VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Fri Jun 08 2012 - 10:09:48 CDT

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