[gmx-users] Re:restart run problem

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 29 17:24:42 CEST 2008

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> 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
> previous

This indicates to me that the minimization and/or equilibration procedure was
not sufficient and you still have some bad contacts, or the parameters you've
chosen for your simulation are incorrect.  So you will likely need to
reconsider how you did things and generate a happier starting structure.


> 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.
> -Justin


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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