Hi Jason,
Thank you very much for your help, but could you tell me about the Bugfix.4
in Ambertools1.4 which is mentioned:
bugfix.4: Fix to parallel *ptraj* when *compressed trajectories* are input.
Is this compressed trajectory corresponds to that netCDF format you have
mentioned?
Regards,
M. Reza
On Sun, Jun 27, 2010 at 4:44 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sun, Jun 27, 2010 at 5:52 AM, M. Reza Ganjalikhany <
> ganjalikhany.gmail.com> wrote:
>
> > Hello all,
> >
> >
> >
> > I want to analyze my compressed trajectory files in Ambertools1.4 with
> > ptraj.MPI but
> > I got the following massage when I used mdcrd.gz files:
> >
> > PTRAJ: Processing input from file new-analysis.in
> >
> > PTRAJ: trajin calb_wat_md1.mdcrd.gz
> > Checking coordinates: calb_wat_md1.mdcrd.gz
> > Compression is not currently supported for parallel ptraj.
> > trajin calb_wat_md1.mdcrd.gz ignored; could not open file
> > (calb_wat_md1.mdcrd.gz)
> > Could not process trajectory calb_wat_md1.mdcrd.gz
> >
> > PTRAJ: trajin calb_wat_md2.mdcrd.gz
> > Checking coordinates: calb_wat_md2.mdcrd.gz
> > Compression is not currently supported for parallel ptraj.
> > trajin calb_wat_md2.mdcrd.gz ignored; could not open file
> > (calb_wat_md2.mdcrd.gz)
> > Could not process trajectory calb_wat_md2.mdcrd.gz
> >
> >
> >
> > Is there any way to use mdcrd.gz file in ptraj.MPI?
> >
>
> No, as the error message indicates. The problem with this is the fact that
> a zipped file is difficult to split up among multiple processors, and has
> not yet been implemented. I think your best bet is to use netCDF format
> trajectories from now on. They're a little bit larger than a zipped file
> (but very compressed compared to an ascii file), but they hold higher
> precision data and are much much faster to both read (in ptraj) and write
> (in sander, pmemd, and ptraj). You can write them as netCDF trajectories
> by
> setting ioutfm=1 in the sander/pmemd input file.
>
> Good luck!
> Jason
>
>
> >
> > Thank you in advance,
> > M. Reza
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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>
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Received on Sun Jun 27 2010 - 14:30:03 PDT
