AMBER Archive (2006)

Subject: Re: AMBER: AMBER mdcrd file bigger than 2GB

From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Jun 01 2006 - 10:41:02 CDT

I do not want to lose my data. So, It is possible to split the amber mdcrd
files in to small files. If yes then how?
thanks
snoze

On 5/31/06, Thomas Cheatham <tec3_at_utah.edu> wrote:
>
>
> > I was reading ross walker comments in net. My file size is also bigger
> then
> > 2GB. Infact it is 2.9GB. Now problem is neither VMD is reading it nor
> ptrj
> > command of amber.
>
> From personal experience, I know that on most 32- and 64- bit platforms
> I've tried, ptraj can happily process files larger than 2GB as long as...
>
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
>
> ...is specified during the compilation.
>
> When you recompiled ptraj with FC4 or FC5 as per the most recent e-mail
> reflector note, are you sure ptraj was recompiled and that the compiler
> flags above were specified/used??? When you ran ptraj, are you sure it
> was the newly compiled version and not an older version?
>
> [Note that although I will strongly second Ross Walker's point that
> working with smaller files makes more sense (due to the potential for
> file corruption, transfer errors, etc), I do acknowledge that sometimes
> large files are needed.]
>
>
> \-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
> -/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
> /-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
> \-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
> -/-
> /-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
> \-/ BPRP295A http://www.chpc.utah.edu/~cheatham
>
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