[gmx-users] g_hbond segmentation fault
Justin A. Lemkul
jalemkul at vt.edu
Thu Sep 30 19:01:24 CEST 2010
Yao Yao wrote:
>
>
> 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.
>
Then simplify the problem. Do you get the same result when processing a single
.gro or .pdb file? What about a shorter .trr file, containing only a few
frames? If the same problem persists, then you can file a bug report with files
that are significantly smaller.
> But anyway, i included the mdp file in the attachment.
>
This doesn't indicate any obvious problem.
-Justin
> Hopefully someone can help me.
>
> Many thanks,
>
> Yao
>
>
>
>
> --- On Wed, 9/29/10, Erik Marklund <erikm at xray.bmc.uu.se
> </mc/compose?to=erikm at xray.bmc.uu.se>> wrote:
>
> > From: Erik Marklund <erikm at xray.bmc.uu.se
> </mc/compose?to=erikm at xray.bmc.uu.se>>
> > Subject: Re: [gmx-users] g_hbond segmentation fault
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org
> </mc/compose?to=gmx-users at 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
> > <spoel at xray.bmc.uu.se </mc/compose?to=spoel at xray.bmc.uu.se>>
> > wrote:
> >
> >
> >
> > From: David van der Spoel <spoel at xray.bmc.uu.se
> </mc/compose?to=spoel at xray.bmc.uu.se>>
> >
> > Subject: Re: [gmx-users] g_hbond
> > segmentation fault
> >
> > To: "Discussion list for GROMACS
> > users"
> > <gmx-users at gromacs.org
> </mc/compose?to=gmx-users at 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.
> >
> > spoel at xray.bmc.uu.se
> </mc/compose?to=spoel at xray.bmc.uu.se>
> > http://folding.bmc.uu.se
> >
> > --
> >
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> >
> >
> >
> > --
> > -----------------------------------------------
> > 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
> > erikm at xray.bmc.uu.se </mc/compose?to=erikm at xray.bmc.uu.se>
> > http://folding.bmc.uu.se/
> >
> >
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> >
> > -----Inline Attachment Follows-----
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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