[gmx-users] Overlapping frames within one .xtc
mark.j.abraham at gmail.com
Wed Aug 15 12:31:35 CEST 2018
Paul's answer is fully correct if you are using the (default) appending
upon restart from checkpoint. If you manage the restart or the filenames
yourself, then trjcat -overwrite can be needed because the first trajectory
can have additional frames after the time of the checkpoint (which mdrun
truncates if needed in the the appending-restart-from-checkpoint case).
On Wed, Aug 15, 2018 at 12:24 PM Sergio Perez <sperezconesa at gmail.com>
> I use gmx 2018.1 .I had just done a restart and I then thought that maybe I
> could have had that problem and I thought maybe that command could solve
> the problem if it had existed. I mean that if in the file there were
> overlapping frames they would be overwritten just as if you are doing
> trjcat on two files. But my problem is irrelevant if gromacs takes care of
> it preventively.
> Thanks a lot!
> On Wed, Aug 15, 2018 at 10:51 AM Paul bauer <paul.bauer.q at gmail.com>
> > Hello,
> > if you restart a run from the checkpoint file than any recent version of
> > GROMACS will make sure that there are no overlapping frames and that the
> > continuation is exact.
> > What were you trying to do on the command line when you wanted to
> > continue the run, and what version have you been using?
> > Cheers
> > Paul
> > On 15/08/18 10:43, Sergio Perez wrote:
> > > Dear GMX comunity,
> > >
> > > I would like to know if a run is interrupted abruptly (killed by the
> > user)
> > > and then is restarted with -append option, is there any chance that
> > > overlapping frames are generated within the .xtc file?
> > >
> > > If this were to happen, would
> > > gmx trjcat -f trj.xtc -o trj2.xtc -overwrite
> > >
> > > solve the problem?
> > >
> > > Thank you all very much in advance!
> > >
> > > Best,
> > >
> > > Sergio Pérez-Conesa
> > --
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