[gmx-users] file too big?

[aldo jongejan]

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)

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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-- 
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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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