[gmx-users] Segmentation fault

pragya chohan pragyachohan at hotmail.com
Sat Dec 29 19:34:58 CET 2007

generally sementation fault occurs due to bad contacts in the system. As suggested by Mark see if the log file lists atom which have the problem.
> From: marcelomuller at hotmail.com
> To: gmx-users at gromacs.org
> Date: Sat, 29 Dec 2007 17:09:10 +0300
> Subject: [gmx-users] Segmentation fault
> Hello,
> I'm getting some problems about segmentation fault. I'm doing a protein simulation during 20 ns on a water cubic box with a total of 23000 atoms.  I'm using the TIP3P water model at 300 K. Interestingly, when I use the Berendsen barostat for pressure coupling, I've got a segmentation fault about 1 ns of trajectory. When I don't use it the simulation extends untill 10 ns, but the fault also occurs. Could it be some problem with memory limitation of the computer? I'm using a cluster to run the simulations, and I'm trying to check the memory capacity of the node that I've used.
> Besides, the message that I've seen is something like that:
> Step #number of the step and time     mdrun -v -deffnm run   Segmentation fault
> Thank so much for the help and happy new year
> Marcelo
> Marcelo Müller dos Santos, Ph.D. student
> Laboratorio de Tecnologia Enzimatica e Biocatalise
> Departamento de Bioquimica e Biologia Molecular, Setor de Ciencias Biologicas, Centro Politecnico, Jardim da Américas, Curitiba - PR, Caixa Postal: 190-46, CEP: 81531-990
> Phone: (+55) 41 3361-1658
> Fax: (+55) 41 3266-2042
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