Are you using iwrap=1? If not, do you see any *****s in your restart file?
If so, this list is full of reports about why it happens and what it means.
HTH,
Jason
On Mon, Oct 17, 2011 at 1:12 AM, Chinh Su Tran To
<chinh.sutranto.gmail.com>wrote:
> Dear Adrian,
>
> I got a similar situation here. I was running unfolding for my protein. It
> was supposed to run for 60ns, but it stopped at the 18th nano-second
> because
> the rst file was not generated at that point of time.
>
> As I checked the results, it shows:
>
> heat3.mdcrd *with the size *1319492081 (~1.3 Gb)
> heat3.out 1047322
> heat3.rst 1982053
>
> Note that the size are the same as the heat2's files accordingly. But the
> heat2 was fine (i.e. heat2.mdcrd has 2000 frames, heat2.rst has 1 frame).
> Then I visualized the heat3.mdcrd and heat3.rst on VMD. Only the
> heat3.mdcrd
> showed up (with 2000 frames), but the heat3.rst did not (0 frame).
> The VMD error said:
>
> Problem when reading the CRD file
>
> We doubted that the problem came from MPI of sander because it showed "the
> mpi exit without calling finalize" when the job ran on 4 nodes (8 ppn).
> Hence, I re-ran the job only on 1 node. There was no such error this time,
> but still nothing was shown in the heat3.rst!!!!
>
> Could you please give me any suggestion? I am using Amber 10.
>
> Thank you.
>
> Regards,
> Chinh
>
> On Thu, Oct 13, 2011 at 4:48 AM, Adrian Roitberg <roitberg.qtp.ufl.edu
> >wrote:
>
> > yes, absolutely
> > now, I am not sure what you mean by 'not usable'
> >
> > if you mean that data is missing or corrupted, then either the file was
> > not fully written when you hit the wallclock
> > or that your molecular is flying outside your box (if you see *** for
> > instance).
> >
> > Now, can you visualize the restart file into vmd ?
> >
> > if that does not work, then the file is truncated/corrupted.
> >
> > If you can visualize it, try running a regular sander/pmemd run without
> > smd. If that works, then the restart is fine...
> >
> > Remember that to restart an SMD run you MUST change the restraint file,
> > since you are now starting your SMD from whatever coordinates you last
> > saved !
> >
> > Adrian
> >
> >
> > On 10/12/11 4:39 PM, Mo Chen wrote:
> > > Hi Adrian,
> > > I understand that. I actually meant to say that I heard the restart
> file
> > of
> > > SMD simulation is not quite usable even if my simulation did not run
> out
> > of
> > > the wall time. Basically I have just heard that, but I am sorry I have
> > not
> > > tried myself and I did not know why. In your last email, do you mean if
> > the
> > > restart file is saved properly before the end of the walltime, I should
> > be
> > > able to use it as a restart file? Thank you very much!
> > >
> > > Best,
> > > Mo
> > >
> > > On Wed, Oct 12, 2011 at 4:30 PM, Adrian Roitberg<roitberg.qtp.ufl.edu
> > >wrote:
> > >
> > >> This has nothing to do with SMD runs.
> > >>
> > >> If you hit the wallclock time, you sometimes do not see the 'last'
> > >> restart fully written.
> > >>
> > >>
> > >> You can pick the last frame form the mdcrd and create your new
> restart.
> > >>
> > >> Adrian
> > >>
> > >>
> > >> On 10/12/11 4:26 PM, Mo Chen wrote:
> > >>> Dear Amber users/developers,
> > >>> I am trying to run SMD simulations on Ranger, but my simulations
> could
> > >> not
> > >>> finish before the maximum runtime (24 hours) even though I would use
> > the
> > >>> optimal number of cores. And I heard the SMD restart file is not
> quite
> > >>> usable, but I did not understand why. May I ask anyone has
> encountered
> > >>> similar situations? And how should I solve this problem? Thank you
> very
> > >>> much!
> > >>>
> > >>>
> > >>> Best,
> > >>> Mo Chen
> > >>> Graduate Student
> > >>> 120 Stocking Hall
> > >>> Cornell University
> > >>> Ithaca, NY 14850
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >> --
> > >> Dr. Adrian E. Roitberg
> > >> Professor
> > >> Quantum Theory Project, Department of Chemistry
> > >> University of Florida
> > >> roitberg.ufl.edu
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > --
> > Dr. Adrian E. Roitberg
> > Professor
> > Quantum Theory Project, Department of Chemistry
> > University of Florida
> > roitberg.ufl.edu
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Oct 16 2011 - 23:30:02 PDT
