[gmx-users] file too big?

[David van der Spoel]

On Tue, 2003-04-29 at 12:29, aldo jongejan wrote:
> Hi,
> 
> Having the same problem (saved too many data :-) ) and being
> in the same group as Anton Feenstra (our GROMACS expert), we were
> able to at least break down the big file into smaller pieces using 'split'.
> You have to know the number of frames, the filesize and then
> divide the filesize by frames+1. This will give you the
> size per frame. And then you can make the chunks you want....
> 
> Hope this helps (at least it worked for me, thanks to Anton)
> 
another workaround for me was to access the file over NFS.

> with kind regards,
> 
> aldo
> 
> 
> >  >
> >>  Hi all,
> >>
> >>  i have a 3Go file.trr
> >>
> >>  when i try to use it whith GROMACS scripts (g_rms, trjconv...)
> >>
> >>  I have the message :
> >>
> >>  File not found.
> >>
> >>  But the file exists.
> >>
> >>  if this file is too big to be used whith the scripts,
> >>  is it possible to obtain 2 files (1.5Go each)?
> >>
> >>  thanks in advance.
> >>
> >>  SEB.
> >>
> >
> >Dear all,
> >i've read the mailing list about the "file too big" topic. I have the
> >same problem, but i think to fall, as Anton said, under a 'very specific
> >things' category: i'm studying the interaction of a little peptide with
> >an asymmetric bilayer for a quite long time (>5 ns). I'm interested also
> >in order parameters calculation, so i'm saving every 100 fs. The
> >trajectory (.xtc) is very large (>3Gb) and i have the "File not found"
> >message when i try to read it (with trjconv for example).
> >I have two question:
> >
> >1. For the order parameters calculation, is it possible to save every
> >200 fs? (In this case the output is halved)
> >2. As Gerrit advices, i've tried to recompile gromacs (actually i'm
> >using the rpm-->deb version) on my kernel (2.4.20-k7 on debian, i
> >suppose it supports very large files). In the output of configure, it
> >seems that the two flags (-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1)
> >are correctly set:
> >
> >.....
> >checking for special C compiler options needed for large files... no
> >checking for _FILE_OFFSET_BITS value needed for large files... 64
> >checking for _LARGE_FILES value needed for large files... no
> >checking for _LARGEFILE_SOURCE value needed for large files... 1
> >checking for fseeko... yes
> >.....
> >
> >But when i try to use trjconv on my trajectory i notice the usual
> >message "File not found"
> >Has anyone some suggestion?
> >
> >Cheers
> >
> >Francesco
> >
> >
> >------------------------------------------
> >
> >Dr. Francesco Tordini
> >Università di Milano-Bicocca
> >Dipartimento di Biotecnologie e Bioscienze
> >P.zza della Scienza, 2 - 20126 Milano
> >Tel.  0264483473 / Fax. 0264483478
> >cell. 3282794451
> >email tordini at tiscalinet.it
> >
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> 
> 
> -- 
> #####################################################
> 
> Aldo Jongejan
> Computational Medicinal Chemistry & Toxicology
> Division of Medicinal Chemistry
> Faculty of Science, Vrije Universiteit
> De Boelelaan 1083, 1081 HV Amsterdam
> The Netherlands
> 
> e-mail:	jongejan at few.vu.nl
> tlf:	+31 (0)20 4447612
> fax:	+31 (0)20 4447610
> 
> #####################################################
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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