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
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>
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Received on Mon Oct 17 2011 - 00:00:03 PDT
