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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