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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Jun 27 2010 - 09:00:03 PDT
