[gmx-users] restarting simulation after segmentation fault

Justin A. Lemkul jalemkul at vt.edu
Tue May 8 17:44:33 CEST 2012

On 5/8/12 11:40 AM, Za Pour wrote:
> Dear gmx users
> I am simulating a system involving carbon nanotube.
> I successfully completed the EM,NVT and NPT equilibration phase and then
> started to run production simulation(NVT ensemble) for 10 ns.However,
> after passing more than 500000 steps(1 ns),I gave the segmentation error.I
> investigated log file but it did not contain any errors so I used tpbconv and
> mdrun to restart the simulation.I would be pleased if you could tell me whether
> restarting the simulation after segmentation fault is correct or not?

More often than not, a segmentation fault indicates the system is unstable and 
will likely crash again.  The log file will not indicate any errors, but 
information printed to stderr/stdout will.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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