Hello,
attached file is for my nmode calculation,including input and script file.
2011/4/15 Jason Swails <jason.swails.gmail.com>
> Can you attach your script that you're using to run it? Based on the
> information given I don't see how that error can be occurring.
>
> 2011/4/14 陳昭同 <dond750507.gmail.com>
>
> > echo $AMBERHOME
> > shows /opt/amber11
> >
> > 2011/4/15 Jason Swails <jason.swails.gmail.com>
> >
> > > None of this addresses the problem you reported. Will you please paste
> > the
> > > results of the command
> > >
> > > echo $AMBERHOME
> > >
> > > here to see if we can locate the problem?
> > >
> > > Thanks,
> > > Jason
> > >
> > > 2011/4/14 陳昭同 <dond750507.gmail.com>
> > >
> > > > Hello,
> > > > yes, it may not take long time for PB(GB)SA calculation using
> MMPBSA.py
> > > in
> > > > serial.
> > > > but nab_nmode calculation is such difference,it take almost 20hrs for
> > "1
> > > > frame" calculation(is it normally?)
> > > > if I want to calculate 5 frame TdeltaS by nab_nmode,I think it's not
> > > > practically.
> > > > That's the reason I think the MMPBSA.py.MPI method is workable or
> not.
> > > >
> > > > Also,I change the execute file name,but it show the same error.
> > > >
> > > > Did it really take such time for nab_nmode calculation by MMPBSA.py
> in
> > > > serial?
> > > > Or it had better using MMPBSA.py.MPI for runnung?
> > > >
> > > > Sorry for my English and such questions
> > > >
> > > > Thans for your help.
> > > >
> > > >
> > > > 2011/4/14 Bill Miller III <brmilleriii.gmail.com>
> > > >
> > > > > Just out of curiosity, why are you using the parallel version of
> > > > MMPBSA.py
> > > > > if you are only running a single thread for the calculation? Have
> you
> > > > tried
> > > > > running the same calculation in serial just using MMPBSA.py without
> > > > mpirun?
> > > > >
> > > > > Oh, and have you tried changing the execute file name? Does this
> make
> > a
> > > > > difference?
> > > > >
> > > > > -Bill
> > > > >
> > > > > On Thu, Apr 14, 2011 at 5:34 AM, 陳昭同 <dond750507.gmail.com> wrote:
> > > > >
> > > > > > Dear Amber user's
> > > > > >
> > > > > > I try to us MMPBSA.py.MPI for nab_nmode calculation
> > > > > > So I install the mpi4py for python version.(Using PGI compile)
> > > > > > I'm sure the MMPBSA.py version have updated to lastest
> > one(5/24/2010)
> > > > > >
> > > > > > My input file is
> > > > > > Input file for running entropy calculations using NMode
> > > > > > &general
> > > > > > endframe=50, keep_files=2,
> > > > > > /
> > > > > > &nmode
> > > > > > nmstartframe=5, nmendframe=45,
> > > > > > nminterval=5, nmode_igb=1, nmode_istrng=0.1,
> > > > > > /
> > > > > > is same as tutorial input file from Amber website
> > > > > >
> > > > > > and the most possible problem is my execute file(named md)
> > > > > >
> > > > > > mpirun -np 1 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa2.in -o
> > > > > > FINAL_RESULTS_MMPBSA.dat -sp 02-S.top -cp 02-com.top -rp
> > receptor.top
> > > > -lp
> > > > > > 02.top -y min3.mdcrd > progress.log
> > > > > > $AMBERHOME is /opt/amber11
> > > > > > When I running execute file(./md)
> > > > > > there is a error message
> > > > > > Error: Command line argument "-p4pg" not recognized!
> > > > > >
> > > > > > I search similiar question on Website
> > > > > > but I don't know what's wrong with it
> > > > > >
> > > > > > What's the possible problem and how can I fixed it
> > > > > >
> > > > > > Thanks for your help
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Bill Miller III
> > > > > Quantum Theory Project,
> > > > > University of Florida
> > > > > Ph.D. Graduate Student
> > > > > 352-392-6715
> > > > > _______________________________________________
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> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
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> > > > 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
> > >
> > _______________________________________________
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> > 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
>
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Received on Thu Apr 14 2011 - 20:00:03 PDT
