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 ?
..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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> > 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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Feb 21 2011 - 10:30:04 PST
