[gmx-users] trjconv -dump buffer overflow

[Mark Abraham]

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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