[gmx-users] Segmentation fault with gromacs 3.3.3

Cesar Avila cavila at fbqf.unt.edu.ar
Sun Jun 29 01:16:45 CEST 2008

It seems to be a problem related to the debian package. I have compiled
gromacs 3.3.3 from source with gcc-4.3 and apparently the problem has
dissapeared. Perhaps, the binaries on the debian package were compiled
with gcc-4.1.

Cesar Avila escribió:
> Dear all,
> I am new to the gromacs simulation package. Thus far I have been using
> Charmm and NAMD, but now I am interested on testing Marrink's
> Coarse-Grained Martini FF. I managed to setup an initial configuration for
> a protein in a water box. After a few minimization steps, I ran the
> simulation for about 10 ns until it crashed with a Segmentation fault
> message.
> Using tpbconv, I resumed the simulation from 10200 ps step. Nevertheless I
> systematically found a segmentation fault  error on step 6530. Using mdrun
> -nocompact gives no additional information about the crash. When I use
> mdrun -debug the simulation is able to run without any problem (until I
> run out of disk space).
> I found the same error to occur on both a Pentium IV (debian etch) and an
> Intel Core 2 Duo (Debian lenny). Both systems
> are running gromacs 3.3.3 from Debian testing packages. If anyone is
> interested on reproducing the error on their own computer, I can send them
> the tpr file (476K compressed).
> Best regards
> Cesar Avila
> Universidad Nacional de Tucuman.
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