[gmx-users] Segmentation fault

Marcelo Müller marcelomuller at hotmail.com
Sat Dec 29 15:09:10 CET 2007


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 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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