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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Received on Thu Apr 14 2011 - 09:00:05 PDT
