[gmx-users] trjconv -dump buffer overflow

Marlon Sidore marlon.sidore at gmail.com
Mon May 30 16:33:10 CEST 2016

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
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

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
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: =========

Marlon Sidore

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

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