[gmx-users] trjconv -dump buffer overflow

[Marlon Sidore]

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