[gmx-users] trjconv gets stuck on frame

[Eric Smoll]

Hi Mark,

Thank you for responding so rapidly. I should note that identical
processing (I use a script) on the trajectories produced by slightly
different chemical systems had no problem and trajconv produced a complete
processed trajectory.

However, when processing the problematic few with trajconv, the trajectory
that is output is incomplete (the trjconv output has fewer frames than the
input trajectory).

This is definitely not problem with the change in output frequency of
progress reports to the terminal.

I am not sure if the -b flag is telling me anything. I move it around and
it still seems to get stuck. I have ~30,000 atoms in my system. The first
120 ps are processed in ~ 5 seconds. The next 4 ps take ~ 30 sec. My
trajectory is many nanoseconds long.

Again, my other chemically similar systems do no hang like this and the
simulation procedure is scripted so it is consistent across my different
chemical systems.

I am using gromacs/4.6.5.

Best,
Eric

On Sun, Oct 26, 2014 at 5:21 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> The output does drop in frequency at some point, so that might be all you
> are seeing. Experiment with -b and values around the putative problem area.
>
> Mark
> On Oct 26, 2014 6:59 PM, "Eric Smoll" <ericsmoll at gmail.com> wrote:
>
> > Hello Gromacs users,
> >
> > I have a trajectory file script18_o.trr that I am trying to process.
> Using
> > gmxcheck, this file appears to be complete. When I execute the command
> > below
> >
> > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o
> > tmp1.trr -pbc whole << EOF
> > 0
> > EOF
> >
> > the code moves quickly through the first few hundred frames only to
> > consistently get stuck on frame 300...
> >
> > trn version: GMX_trn_file (single precision)
> >  ->  frame    320 time  128.000        ->  frame    300 time  120.000
> >
> > How do I troubleshoot the problem?
> >
> > -Eric
> > --
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