[gmx-users] trjconv -pbc

[Andre Farias de Moura]

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
> > /./././././././././././././././././
> >
> >
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