Dear Jason,
Thanks very much for your suggestion. Next time I will have a try. For this
time, how should I check the trajectory, RMSD and RMSF? Thanks!
Best Regards,
Qinghua
On Wed, Dec 14, 2011 at 10:55 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Dec 14, 2011 at 4:31 PM, Qinghua Liao <fantasticqhl.gmail.com
> >wrote:
>
> > Dear amber users,
> >
> > I did simulations using a simple script like this:
> >
> > #!/bin/bash
> >
> > mpiexec -np 24 sander.MPI -O -i min1.in -o min1.out -p com_solv.prmtop
> -c
> > com_solv.inpcrd -r min1.rst -ref com_solv.inpcrd
> > mpiexec -np 24 sander.MPI -O -i min2.in -o min2.out -p com_solv.prmtop
> -c
> > min1.rst -r min2.rst -ref min1.rst
> > mpiexec -np 24 sander.MPI -O -i min3.in -o min3.out -p com_solv.prmtop
> -c
> > min2.rst -r min3.rst -ref min2.rst
> > mpiexec -np 24 sander.MPI -O -i heat.in -o heat.out -p com_solv.prmtop
> -c
> > min3.rst -r heat.rst -x heat.mdcrd -ref min3.rst
> > mpiexec -np 24 sander.MPI -O -i density.in -o density.out -p
> > com_solv.prmtop -c heat.rst -r density.rst -x density.mdcrd -ref heat.rst
> > mpiexec -np 24 sander.MPI -O -i equil.in -o equil.out -p com_solv.prmtop
> > -c
> > density.rst -r equil.rst -x equil.mdcrd -ref density.rst
> > mpiexec -np 24 pmemd.MPI -O -i md.in -o md1.out -p com_solv.prmtop -c
> > equil.rst -r md1.rst -x md1.mdcrd -ref equil.rst
> > mpiexec -np 24 pmemd.MPI -O -i md.in -o md2.out -p com_solv.prmtop -c
> > md1.rst -r md2.rst -x md2.mdcrd -ref md1.rst
> > mpiexec -np 24 pmemd.MPI -O -i md.in -o md3.out -p com_solv.prmtop -c
> > md2.rst -r md3.rst -x md3.mdcrd -ref md2.rst
> > mpiexec -np 24 pmemd.MPI -O -i md.in -o md4.out -p com_solv.prmtop -c
> > md3.rst -r md4.rst -x md4.mdcrd -ref md3.rst
> > mpiexec -np 24 pmemd.MPI -O -i md.in -o md5.out -p com_solv.prmtop -c
> > md4.rst -r md5.rst -x md5.mdcrd -ref md4.rst
> >
> > I found that simulation of md3 was initiated even when md2 was not
> > finished. Why did this situation happen? I just can't understand, I
> believe
> > that it should be done one by one.
> >
>
> I'm guessing your md2 calculation died. If the script you gave us above is
> accurate, that's the only explanation that makes sense to me. You can use
> "top" to analyze the running processes to verify this if you'd like.
>
> My suggestion is to look for the error message (where would the standard
> error stream have gone?). The issue is that each step will continue even
> if the step before it failed. You can do something like this:
>
> #!/bin/bash
>
> error() {
> echo "pmemd failed!"
> exit 1
> }
>
> mpiexec -np 24 sander.MPI -O -i min1.in -o min1.out -p com_solv.prmtop -c
> com_solv.inpcrd -r min1.rst -ref com_solv.inpcrd || error
> ... etc.
>
> That way, if a process fails, then it's picked up by the error() function
> you defined and it bails out. (I'm not positive this will work with all
> MPIs, but I think it should be fine)
>
> HTH,
> Jason
>
> --
> 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 Thu Dec 15 2011 - 00:30:03 PST
