[gmx-users] trajectory tools don't work with large .xtc / .trr files

[Mark Abraham]

Hi,

Rafael is probably on the right track. Using a file system with a limit of
2^32 bytes (=2GB) is just not going to work. One way that might happen is
if you used a 32-bit Ubuntu, but that's just a guess. Bottom line - get a
real 64-bit file system.

Mark

On Wed, Feb 11, 2015 at 2:26 PM, Rafael R. Pappalardo <rafapa at us.es> wrote:

> Just one dumb idea. Your ubuntu is 32 or 64 bits?
>
> Rafael Rodríguez Pappalardo
> Depto. Química Física, Univ. de Sevilla
>
> > El 11/2/2015, a las 13:57, Wojciech Kopeć <9000nin at gmail.com> escribió:
> >
> > Dear all,
> >
> > I've been using GROMACS successfully for quite some time on several
> > platforms, although after a recent upgrade my main linux workstation to
> > Ubuntu 14.04 and new installation of latest GROMACS (5.0.4) I noticed
> very
> > strange behaviour of several tools (mainly trjconv and gmxcheck).
> Basically
> > when I try to use them on my trajectories, in simplest case
> >
> > trjconv -f traj.xtc
> >
> > I get the error:
> > Source code file
> > /home/wojciech2/GROMACS-5.0.4/gromacs-5.0.4/src/gromacs/fileio/gmxfio.c,
> > line: 513
> >
> > Can not open file:
> > traj.xtc
> >
> > Needless to say the file exists in the given directory. It happens to all
> > files that I've accumulated over the years (with different GROMACS
> > versions); files themselves are not damaged as they work perfectly on my
> > mac with the same GROMACS version, installed in the same way. Also when I
> > reduced the size (simply using -skip) command of the trajectories on my
> mac
> > and transferred them to my workstation, the very same tools work without
> > any problems. However, as soon as the file size is above ~2 GB, it throws
> > me the above mentioned error. Any clues?
> >
> > Thanks,
> > Wojciech
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