I tried to do in manually in fallowing steps :
grep "Total:" for _MMPBSA_complex_nm.out.[0-3],
_MMPBSA_receptor_nm.out.[0-3], _MMPBSA_ligand_nm.out.[0-3].
there were 488, 487, 887 lines for complex, receptor and ligand
respectively. I ran 500 snapshots so It seems to be correct that that values
corresponds to each snapshot. Now I am taking average over of entropy
(Complex-receptor-ligand) over 487 snapshots but it does not seems to be
correct. The values are fluctuating between 15 to 25 with an average of
about 18. If i compare from previous calculations then it should be about
14. Is there something wrong I am doing in calculations or the statistics
from the script is not as strait forward as I am doing ?
Sincerely
..mish
On Tue, Feb 22, 2011 at 10:51 AM, mish <smncbr.gmail.com> wrote:
> I ran with the statistics calculation with flag "-rewrite-output" like :
>
> mpiexec -np 4 -machinefile MMPBSA.py.MPI -rewrite-output -O -i
> mmpbsa_nm.in-o FINAL_RESULTS_MMPBSA.dat -sp rsl_lig2_wat.prmtop -cp
> rsl_lig2.prmtop -rp
> rsl.prmtop -lp lig2.prmtop -y prod_lig2.mdcrd > progress.log
>
> but its running from last 20 hours and the only output i can see in the log
> file is "MMPBSA.py.MPI being run on 4 processors
> ". Do u think it should take so much time ?
>
> Sincerely
> ..mish
>
> On Mon, Feb 21, 2011 at 8:05 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Mon, Feb 21, 2011 at 1:18 PM, mish <smncbr.gmail.com> wrote:
> >
> > > If we look at output file (_MMPBSA_complex_nm.out.[0-3]), it have the
> > > fallowing statistics for each snapshot (probably) -
> > >
> > >
> > > freq. E Cv S
> > > cm**-1 kcal/mol cal/mol-K cal/mol-K
> > > Total: 20127.098 7989.218 9654.238
> > > translational: 0.888 2.979 56.561
> > > rotational: 0.888 2.979 57.775
> > > vibrational: 21829.391 7983.261 9539.901
> > > ff energy: -1704.069
> > >
> > > Do you think that average of all the terms (or Total) and computing the
> > > delta (complex-receptor-ligand) over all the snapshots for all 4
> thread
> > > will give the entropy term ? or there is some other statistics /
> formulae
> > > used to get the entropy from these values ?
> > >
> >
> > That will work, but I don't know if MMPBSA.py.MPI actually uses the
> length
> > of the arrays or if it uses the number taken from the ptraj output files
> to
> > determine how many frames were analyzed. I can't remember how it's done
> in
> > the currently released version anymore.
> >
> > Good luck!
> > Jason
> >
> >
> > >
> > > ..mish
> > >
> > >
> > > On Mon, Feb 21, 2011 at 6:08 PM, Jason Swails <jason.swails.gmail.com
> > > >wrote:
> > >
> > > > Hello,
> > > >
> > > > All threads should be running concurrently (which is why you have the
> > > files
> > > > for all 4 threads; .0, .1, .2, and .3). You would have to look at
> each
> > > of
> > > > those input files separately to see where the calculation died (on
> > which
> > > > frame).
> > > >
> > > > There is no way of *easily* computing the statistics from *finished*
> > > > frames,
> > > > I don't think. You can try using the same command you used to run
> > > > MMPBSA.py.MPI the first time and just add the flag "-rewrite-output"
> to
> > > the
> > > > command line. I can't remember whether it counts the frames as it
> adds
> > > > them, or parses it from the ptraj output files.
> > > >
> > > > Just be careful and make sure that the output makes sense.
> > > >
> > > > Good luck!
> > > > Jason
> > > >
> > > > On Mon, Feb 21, 2011 at 10:38 AM, mish <smncbr.gmail.com> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I was doing Entropy calculation in nabmode. I used parallel version
> > of
> > > > the
> > > > > python script to do so using 4CPU. Unfortunately my calculation got
> > > > killed
> > > > > due to lime limit and now it copied only -
> > > > >
> > > > > _MMPBSA_complex_nm.out.[0-3]
> > > > > _MMPBSA_receptor_nm.out.[0-3]
> > > > > _MMPBSA_ligand_nm.out.[0-3]
> > > > >
> > > > > If I look in the progress.log then i can see that calculation were
> > > killed
> > > > > during last thread so I think It will have the data up to second
> last
> > > > > thread. Is it possible by someway to generate the final results
> from
> > > this
> > > > > data stored in these 12 files ?
> > > > >
> > > > >
> > > > > Sincerely
> > > > > ..mish
> > > > > _______________________________________________
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> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > 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
> > > >
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> > >
> >
> >
> >
> > --
> > 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
> >
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Received on Tue Feb 22 2011 - 03:00:02 PST
