There is not a specific version of MMPBSA.pl that is parallel, per se.
However, remember that the MMPBSA method is trivially parallel in the fact
that you can send multiple jobs to the queue each analyzing different parts
of your trajectory file and then manually combine the statistics results
afterward. This method would be perfectly valid if you are having problems
with your calculation hitting a maximum wall clock.
Alternatively, MMPBSA.py is not just restricted to three processors. The
python version of MMPBSA is programmed to use 3 processors (one processor
per complex, receptor, and ligand) for systems in which the ligand is not
significantly smaller than the receptor OR it can be done on an *any* even
number of processors as you have described. The MMPBSA.py tutorial (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/) describes and
shows examples for both of these methods in Section 1 and Section 2.
Good luck!
-Bill Miller
On Mon, Feb 1, 2010 at 6:43 AM, s. Bill <s_bill36.yahoo.co.uk> wrote:
> Dear AMBER
> I was wonder if there is any one has a parrallel version of MMPBSA.pl. I
> know the new MMPBSA.py is parrallel, but it is just restricted to 3
> processors (2 in real worl, where ligand is so small).
> Also, how can I restart the job? my jobs have been killed because of the
> wall clock time, so I would like to continue my jobs rather than to start it
> from scratch again. How can I do it?
> Thanks in advance
> S. Bill
>
>
>
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Received on Mon Feb 01 2010 - 04:30:02 PST
