[gmx-users] trjconv -dump buffer overflow

[Marlon Sidore]

It happens even with the first frame of the .xtc

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-05-31 19:35 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> It's hard to say. Does it happen with earlier frames?
>
> Mark
>
> On Mon, May 30, 2016 at 4:33 PM Marlon Sidore <marlon.sidore at gmail.com>
> wrote:
>
> > Dear Gromacs users,
> >
> > I'm trying to output frames of my trajectory to individual .gro files and
> > have been trying to use trjconv -dump (or -sep, which gives the same
> > outcome).
> > My system is a martini CG membrane with a protein inside, although I
> don't
> > think the system is the problem as I could run other tools, or the same
> > one, through it (cutting the trajectory is also fine with the very same
> > tool).
> >
> > Once trjconv reaches the appropriate time ... it crashes with a buffer
> > overflow. I've attached a small part of the error at the end (not sure if
> > the whole error is needed ?).
> > The command I'm using is this:
> > "gmx trjconv -f vicl.xtc -pbc whole -s vicl.tpr -o frame_dump_0.gro -dump
> > 3600000"
> > I'm using Gromacs 5.1 (the trajectory comes from it) - and the error is
> > also there with Gromacs 5.1.2.
> >
> > Thanks in advance
> >
> > """
> > Back Off! I just backed up frame_dump_0.gro to ./#frame_dump_0.gro.3#
> > Reading frame    1000 time 3600000.000
> > Dumping frame at t= 3.6e+06 ps
> > *** buffer overflow detected ***:
> > /home/ubuntu/progs/gromacs-5.1.2/build/bin/gmx terminated
> > ======= Backtrace: =========
> > /lib/x86_64-linux-gnu/libc.so.6(+0x7333f)[0x7f70e1e6933f]
> > /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f70e1f00ccc]
> > ...
> > """
> >
> > Marlon Sidore
> >
> >
> > PhD Student
> > Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
> > CNRS - UMR7255
> > 31, Chemin Joseph Aiguier
> > 13402 cedex 20 Marseille
> > France
> > --
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