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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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
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Received on Mon Feb 21 2011 - 11:30:02 PST
