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
> > > > _______________________________________________
> > > > 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
Received on Tue Feb 22 2011 - 02:00:03 PST
