[gmx-users] file too big?

Francesco Tordini tordini at tiscalinet.it
Tue Apr 29 10:56:01 CEST 2003

> 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?




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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