VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Mon Jun 11 2012 - 18:05:32 CDT

Hi Jerome,

Thanks for your reply. I think that means we must have some other
issue to figure out!

Best,
Ed

On Mon, Jun 11, 2012 at 10:54 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> 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