Hi Gmxers,
Sorry, Eric and David, I cannot transfer my trr file to report a bug because of its huge size. It is just a regular protein with 70 Angstrom cubic TIP5P water box in Charmm27 force field. That's all of the system. But anyway, i included the mdp file in the attachment. Hopefully someone can help me. Many thanks, Yao --- On Wed, 9/29/10, Erik Marklund <er...@xray.bmc.uu.se> wrote: > From: Erik Marklund <er...@xray.bmc.uu.se> > Subject: Re: [gmx-users] g_hbond segmentation fault > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Wednesday, September 29, 2010, 7:55 AM > > > > > > > > Hi, > > > > 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. > > > > Erik > > > > Yao Yao skrev 2010-09-29 08.22: > > > > > > > > > > > > I tried without -dt or -e, still the same > problem exists > in either case. > > > > Thanks, > > > > Yao > > > > --- On Wed, 9/29/10, David van der Spoel > <sp...@xray.bmc.uu.se> > wrote: > > > > From: David van der Spoel <sp...@xray.bmc.uu.se> > > Subject: Re: [gmx-users] g_hbond > segmentation fault > > To: "Discussion list for GROMACS > users" > <gmx-users@gromacs.org> > > Date: Wednesday, September 29, 2010, 6:11 > AM > > > > On > 2010-09-29 08.02, Yao Yao > wrote: > > > Hi Gmxers, > > > > > > I used the command line, > > > > > > g_hbond -f tst.trr -s tst.tpr -ac > test -e 500 > -dt 1 > > > > > > and I got the message like, > > > > > try without the -dt 1 > > > > > > ---------------------------------- > > > Found 1048 different hydrogen > bonds in > trajectory > > > Found 2292 different atom-pairs > within hydrogen > bonding distance > > > Merging hbonds with Acceptor and > Donor swapped > > > 2/10915 *Segmentation fault* > > > > __________________________________ > > > > > > Anyone knows what could be the > reason for this > Segmentation Fault ? > > > > > > A couple of Q's I am also > curious, > > > > > > why do we need to swap Acceptors > and Acceptors > when merging hbonds? > > > > > > Does gromacs suggest that the > number of > different hydrogen bonds in > > > trajectory > > > should be the same as that of > different > atom-pairs within hydrogen > > > bonding distance? > > > > > > Thanks, > > > > > > Yao > > > > > > > > > > > > > > > -- > > David van der Spoel, Ph.D., Professor > of Biology > > Dept. of Cell & Molec. Biol., > Uppsala > University. > > Box 596, 75124 Uppsala, Sweden. > Phone: > +46184714205. > > sp...@xray.bmc.uu.se > http://folding.bmc.uu.se > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search > before posting! > > Please don't post (un)subscribe > requests to the > list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read >http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > -- > ----------------------------------------------- > 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 > er...@xray.bmc.uu.se > http://folding.bmc.uu.se/ > > > > > -----Inline Attachment Follows----- > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search > before posting! > Please don't post (un)subscribe requests to the list. Use > the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
nvt.mdp
Description: Binary data
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