2011/8/29 Jesper Sørensen <lists.jsx.dk>
> Great. I gave it a go and the MMPBSA calculation is performed over 480
> frames.
> When I run it through ptraj - i get out 505 frames.
> This seems to be the 480 frames + 1 extra frame per CPU core (24) + 1
> extra.
>
> Is there some overlap between the files, or do I need to specify the input
> to ptraj in a particular way.
>
There should be no overlap between the files, and you should be able to add
up each file in numerical order to build the original trajectory. I'm
confused about what exactly you're doing here... Did you remember to trajin
the 0th trajectory? Based on the sizes you gave above, I would expect the
0th trajectory to have 1 more frame than each other (since the total number
of frames mod the number of processors was 1), so it seems that you didn't
run the 0th frame through MMPBSA, which will account for what you are
seeing...
HTH,
Jason
> Thanks,
> Jesper
>
>
> Den 29/08/2011 kl. 16.22 skrev Bill Miller III:
>
> > Yes, that should be correct.
> >
> > -Bill
> >
> > 2011/8/29 Jesper Sørensen <lists.jsx.dk>
> >
> >> Hi,
> >>
> >> When I run MMPBSA.py in parallel it splits up the file for each
> CPU-core,
> >> to something like this below.
> >>
> >> 2.4M _MMPBSA_mutant_receptor.mdcrd.0
> >> 2.3M _MMPBSA_mutant_receptor.mdcrd.1
> >> 2.3M _MMPBSA_mutant_receptor.mdcrd.2
> >> 2.3M _MMPBSA_mutant_receptor.mdcrd.3
> >> 2.3M _MMPBSA_mutant_receptor.mdcrd.4
> >> 2.3M _MMPBSA_mutant_receptor.mdcrd.5
> >> 2.3M _MMPBSA_mutant_receptor.mdcrd.6
> >> 2.3M _MMPBSA_mutant_receptor.mdcrd.7
> >>
> >> If I wanted to cat these together using ptraj, is the ordering of the
> files
> >> so that I can just cat 0, 1, 2, 3 etc. and the frames will be in the
> >> correct order as in the initial MD trajectory?
> >>
> >> Best regards,
> >> Jesper
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> >>
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
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> > 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 Aug 29 2011 - 20:00:02 PDT
