[gmx-users] Segmentation fault
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
Confira vídeos com notícias do NY Times, gols direto do Lance, videocassetadas e muito mais no MSN Video!
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users