> On Feb 17, 2015, at 1:17 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>>
>> On Feb 17, 2015, at 10:30 AM, Marek Maly <marek.maly.ujep.cz <mailto: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.
One comment here -- if you make this change, type “make install” in the mmpbsa_py/ directory to make sure that you *install* that program with the appropriate change.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 17 2015 - 10:30:03 PST
