[gmx-users] Periodic boundary problem

[Berk Hess]

> >
> > But
> > trjconv -s -pbc nojump
> > should fix the problem when the tpr file given with -s has the correct
> > complex conformation.
>
>So i only need to take an input file with the "correct" look (both dimers
>together), and then it should work?

Yes.
That is what the manual page says.
And that is how I programmed it.
It has always worked for me.
If it doesn't work for you, please tell us.

>
> > Note that your problem is not really a problem, unless you want to make
> > nice
> > pictures
> > or do a visual inspection.
>
>So how can i fix it, if i want to make nice pictures or animations?

With the method desdribed above.
And probably also with the cluster option as mailed by Kay Gottschalk.

Berk.

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