AMBER Archive (2006)

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

From: Thomas Cheatham (
Date: Wed May 31 2006 - 18:27:16 CDT

> 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 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
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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