[gmx-users] Re:restart run problem

sudheer babu sudheer.pbm07 at gmail.com
Tue Apr 29 17:04:12 CEST 2008

Thanks for reply Justin,
I have given run 375000 steps but in between simulation stopped, in terminal
showed that segmentation fault and in .log file showed that
"t = 650.000 ps: Water molecule starting at atom 14549 can not be settled.
Check for bad contacts and/or reduce the time step.Wrote pdb files with
and current coordinates"
I have start from the scratch?
Thanks for your appreciation.

>* HI all,
*>* My simulation crashed mid of the run , I genrated restart.tpr by using
*>* tpbconv command for restart my simulation, Then I when I give mdrun -v
*>* -deffnm restart.tpr
*>* It showed below mentioned two lines  and stopped.
*>* "Wrote pdb files with previous and current coordinates
*>* step 0, will finish at Sat May  3 02:07:06 2008Segmentation fault"
*>* Could you tell me the reason
*>* Thanks for your appreciation
Did your simulation crash with a segmentation fault/LINCS warnings, etc?  If so,
tpbconv won't magically rescue your simulation, there's something physically
unreasonable about it and you need to reconsider your
minimization/equilibration scheme.

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