Thanks Jason!
On Fri, Jun 18, 2010 at 6:29 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> The entropy will be similar, but not necessarily identical. You will also
> not get identical results if you compile nab with and without the intel MKL
> using just MMPBSA.py. The only difference between the two programs that I
> can see is that different diagonalization algorithms are used, but we've
> verified that both algorithms give exactly the same answer (the one chosen
> in MMPBSA.py was chosen because it performed faster in our test set).
>
> A couple things to keep in mind: mm_pbsa.pl can run in parallel via a
> "forking" method that spawns new compute threads. This is restricted, as
> far as I can tell, to shared memory machines. MMPBSA.py runs in parallel
> via MPI, so it can run on distributed memory systems (i.e. it is not
> confined to a single node). Only the most recent version of MMPBSA.py
> available has the ability to run in parallel. You can find it at
> ambermd.org/tutorials/advanced/tutorial3/py_script/ . Do not forget to
> add
> the patches to the script. Also in order to run in parallel, you have to
> compile the mpi4py package (instructions on the website).
>
> Good luck!
> Jason
>
> On Fri, Jun 18, 2010 at 7:30 AM, RANAJIT SHINDE <
> science.ranajitshinde.gmail.com> wrote:
>
> > Dear Amber members,
> >
> > I have done free energy calculations with the mm_pbsa.pl script. Now i
> > want
> > to calculate the entropy with the MMPBSA.py script as it can be save time
> > by
> > run in parallel. Will both scripts provide same entropy if parameters are
> > kept constant?
> >
> > Regards,
> >
> > Ranajit Shinde
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jun 18 2010 - 22:30:05 PDT
