[gmx-users] trjconv gets stuck on frame

[Mark Abraham]

On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll <ericsmoll at gmail.com> wrote:

> 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.
>

The point is to try to see whether the issue happens x steps into the
trajectory, or only at around t=120ps. Does it happen if you are using -pbc
somethingelse? Does it happen if you copy the file to some other filesystem
before using -pbc whole? One needs to find a pattern before one can guess
where the problem might lie.


> 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.
>

OK. It's possible your simulation system is doing something pathological in
that trajectory, which somehow does not agree with the implementation of
-pbc whole (I'm guessing wildly here), but one would need to try the above
kinds of experiments to probe that, and or visualize the trajectory in some
viewing program.

Mark

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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