[gmx-users] Crush after ~135 ps
yesint4 at yahoo.com
Thu Jul 10 08:08:01 CEST 2003
Dear GMX users,
Thanks to your help I've set up a simulation of my
protein. It was expected to be 1ns run, however it
crashed after ~135 ps.
The last message in the log was something like this:
"Can't set a water molecule starting from atom ###,
fatal error at bla-bla-bla.c line ###", than I was
asked to reduce the step size or to check the system.
The system was solwated by ~8000 water molecules in a
rectangular box. PME with the defauls params from the
manual was used.
So far I've found several suspicious points:
1) Too short equilibration of the solvent with
2) Exposure of the hydrophobic areas in the protein
(it is a membrane protein, but I put it into the box
3) The system is not neutral (+7)
However, I still can't understand why the simulation
crashed after quite long successful run.
Any ideas how to fix this problem?
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