[gmx-users] trjconv -pbc

[Rainer Boeckmann]

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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