hi 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: [EMAIL PROTECTED] > To: gmx-users@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 > ________________________________ > Notícias direto do New York Times, gols do Lance, videocassetadas e muitos > outros vídeos no MSN Videos! Confira já!
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