic TIP5P water box in Charmm27 force field. That's all of the system.<br><br>But anyway, i included the mdp file in the attachment.<br><br>Hopefully someone can help me.<br><br>Many thanks,<br><br>Yao <br><br><br><br><br>--- On Wed, 9/29/10, Erik Marklund <<a ymailto="mailto:erikm@xray.bmc.uu.se" href="/mc/compose?to=erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>> wrote:<br><br>> From: Erik Marklund <<a ymailto="mailto:erikm@xray.bmc.uu.se" href="/mc/compose?to=erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>><br>> Subject: Re: [gmx-users]
g_hbond segmentation fault<br>> To: "Discussion list for GROMACS users" <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Date: Wednesday, September 29, 2010, 7:55 AM<br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> Hi,<br>> <br>> <br>> <br>> Could you file a bugzilla and attach the trr and tpr<br>> files please?<br>> If you do I'll try to sort it out today or at least<br>> this week.<br>> <br>> <br>> <br>> Erik<br>> <br>> <br>> <br>> Yao Yao skrev 2010-09-29 08.22:<br>> <br>>
<br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> I tried without -dt or -e, still the same<br>> problem exists<br>> in either case.<br>> <br>> <br>> <br>> Thanks,<br>>
<br>> <br>> <br>> Yao<br>> <br>> <br>> <br>> --- On Wed, 9/29/10, David van der Spoel<br>> <<a ymailto="mailto:spoel@xray.bmc.uu.se" href="/mc/compose?to=spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>> wrote:<br>> <br>> <br>> <br>> From: David van der Spoel <<a ymailto="mailto:spoel@xray.bmc.uu.se" href="/mc/compose?to=spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>> <br>>
Subject: Re: [gmx-users] g_hbond<br>> segmentation fault<br>> <br>> To: "Discussion list for GROMACS<br>> users"<br>> <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <br>> Date: Wednesday, September 29, 2010, 6:11<br>> AM<br>> <br>> <br>> <br>> On<br>> 2010-09-29 08.02, Yao Yao<br>> wrote:<br>> <br>>
> Hi Gmxers,<br>> <br>> ><br>> <br>> > I used the command line,<br>> <br>> ><br>> <br>> > g_hbond -f tst.trr -s tst.tpr -ac<br>> test -e 500<br>> -dt 1<br>> <br>> ><br>> <br>> > and I got the message like,<br>> <br>> ><br>>
<br>> try without the -dt 1<br>> <br>> <br>> <br>> ><br>> ----------------------------------<br>> <br>> > Found 1048 different hydrogen<br>> bonds in<br>> trajectory<br>> <br>> > Found 2292 different atom-pairs<br>> within hydrogen<br>> bonding distance<br>> <br>> >
Merging hbonds with Acceptor and<br>> Donor swapped<br>> <br>> > 2/10915 *Segmentation fault*<br>> <br>> ><br>> __________________________________<br>> <br>> ><br>> <br>> > Anyone knows what could be the<br>> reason for this<br>> Segmentation Fault ?<br>> <br>> ><br>> <br>> > A couple of Q's I am also<br>> curious,<br>>
<br>> ><br>> <br>> > why do we need to swap Acceptors<br>> and Acceptors<br>> when merging hbonds?<br>> <br>> ><br>> <br>> > Does gromacs suggest that the<br>> number of<br>> different hydrogen bonds in<br>> <br>> > trajectory<br>> <br>> > should be the same as
that of<br>> different<br>> atom-pairs within hydrogen<br>> <br>> > bonding distance?<br>> <br>> ><br>> <br>> > Thanks,<br>> <br>> ><br>> <br>> > Yao<br>> <br>> ><br>> <br>> ><br>> <br>>
><br>> <br>> <br>> <br>> <br>> <br>> -- <br>> <br>> David van der Spoel, Ph.D., Professor<br>> of Biology<br>> <br>> Dept. of Cell & Molec. Biol.,<br>> Uppsala<br>> University.<br>> <br>> Box 596, 75124 Uppsala, Sweden.<br>> Phone: <br>>
+46184714205.<br>> <br>> <a ymailto="mailto:spoel@xray.bmc.uu.se" href="/mc/compose?to=spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <br>> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>> <br>> -- <br>> <br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> <br>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a><br>> before posting!<br>> <br>> Please don't post (un)subscribe<br>> requests to the<br>> list. Use the <br>> <br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>>
<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> -- <br>> -----------------------------------------------<br>> Erik Marklund, PhD student<br>>
Dept. of Cell and Molecular Biology, Uppsala University.<br>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>> phone: +46 18 471 4537 fax: +46 18 511 755<br>> <a ymailto="mailto:erikm@xray.bmc.uu.se" href="/mc/compose?to=erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br>> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a><br>> <br>> <br>> <br>> <br>> -----Inline Attachment Follows-----<br>> <br>> -- <br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search"
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