Can you attach your prmtop and "bad" restart file here? There's little hope
of determining the problem if we can't reproduce it.
All the best,
Jason
On Mon, Oct 17, 2011 at 2:29 AM, Chinh Su Tran To
<chinh.sutranto.gmail.com>wrote:
> Hi Jason,
>
> I did not use iwrap=1. This is my input.in file:
>
> #heating in 6ns at 500K without restraint on the model to unfold the
> protein
> &cntrl
> imin=0,
> irest=0,
> ntx=1,
> ntb=1,
> cut=10.0,
> ntr=0,
> ntc=2,
> ntf=2,
> tempi=500.0,
> temp0=500.0,
> ntt=3,
> gamma_ln=1.0,
> nstlim=3000000, dt=0.002,
> ntpr=1500, ntwx=1500,ntwr=1000
> /
>
> And I did not find any *****s in the restart file as you said. This is my
> rst file result:
>
> 27149 0.1800000E+05
> 35.0751404 19.2096947 42.9562043 34.6961887 19.3553339 42.0313836
> 35.2834506 18.2235648 42.8909497 34.2289842 19.3807513 43.4804746
> 36.2015190 20.0948059 43.2344232 35.9385919 21.0028435 42.6918014
> .....
> -0.9359383 -1.0136912 0.9858400
> 73.8806979 73.8806979 73.8806979 109.4712190 109.4712190 109.4712190
>
> It looks like a complete output, but no frame shown when I visualized it in
> VMD.
> And consequently, it caused error for the next 6ns-run.
>
> Please help. Thanks.
>
> Chinh
>
>
>
> On Mon, Oct 17, 2011 at 1:58 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > 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
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 17 2011 - 04:00:02 PDT
