[gmx-users] trjconv -pbc

[Rainer Boeckmann]

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.

cheers,
rainer

Andre Farias de Moura wrote:

> hello rainer,
>
> my tpr-file is ok, lipid molecules are not broken after
> "-pbc whole" option is applied. any other clue?
>
> thanks again,
>
> andre
>
> On Sat, 8 Mar 2003, Rainer Boeckmann wrote:
>
> > Hi Andre,
> >
> > sounds like as if your tpr-file has already broken molecules/lipids. Are
> > the lipid molecules broken, too, after applying '-pbc whole' only? That
> > works only in case your tpr-file shows whole molecules.
> >
> > cheers,
> > rainer
> >
> > On Fri, 7 Mar 2003, Andre Farias de Moura wrote:
> >
> > >
> > > hello all,
> > >
> > > I've performed some simulations of a micellar system and
> > > I would like to make animations of these trajectories,
> > > but some lipids jump across the box boundaries all the
> > > time. I'm using trjconv -pbc whole, followed by trjconv
> > > -pbc nojump, but then the lipid molecules break up in the
> > > boundary region. What am I doing wrong?
> > >
> > > thanks in advance,
> > >
> > > Andre'
> > >
> > >
> > > /./././././././././././././././././
> > >      Andre' Farias de Moura
> > >         Graduate Student
> > >       Departamento de Quimica
> > >  Universidade Federal de Sao Carlos
> > > /./././././././././././././././././
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

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

tel:    +49(551)201-1141
mobile: +49(172)9531168
fax:    +49(551)201-1089

email: rboeckm at gwdg.de

http://www.mpibpc.gwdg.de/abteilungen/071/rainer/index.html