Marcelo Müller wrote:
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
Check out the .log file for the real error message, rather than stderr.
I expect you will see LINCS warnings, and that your system hasn't been
prepared/minimized/equilibrated carefully enough, which is causing
problems down the road. See
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings and
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
There are many other more likely sources of problems than a memory
limitation.
Mark
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