What I meant was that your mm_pbsa.pl input file did not specify a
decomposition option. It should be much faster _not_ to use PB when doing
decomposition.
All the best,
Jason
On Fri, Dec 16, 2011 at 1:56 AM, Qinghua Liao <fantasticqhl.gmail.com>wrote:
> Dear Jason,
>
> Thanks very much. what you mean is that I am doing decomposition with the
> serial version but not the parallel one? I will try to turn off PB when
> doing decomposition, and calculate the binding energy and decomposition
> seperately. Thanks very much!
>
>
>
> --
> Best Regards,
>
> Qinghua
>
>
>
>
>
> On Thu, Dec 15, 2011 at 10:30 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > You're running a decomposition analysis with MMPBSA.py, but not with
> > mm_pbsa.pl. Decomposition adds significant time to the calculation
> > (especially for PB, I believe).
> >
> > HTH,
> > Jason
> >
> > On Thu, Dec 15, 2011 at 3:44 PM, Qinghua Liao <fantasticqhl.gmail.com
> > >wrote:
> >
> > > Dear Jason,
> > >
> > > Thanks again. Here is my input file for the mm_pbsa.pl calculation:
> > >
> > > .GENERAL
> > > #
> > > VERBOSE 0
> > > PARALLEL 8
> > > #
> > > PREFIX snapshot
> > > PATH ../snapshots/
> > > START 1
> > > STOP 400
> > > OFFSET 1
> > > #
> > > COMPLEX 1
> > > RECEPTOR 1
> > > LIGAND 1
> > > #
> > > COMPT ../com.prmtop
> > > RECPT ../rec.prmtop
> > > LIGPT ../lig.prmtop
> > > #
> > > GC 0
> > > AS 0
> > > DC 0
> > > #
> > > MM 1
> > > GB 1
> > > PB 1
> > > MS 1
> > > #
> > > NM 0
> > > #
> > >
> > >
> >
> ################################################################################
> > > .PB
> > > #
> > > PROC 2
> > > REFE 0
> > > INDI 1.0
> > > EXDI 80.0
> > > SCALE 2
> > > LINIT 1000
> > > PRBRAD 1.4
> > > ISTRNG 0.10
> > > RADIOPT 1
> > > INP 1
> > > #
> > > SURFTEN 0.00542
> > > SURFOFF -1.008
> > > #
> > > IVCAP 0
> > > CUTCAP -1.0
> > > XCAP 0.0
> > > YCAP 0.0
> > > ZCAP 0.0
> > > #
> > >
> > >
> >
> ################################################################################
> > > .MM
> > > #
> > > DIELC 1.0
> > > #
> > >
> > >
> >
> ################################################################################
> > > .GB
> > > #
> > > #
> > > IGB 5
> > > GBSA 2
> > > SALTCON 0.10
> > > EXTDIEL 80.0
> > > INTDIEL 1.0
> > > #
> > > SURFTEN 0.0072
> > > SURFOFF 0.00
> > > #
> > >
> > >
> >
> ################################################################################
> > > .MS
> > > #
> > > #
> > > PROBE 0.0
> > > #
> > >
> > >
> >
> ################################################################################
> > > .PROGRAMS
> > > #
> > > # Additional program executables can be defined here
> > > #
> > > #
> > >
> > >
> >
> ################################################################################
> > >
> > > How should I check the temporary files? In mm_pbsa.pl's calculation, I
> > can
> > > check the output files for the process, but in the python version, how
> > > should I checnk the process?
> > >
> > > Right now, I guess that the calculation was died, however, the sander
> are
> > > still working. Is it possible for the python version?
> > > Here are the temporary files in the working folder:
> > >
> > > _MMPBSA_avgcomplex.pdb _MMPBSA_comtraj.in.0
> > > _MMPBSA_ligandinpcrd.in _MMPBSA_pb_decomp_rec.mdin
> > > _MMPBSA_ptraj5.out _MMPBSA_receptor.pdb
> > > _MMPBSA_cenptraj.in _MMPBSA_dummycomplex.inpcrd.1
> > > _MMPBSA_ligand.mdcrd _MMPBSA_ptraj1.out
> > > _MMPBSA_ptraj6.out _MMPBSA_rectraj.in
> > > _MMPBSA_complex_gb.mdout.0 _MMPBSA_dummyligand.inpcrd.1
> > > _MMPBSA_ligand.mdcrd.0 _MMPBSA_ptraj1.out.0 mmpbsa_py.in
> > > _MMPBSA_rectraj.in.0
> > > _MMPBSA_complexinpcrd.in _MMPBSA_dummyreceptor.inpcrd.1
> > > _MMPBSA_ligand.pdb _MMPBSA_ptraj2.out
> > > _MMPBSA_receptor_gb.mdout.0 _MMPBSA_.restrt.0
> > > _MMPBSA_complex.mdcrd _MMPBSA_gb_decomp_com.mdin
> > > _MMPBSA_ligtraj.in _MMPBSA_ptraj2.out.0
> > > _MMPBSA_receptorinpcrd.in mpd.hosts
> > > _MMPBSA_complex.mdcrd.0 _MMPBSA_gb_decomp_lig.mdin
> > > _MMPBSA_ligtraj.in.0 _MMPBSA_ptraj3.out
> > > _MMPBSA_receptor.mdcrd nohup.out
> > > _MMPBSA_complex_pb.mdout.0 _MMPBSA_gb_decomp_rec.mdin
> > > _MMPBSA_pb_decomp_com.mdin _MMPBSA_ptraj3.out.0
> > > _MMPBSA_receptor.mdcrd.0
> > > _MMPBSA_complex.pdb _MMPBSA_ligand_gb.mdout.0
> > > _MMPBSA_pb_decomp_lig.mdin _MMPBSA_ptraj4.out
> > > _MMPBSA_receptor_pb.mdout.0
> > >
> > >
> > > It seems no change for sometime now. I am going to kill one and redo
> it.
> > > Thanks!
> > >
> > >
> > > Best Regards,
> > >
> > > Qinghua
> > >
> > >
> > >
> > > On Thu, Dec 15, 2011 at 7:50 PM, Jason Swails <jason.swails.gmail.com
> > > >wrote:
> > >
> > > > What was your mm_pbsa.pl input file? Are temporary files
> (_MMPBSA_*)
> > > > still
> > > > being written to for MMPBSA.py?
> > > >
> > > > On Thu, Dec 15, 2011 at 11:21 AM, Qinghua Liao <
> fantasticqhl.gmail.com
> > > > >wrote:
> > > >
> > > > > Dear amber users,
> > > > >
> > > > > Is it very slow for calculating binding energy and decomposition
> > > > > simultaneously? It has been more than 24 hours for the calculation
> > > using
> > > > 16
> > > > > cores' MMPBSA.MPI, and it has already finished using 8 core's
> > > > > mm_pbsa.plfor the calculation of binding energy. Here is the input
> > > > > file:
> > > > >
> > > > > &general
> > > > > startframe=1, endframe=400, interval=1,
> > > > > verbose=1, keep_files=1,
> > > > > /
> > > > > &gb
> > > > > igb=5, saltcon=0.10, surften=0.0072, surfoff=0.00,
> > > > > /
> > > > > &pb
> > > > > indi=1.0, exdi=80.0, scale=2.0, linit=1000, prbrad=1.4,
> > > > > inp=1, istrng=0.10, cavity_surften=0.00542, cavity_offset=-1.008,
> > > > > fillratio=4.0,
> > > > > /
> > > > > &decomp
> > > > > idecomp=2, dec_verbose=3,
> > > > > /
> > > > >
> > > > > I guess that there may be some problem with my input file, could
> > > someone
> > > > > give me a suggestion? Thanks very much!
> > > > >
> > > > > --
> > > > > Best Regards,
> > > > >
> > > > > Qinghua
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Candidate
> > > > 352-392-4032
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 16 2011 - 06:00:06 PST
