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
> > > _______________________________________________
> > > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Apr 14 2011 - 19:30:03 PDT
