Unfortunately, you should just re-run the entire calculation again unless
you wanted to do all of the statistics on your own.
-Bill
On Mon, Apr 16, 2012 at 12:31 PM, Victor Ma <victordsmagift.gmail.com>wrote:
> So can I still finish the few terminated jobs from the beginning and then
> use MMPBSA.MPI to merge them in the end?
>
> Thanks,
> Victor
>
> On Mon, Apr 16, 2012 at 11:21 AM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
>
> > Unfortunately, the calculation must be restarted from the beginning if
> one
> > or more threads ended unexpectedly. The restart files that are created
> are
> > used during the calculations, and are not actually restart files used to
> > restart the calculation.
> >
> > Also, MMPBSA.py.MPI will merge all the results in the end to make the
> final
> > output file.
> >
> > -Bill
> >
> > On Mon, Apr 16, 2012 at 12:12 PM, Victor Ma <victordsmagift.gmail.com
> > >wrote:
> >
> > > hi
> > >
> > > I'm doing energy decomposition in mmpbsa. Since it's really slow
> running
> > in
> > > serial, so I'm doing the calculation with MMPBSA.MPI on 24 nodes.
> > HOwever,
> > > among the 24 parallel jobs, a few of them terminated unexpectedly. Is
> > there
> > > anyway to rescue the calculation instead of starting from scratch
> again?
> > I
> > > imagine I could try something like this:
> > >
> > > mpiexec_ssh -np 24 MMPBSA.MPI -O -i _MMPBSA_pb_decomp_com.mdin -o
> > > _MMPBSA_complex_pb.mdout.1 -sp complex_wat.prm -cp complex_new.prm -rp
> > > receptor.prm -lp lig.prm -y _MMPBSA_complex.mdcrd.1 -r
> _MMPBSA_.restrt.1
> > >
> > > Or since there is a restart file "_MMPBSA_.restrt.1", can I resume the
> > > calculation?
> > >
> > > Also how do i merge all these separate calculations in the end?
> Thanks!!
> > >
> > > Best,
> > > Victor
> > > _______________________________________________
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> > >
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Apr 16 2012 - 14:00:03 PDT
