Hello,
On Thu, Sep 29, 2011 at 5:32 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> Dear all,
> I just started today with MMPBSA.py (until now I used mm_pbsa.pl).
>
> After the relevant tutorial and brief reading of MMPBSA.py manual I have
> these two questions.
>
> #1
>
> How to proceed with MMPBSA.py if I want to calculate just (absolute) free
> energy of the given molecule
> (not dG of binding between receptor and ligand molecules).
>
Just supply a complex prmtop file. If you don't provide a receptor or
ligand topology file, you will get this same behavior.
>
>
> In case of mm_pbsa.pl one could set just COMPLEX, RECEPTOR, LIGAND flags
> in input file like this:
>
>
>
> COMPLEX 0
> RECEPTOR 1
> LIGAND 0
>
>
> and mm_pbsa.pl will consider here the stand-alone molecule provided as
> the "formal receptor" without any complains
> that complex or ligand are not specified and calculate just H or S of that
> molecule. Is there any way how to
> tell MMPBSA.py that I want just calculate H, S or whole G for the given
> molecule ?
>
>
>
> #2
>
> In mm_pbsa.pl there is available flag PARALLEL which is very useful as it
> allows to define howmany frames
> from the given trajectory will be processed simultaneously. So for example
> if one has node
> with 8 CPU cores, setting:
>
> PARALLEL 8
>
> allow to process 8 MD frames simultaneously (probably without need of MPI
> ?).
>
Yes. The way mm_pbsa.pl works is by forking off processes. This limits
parallel performance to a single node, though, since the simple forker
doesn't know enough to launch processes on remote nodes. MPI, on the other
hand, is built for normal, parallel Amber simulations and is easily run on
distributed systems (across multiple nodes). Since there were good python
bindings for MPI, we decided to use MPI to parallelize MMPBSA.py.
> In case of python version just usage of MMPBSA.py.MPI instead MMPBSA.py
> brings the similar
> possibility am I right ?
>
Correct. mpi4py is built automatically with AmberTools 1.5. I would
suggest using AmberTools 1.5 version, in which case you have to use MMPBSA
and MMPBSA.MPI, which are shell scripts that invoke MMPBSA.py and
MMPBSA.py.MPI with the appropriate variables.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 29 2011 - 15:30:02 PDT
