Thanks for explanation ! However after my short experiments with MMPBSA_PY
I have
another two interesting problems here. I did GB/PB MMPBSA_PY analysis of
cationic molecule (PPI dendrimer G4, with total charge 32) to see the
effect of
salt parameters in GB/PB calculations. And I got these results.
#1
GB seems to be much much more sensitive on salt concentration (saltcon)
that PB (istrng).
#2
Change in setting of param. "use_sander" (0/1) has practically zero
influence on GB result but
in case of PB there are some non-negligible differences, although these
might vanish in case
of calculation dH if the same shift is for complex, and (receptor+ligand).
#1 and #2 are nicely illustrated by table below (H analysis of above
mentioned molecule).
Is there any explanation for #1 and/or #2 ?
Thanks a lot in advance !
Best wishes,
Marek
use_sander=0
GB saltcon=0.0
TOTAL -307.6173 20.0845
2.0085
GB saltcon=0.1
TOTAL -395.5508 20.0667
2.0067
PB istrng=0.0
TOTAL -447.0705 18.9268
1.8927
PB istrng=0.1
TOTAL -447.5793 18.9518
1.8952
use_sander=1
GB saltcon=0.0
TOTAL -307.6805 20.0847
2.0085
GB saltcon=0.1
TOTAL -395.6140 20.0669
2.0067
PB istrng=0.0
TOTAL -454.1829 18.8272
1.8827
PB istrng=0.1
TOTAL -454.7201 18.8393
1.8839
Dne Fri, 30 Sep 2011 21:27:36 +0200 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> 2011/9/30 Marek Maly <marek.maly.ujep.cz>
>
>> Hi Jason,
>>
>> Thanks a lot ! The problem is solved and MMPBSA.MPI works perfectly !
>>
>> I would like to ask you about "saltcon" GB parameter. I am doing
>> simulations under
>> 0.15 M of NaCl. Is it in your opinion this concentration still
>> acceptable
>> for GB,
>> or is better to go on 0.1 to be still in safe range regarding
>> assumptions/approximations
>> in GB theory ?
>>
>
> 0.15 seems safe, I'm not sure. GB is fast enough that you could try
> different values and see if it really makes a difference.
>
>
>>
>>
>> I am also curious why usage of sander ( use_sander=1 ) causes so
>> significant slowdown comparing
>> to case when mmpbsa_py_energy is used ( use_sander=0 ) .
>>
>
> I think this is because sander calculates the energy twice for some
> reason
> (an "initial" call and then one on the first step, perhaps). In any
> case,
> we've found that using the nab program gives ~2x speedup for both GB and
> PB. I haven't done my own code investigation to find out where this is
> being done, I just took it on faith based on what someone (I've forgotten
> who at this point) told me. We suggest *not* setting use_sander=1 unless
> you absolutely have to (for instance, if you're using chamber prmtops, or
> some of the GB models not implemented in nab, or QM/MM-GBSA).
>
> HTH,
> Jason
>
>
>> Thanks once again !
>>
>> Best wishes,
>>
>> Marek
>>
>>
>>
>>
>>
>> Dne Fri, 30 Sep 2011 07:10:47 +0200 Jason Swails
>> <jason.swails.gmail.com>
>> napsal/-a:
>>
>> > Hi,
>> >
>> > MMPBSA.py.MPI is built when you build AmberTools 1.5 in parallel, not
>> > Amber
>> > 11. Thus, running "make parallel" in $AMBERHOME/AmberTools/src after
>> > running ./configure -mpi gnu is what you need to do. (You could also
>> go
>> > to
>> > the $AMBERHOME/AmberTools/src/mmpbsa_py directory and run the "make
>> > parallel" command -- it should build it for you).
>> >
>> > About the errors you're seeing -- this is a sign that your environment
>> > variables or something may be out of whack. I suggest trying to
>> > recompile
>> > AmberTools 1.5 in serial, then in parallel.
>> >
>> > HTH,
>> > Jason
>> >
>> > 2011/9/29 Marek Maly <marek.maly.ujep.cz>
>> >
>> >> Hi Jason,
>> >> thanks for a prompt reply !
>> >>
>> >> Regarding #1 I tried your suggestion and it works perfectly !
>> >>
>> >> Regarding #2 I didn't find MMPBSA.MPI in $AMBERHOME/bin nor
>> >>
>> >> MMPBSA.py.MPI which I suppose to be located in
>> >> $AMBERHOME/AmberTools/src/mmpbsa_py
>> >> where I found MMPBSA.py script. Then I found in Amber11 manual :
>> >>
>> >>
>> >>
>> -------------------------------------------------------------------------------------
>> >> 10.3.3.2 Parallel (MPI) version
>> >> This version is installed with Amber during the parallel install. The
>> >> python package mpi4py is included with the MMPBSA.py source code and
>> >> must
>> >> be successfully installed in order to run the MPI version of MMPBSA
>> >> ......
>> >>
>> >>
>> >>
>> --------------------------------------------------------------------------------------
>> >>
>> >> So I successfully installed also parallel version (./configure -mpi
>> gnu)
>> >> of Amber11 ( having before just serial one in combination with
>> >> AmberTools1.5 just for analyses of MD trajectories calculated with
>> >> pmemd.CUDA on separate CUDA WorkStations. ), but unfortunately
>> situation
>> >> didn.t change i.e. no MMPBSA.MPI appeared in $AMBERHOME/bin. So I
>> went
>> >> to
>> >> $AMBERHOME/AmberTools/src/mmpbsa_py and tried "make install"
>> >> after this I have obtained plethora of errors please see below. I
>> would
>> >> be
>> >> really grateful for any helpful suggestion ! Anyway that "forking"
>> >> parallel approach from mm_pbsa.pl might be fully sufficient and
>> useful
>> >> alternative for those who don.t care about parallel Amber11
>> >> installation or even don.t care about MPI on their machine or they
>> have
>> >> simply problem to install these things.
>> >> For those might be parallelization of MMPBSA jobs although limited
>> to
>> >> given node sufficient solution.
>> >> But there are for sure much more important development tasks in the
>> >> queue
>> >> I guess :))
>> >>
>> >> Thanks in advance for your help !
>> >>
>> >>
>> >> Best wishes,
>> >>
>> >> Marek
>> >>
>> >>
>> >> mmaly.node25 ~/_applications/amber11_node25/AmberTools/src/mmpbsa_py
>> $
>> >> make install
>> >> make: Warning: File `../config.h' has modification time 8.3e+03 s in
>> the
>> >> future
>> >> /bin/bash setup.sh
>> >> Using AmberTools' python
>> >> /home/mmaly/_applications/amber11_node25/bin/nab -o
>> mmpbsa_py_nabnmode
>> >> mmpbsa_entropy.nab
>> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o): In function
>> >> `dsaupd_':
>> >> dsaupd.f:(.text+0x11d): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaupd.f:(.text+0x5f9): undefined reference to `_gfortran_st_write'
>> >> dsaupd.f:(.text+0x601): undefined reference to
>> `_gfortran_st_write_done'
>> >> dsaupd.f:(.text+0x64d): undefined reference to `_gfortran_st_write'
>> >> dsaupd.f:(.text+0x65f): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dsaupd.f:(.text+0x671): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dsaupd.f:(.text+0x683): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dsaupd.f:(.text+0x695): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dsaupd.f:(.text+0x6a7): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >>
>> >>
>> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o):dsaupd.f:(.text+0x6b9):
>> >> more undefined references to `_gfortran_transfer_integer' follow
>> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o): In function
>> >> `dsaupd_':
>> >> dsaupd.f:(.text+0x6cb): undefined reference to
>> `_gfortran_transfer_real'
>> >> dsaupd.f:(.text+0x6dd): undefined reference to
>> `_gfortran_transfer_real'
>> >> dsaupd.f:(.text+0x6ef): undefined reference to
>> `_gfortran_transfer_real'
>> >> dsaupd.f:(.text+0x701): undefined reference to
>> `_gfortran_transfer_real'
>> >> dsaupd.f:(.text+0x713): undefined reference to
>> `_gfortran_transfer_real'
>> >>
>> >>
>> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o):dsaupd.f:(.text+0x725):
>> >> more undefined references to `_gfortran_transfer_real' follow
>> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o): In function
>> >> `dsaupd_':
>> >> dsaupd.f:(.text+0x787): undefined reference to
>> `_gfortran_st_write_done'
>> >> dsaupd.f:(.text+0x7a3): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaupd.f:(.text+0x7c2): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaupd.f:(.text+0x7e1): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaupd.f:(.text+0x800): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaupd.f:(.text+0x857): undefined reference to
>> >> `_gfortran_compare_string'
>> >>
>> >>
>> /home/mmaly/_applications/amber11/lib/arpack.a(dseupd.o):dseupd.f:(.text+0x110):
>> >> more undefined references to `_gfortran_compare_string' follow
>> >> /home/mmaly/_applications/amber11/lib/arpack.a(dseupd.o): In function
>> >> `dseupd_':
>> >> dseupd.f:(.text+0xb6d): undefined reference to
>> `_gfortran_copy_string'
>> >> dseupd.f:(.text+0xb8e): undefined reference to
>> `_gfortran_copy_string'
>> >> dseupd.f:(.text+0xc38): undefined reference to
>> `_gfortran_copy_string'
>> >> dseupd.f:(.text+0xc59): undefined reference to
>> `_gfortran_copy_string'
>> >> dseupd.f:(.text+0xcc2): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dseupd.f:(.text+0xd60): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dseupd.f:(.text+0xe23): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dseupd.f:(.text+0xf6d): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dseupd.f:(.text+0xf91): undefined reference to
>> >> `_gfortran_compare_string'
>> >>
>> >>
>> /home/mmaly/_applications/amber11/lib/arpack.a(dseupd.o):dseupd.f:(.text+0xfb5):
>> >> more undefined references to `_gfortran_compare_string' follow
>> >> /home/mmaly/_applications/amber11/lib/arpack.a(ivout.o): In function
>> >> `ivout_':
>> >> ivout.f:(.text+0xb7): undefined reference to `_gfortran_st_write'
>> >> ivout.f:(.text+0xc6): undefined reference to
>> >> `_gfortran_transfer_character'
>> >> ivout.f:(.text+0xd3): undefined reference to
>> >> `_gfortran_transfer_character'
>> >> ivout.f:(.text+0xdb): undefined reference to
>> `_gfortran_st_write_done'
>> >> ivout.f:(.text+0x134): undefined reference to
>> `_gfortran_st_write_done'
>> >> ivout.f:(.text+0x19b): undefined reference to `_gfortran_st_write'
>> >> ivout.f:(.text+0x1b0): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x1c5): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x1f7): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x239): undefined reference to `_gfortran_st_write'
>> >> ivout.f:(.text+0x241): undefined reference to
>> `_gfortran_st_write_done'
>> >> ivout.f:(.text+0x2aa): undefined reference to
>> `_gfortran_st_write_done'
>> >> ivout.f:(.text+0x311): undefined reference to `_gfortran_st_write'
>> >> ivout.f:(.text+0x326): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x33b): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x373): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x3ca): undefined reference to
>> `_gfortran_st_write_done'
>> >> ivout.f:(.text+0x431): undefined reference to `_gfortran_st_write'
>> >> ivout.f:(.text+0x446): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x45b): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x48d): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x4d8): undefined reference to
>> `_gfortran_st_write_done'
>> >> ivout.f:(.text+0x53f): undefined reference to `_gfortran_st_write'
>> >> ivout.f:(.text+0x554): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x569): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x59b): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x5da): undefined reference to
>> `_gfortran_st_write_done'
>> >> ivout.f:(.text+0x641): undefined reference to `_gfortran_st_write'
>> >> ivout.f:(.text+0x656): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x66b): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x69d): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x6e4): undefined reference to
>> `_gfortran_st_write_done'
>> >> ivout.f:(.text+0x74b): undefined reference to `_gfortran_st_write'
>> >> ivout.f:(.text+0x760): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x775): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x7a7): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x7ee): undefined reference to
>> `_gfortran_st_write_done'
>> >> ivout.f:(.text+0x855): undefined reference to `_gfortran_st_write'
>> >> ivout.f:(.text+0x86a): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x87f): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x8b1): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x8ed): undefined reference to
>> `_gfortran_st_write_done'
>> >> ivout.f:(.text+0x954): undefined reference to `_gfortran_st_write'
>> >> ivout.f:(.text+0x969): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x97e): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> ivout.f:(.text+0x9b0): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> /home/mmaly/_applications/amber11/lib/arpack.a(dvout.o): In function
>> >> `dvout_':
>> >> dvout.f:(.text+0xb7): undefined reference to `_gfortran_st_write'
>> >> dvout.f:(.text+0xc6): undefined reference to
>> >> `_gfortran_transfer_character'
>> >> dvout.f:(.text+0xd3): undefined reference to
>> >> `_gfortran_transfer_character'
>> >> dvout.f:(.text+0xdb): undefined reference to
>> `_gfortran_st_write_done'
>> >> dvout.f:(.text+0x134): undefined reference to
>> `_gfortran_st_write_done'
>> >> dvout.f:(.text+0x19b): undefined reference to `_gfortran_st_write'
>> >> dvout.f:(.text+0x1b0): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x1c5): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x1f7): undefined reference to
>> `_gfortran_transfer_real'
>> >> dvout.f:(.text+0x239): undefined reference to `_gfortran_st_write'
>> >> dvout.f:(.text+0x241): undefined reference to
>> `_gfortran_st_write_done'
>> >> dvout.f:(.text+0x298): undefined reference to
>> `_gfortran_st_write_done'
>> >> dvout.f:(.text+0x2ff): undefined reference to `_gfortran_st_write'
>> >> dvout.f:(.text+0x314): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x329): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x35b): undefined reference to
>> `_gfortran_transfer_real'
>> >> dvout.f:(.text+0x3a1): undefined reference to
>> `_gfortran_st_write_done'
>> >> dvout.f:(.text+0x408): undefined reference to `_gfortran_st_write'
>> >> dvout.f:(.text+0x41d): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x432): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x464): undefined reference to
>> `_gfortran_transfer_real'
>> >> dvout.f:(.text+0x4a9): undefined reference to
>> `_gfortran_st_write_done'
>> >> dvout.f:(.text+0x510): undefined reference to `_gfortran_st_write'
>> >> dvout.f:(.text+0x525): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x53a): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x56c): undefined reference to
>> `_gfortran_transfer_real'
>> >> dvout.f:(.text+0x5aa): undefined reference to
>> `_gfortran_st_write_done'
>> >> dvout.f:(.text+0x611): undefined reference to `_gfortran_st_write'
>> >> dvout.f:(.text+0x626): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x63b): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x66d): undefined reference to
>> `_gfortran_transfer_real'
>> >> dvout.f:(.text+0x6aa): undefined reference to
>> `_gfortran_st_write_done'
>> >> dvout.f:(.text+0x711): undefined reference to `_gfortran_st_write'
>> >> dvout.f:(.text+0x726): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x73b): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x76d): undefined reference to
>> `_gfortran_transfer_real'
>> >> dvout.f:(.text+0x7b5): undefined reference to
>> `_gfortran_st_write_done'
>> >> dvout.f:(.text+0x81c): undefined reference to `_gfortran_st_write'
>> >> dvout.f:(.text+0x831): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x846): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x878): undefined reference to
>> `_gfortran_transfer_real'
>> >> dvout.f:(.text+0x8a6): undefined reference to
>> `_gfortran_st_write_done'
>> >> dvout.f:(.text+0x90c): undefined reference to `_gfortran_st_write'
>> >> dvout.f:(.text+0x921): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x936): undefined reference to
>> >> `_gfortran_transfer_integer'
>> >> dvout.f:(.text+0x968): undefined reference to
>> `_gfortran_transfer_real'
>> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsaup2.o): In function
>> >> `dsaup2_':
>> >> dsaup2.f:(.text+0xb4d): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaup2.f:(.text+0xb71): undefined reference to
>> `_gfortran_copy_string'
>> >> dsaup2.f:(.text+0xcde): undefined reference to
>> `_gfortran_copy_string'
>> >> dsaup2.f:(.text+0xd77): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaup2.f:(.text+0xd9b): undefined reference to
>> `_gfortran_copy_string'
>> >> dsaup2.f:(.text+0xef8): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaup2.f:(.text+0xf19): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaup2.f:(.text+0xf3a): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaup2.f:(.text+0xf5b): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsaup2.f:(.text+0x104a): undefined reference to
>> `_gfortran_copy_string'
>> >> dsaup2.f:(.text+0x106b): undefined reference to
>> `_gfortran_copy_string'
>> >> dsaup2.f:(.text+0x108c): undefined reference to
>> `_gfortran_copy_string'
>> >> dsaup2.f:(.text+0x10ad): undefined reference to
>> `_gfortran_copy_string'
>> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsesrt.o): In function
>> >> `dsesrt_':
>> >> dsesrt.f:(.text+0x55): undefined reference to
>> `_gfortran_compare_string'
>> >> dsesrt.f:(.text+0x18c): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsesrt.f:(.text+0x2e0): undefined reference to
>> >> `_gfortran_compare_string'
>> >> dsesrt.f:(.text+0x3fe): undefined reference to
>> >> `_gfortran_compare_string'
>> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsgets.o): In function
>> >> `dsgets_':
>> >> dsgets.f:(.text+0x5d): undefined reference to
>> `_gfortran_compare_string'
>> >> cc failed!
>> >> make: *** [install] Error 1
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Dne Fri, 30 Sep 2011 00:12:20 +0200 Jason Swails
>> >> <jason.swails.gmail.com>
>> >> napsal/-a:
>> >>
>> >> > 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
>> >> >
>> >>
>> >>
>> >> --
>> >> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> >> http://www.opera.com/mail/
>> >>
>> >> _______________________________________________
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>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> >
>>
>>
>> --
>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> http://www.opera.com/mail/
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
--
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Received on Fri Sep 30 2011 - 14:00:03 PDT
