[gmx-users] trjconv -pbc

[Rainer Boeckmann]

trjconv -pbc nojump starts indeed with the coordinates of the tpr-file. Therefore you
end up with broken molecules if the time gap between tpr-coordinates and coordinates
of the first frame of the trajectory is too large. (I wouldn't call it a bug, it is
even useful.)
rainer

Anton Feenstra wrote:

> Rainer Boeckmann wrote:
> > Hi Andre,
> >
> > do you apply -pbc whole/-pbc nojump on the whole trajectory or only on snapshots
> > or parts of the trajectory (with the initial tpr-file)? In the latter cases you
> > might get broken molecules due to a change in box vector length. The nojump-flag
> > uses the box parameters from the trajectory and not from the tpr-file. A
> > solution would thus be to apply the procedure with whole & nojump on the whole
> > trajectory (or on a small part with a changed tpr-file). trjconv -pbc nojump
> > uses the tpr-file coordinates as a reference for the first frame but the box
> > parameters from the first frame of the trajectory.
>
> That doesn't sound quite right. If that is really the case, it might be a bug.
> Can someone look into that?
>
> --
>

--
Dr. Rainer Böckmann
Theoretical Molecular Biophysics Group
Max-Planck-Institute for Biophysical Chemistry
Am Faßberg 11
D-37077 Göttingen

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email: rboeckm at gwdg.de

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