All, thank you. To keep it short, In the end using NetCDF is working smoothly!
Nicole
Dr. Nicole Horenstein
Associate Professor of Chemistry
Department of Chemistry
University of Florida
Gainesville FL, 32611
U.S.A.
----- Original Message -----
From: "Jason Swails" <jason.swails.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Friday, April 29, 2011 8:10:59 AM
Subject: Re: [AMBER] ptraj trajectory file size limits?
To avoid all of this, I would just use NetCDF trajectories :).
Uncompressed, formatted trajectories gave problems before AmberTools 1.4
patch level 16 (as Bill said), but NetCDF trajectories are so so much better
in every way that it's almost never worth using ASCII trajectory files
anymore.
All the best,
Jason
On Fri, Apr 29, 2011 at 6:21 AM, juzer stationwala <juzer.niper.gmail.com>wrote:
> I too faced similar problem but was solved when using compressed trajectory
> file.
>
> use gzip command to compress your trajectory file then use it in ptraj.
>
> even if you want to combine two trajectories I would suggest to have out
> put
> in mdcrd.gz form & then you may uncompress it by command line & visualise
> it
> using VMD
>
> --
> Warm Regards:
>
> Juzer Stationwala,
> Dept. of Pharmacoinformatics,
> National Institute of Pharmaceutical Education & Research
> (NIPER)
> Mohali,
> Punjab.
> India
> _______________________________________________
> 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
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Received on Sun May 01 2011 - 09:00:02 PDT
