Yes, the new release of MMPBSA.py (and MMPBSA.py.MPI) no longer utilizes
sander.MPI. MMPBSA.py.MPI now divides the total amount of frames into the
number of threads desired and runs that many separate sander calculations.
Since a user can now, in theory, use one processor per frame then the use of
sander vs. sander.MPI is not substantial. Furthermore, sander.MPI gives no
actual speedup when performing a PB calculation, so sander.MPI would only be
useful for GB calculations, which are already computationally very cheap in
comparison.
-Bill
On Tue, May 25, 2010 at 6:17 AM, Alan <alanwilter.gmail.com> wrote:
> Hi there,
>
> So I am playing with new released MMPBSA.py.MPI and the first I noticed
> when
> running test with DO_PARALLEL (-np 2) is that I got two 'sander' (serial
> version) running when I was expecting sander.MPI with 2 threads.
>
> Is this behaviour correct?
>
> Thanks,
>
> Alan
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue May 25 2010 - 04:30:04 PDT
