> On Feb 17, 2015, at 10:30 AM, Marek Maly <marek.maly.ujep.cz> wrote:
>
> Hello,
>
> #1
> I succeeded to solve my problem with entropy analysis of my big system
> (see below) using "obsolete" mm_pbsa.pl (PROC = 1 i.e. using NAB
> implementation of nmode - mm_pbsa_nabnmode)
> ( no chance with PROC = 2, i.e. "original" nmode implementation)
>
> This means that the problem with MMPBSA.py.MPI or just MMPBSA.py which I
> described sooner (see below) is connected with i) Python "skeleton" or ii)
> the problem might be in "mmpbsa_py_nabnmode" if
> there are some bigger differences comparing to "mm_pbsa_nabnmode".
> Based on my experiences/tests I assume that i) is true.
Actually it’s almost definitely not i). MMPBSA.py and mm_pbsa.pl are glorified scripts that basically organize the various tasks that need to be done, call external programs, and parse the results.
There is only one *real* functional difference between mm_pbsa.pl and MMPBSA.py’s nmode NAB programs. MMPBSA.py uses dsyevd to diagonalize the Hessian (which is faster, but takes quite a bit more memory), and mm_pbsa.pl uses dsyev (which is slower, but takes quite a bit less memory).
This is almost certainly why mm_pbsa.pl works for your large system and MMPBSA.py does not. If you want, you can modify mmpbsa_entropy.nab inside $AMBERHOME/AmberTools/src/mmpbsa_py and change the line:
nmode(xyz, 3*natm, mme2, 0, 1, 0.0, 0.0, 0); //calc entropy
to
nmode(xyz, 3*natm, mme2, 0, 0, 0.0, 0.0, 0); //calc entropy
(note the 1-->0 change). I *suspect* that will make things work (given that mm_pbsa.pl works). I will look more into the scratch memory requirements of dsyevd vs. dsyev and see if I can make a smarter default that will use the faster routine only when there is enough memory.
> #2
> The problem is that mm_pbsa.pl (PROC = 1 i.e. using NAB implementation of
> nmode - mm_pbsa_nabnmode)
> provides different results (significantly different !) than MMPBSA.py.MPI
> or just MMPBSA.py as I tested on my small "testing" molecular system (just
> one single fraim) in spite the fact that I set the same input parameters
> in both cases (please see below).
>
> I would be grateful for any useful suggestions what to change/add in
> mm_pbsa.pl
Ideally you can just change the mmpbsa_entropy.nab script in MMPBSA.py as shown above and have that *just work*.
> settings/(input file) to obtain similar results from both mmpbsa routines.
> I hope it is just
> the problem of some different defaults in additional parameters and that
> for the
> same input both NAB routines ("mmpbsa_py_nabnmode", "mm_pbsa_nabnmode")
> have to
> return very similar output.
I agree that they should give similar output. In the early days when MMPBSA.py was first written, it was compared carefully to mm_pbsa.pl to make sure that it gave comparable results with very similar (if not identical) defaults. However, mmpbsa_py_nabnmode and mm_pbsa_nabnmode were both written well after that comparison was done (and in fact, I think mmpbsa_py_nabnmode was written shortly before the perl version was).
Since mmpbsa_py_nabnmode was written first, it wasn’t compared against the GB-enabled version of the perl nab program. The key to identifying the source of the differences between the two scripts will be in the NAB output of the two scripts. You should compare those and make sure that the mm_options are being set the same in both cases and that the overall minimization is similar (in addition to the first few eigenvectors and eigenvalues).
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 17 2015 - 10:30:02 PST
