It could be that some of the default parameters are different for
use_sander=0 and use_sander=1 (since the inputs are handled differently
between nab and sander).
I'll check into this. I believe DELTAs make this effect basically go away,
though.
Thanks!
Jason
2011/9/30 Marek Maly <marek.maly.ujep.cz>
> 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/
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Sep 30 2011 - 14:30:03 PDT
