VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Jun 11 2012 - 09:54:00 CDT

Hi Edward,

Unwrap tries to produce a trajectory without any jumps larger than
half the cell size. It does this by wrapping each frame around the
(unwrapped) coordinates of the previous frame.

At not point does it try to put atoms back into a unit cell, so atoms
may diffuse as far from the origin as they want, possibly many cell
sizes away.

Best,
Jerome

On 8 June 2012 17:09, Edward Lyman <edward.lyman_at_gmail.com> wrote:
> Hi All,
>
> We are trying to track some weirdness in a long trajectory which we
> would like to unwrap. We are not unwrapping whole molecules just
> single atoms---we have a trajectory of the phosphates only from a
> bilayer simulation.
>
> What we would like to know is if pbc unwrap will recognize when an
> atom crosses a boundary twice consecutively in the same direction. In
> other words the atom crosses the xmax boundary, then its unwrapped
> image continues diffusing away and crosses the **image** of xmax.
>
> Let's say the system size is L, and the x max boundary is at L/2. At
> some time an atom crosses the boundary at x=L/2. Some time later, it
> crosses the *same* boundary from the same direction. (without having
> turned around and recrossed) At that point, its unwrapped image is
> crossing an image of the boundary at 3L/2. Does pbc unwrap continue
> the unwrapped image atom happily on his way? Or does he jump back to
> the minimum image position, just across the boundary at L/2?
>
> Thx,
> Ed