[gmx-users] Segmentation fault in mdrun!!!!!!!!!!!!

David spoel at xray.bmc.uu.se
Sun Feb 23 21:15:52 CET 2003

On Sun, 2003-02-23 at 05:38, nanyu101 wrote:
> Dear gmx-users,
>  I don't know what happened to my system.I just try to minimize my bilayer(POPC128a.PDB) downloaded from Dr.Tieleman't web.I think I'v succeeded in energy minimization and tried to run some dynamics simulation.But when I run,
> mdrun -s popcmd.tpr -o popcmd.trr -c popcmd.gro
> The system told as follows. The file popcmd.tpr comes from my energy minization's results.
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
> starting mdrun 'popc'
> 20000 steps,     20.0 ps.
> Back Off! I just backed up popcem.trr to ./#popcem.trr.1#
> Segmentation fault
> Would you please tell me what happened?
What happened is a memory violation in the program. Writing an array
outside its bounds. This can be due to two things: bugs, or large
forces. Since you have reported problems equilibrating your system the
latter seems most likely.

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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