From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Fri Jun 15 2012 - 23:35:58 CDT

as it turns out, my problem was a red herring: pbc unwrap has no issues for
long trajectories, my issue was elsewhere. I found the discussion very
useful anyway; now I understand much better the pbctools.

On Thu, Jun 14, 2012 at 2:51 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Thu, Jun 14, 2012 at 1:34 PM, Joshua D. Moore <joshuadmoore_at_gmail.com>
> wrote:
> > Not sure if you are having the same issue as I've had before, but I
> > always had trouble with pbcunwrap if my starting frame was not already
> > unwrapped. So if I had a trajectory where frame 0 had everything
> > nicely in the box, with no bonds, etc. crossing periodic boundaries,
> > it seemed to work well, but if my frame 0 was wrapped and had
> > molecules with bonds that stretched across the PBCs, I would get
> > strange results.
>
> yes. that is by design. for this step there is _pbc join_
> (with two different algorithms, btw) and once you've
> done that, you can unwrap based on that reference.
> most of the time, you actually don't want to run
> pbc unwrap, but rather pbc join. however, this is very
> slow, while running pbc join on one frame and then
> pbc unwrap and finally pbc wrap -compound fragment
> or pbc wrap -compound residue is much more efficient.
>
> > I think from what Jerome says (It does this by wrapping each frame
> > around the (unwrapped) coordinates of the previous frame.", maybe this
> > implies that you always need the first frame to be unwrapped?
>
> yes, but "joined" not "unwrapped". unwrapping always works
> by comparing two frames to detect, which particles moved
> farther than half a box length.
>
> axel.
>
> > On Mon, Jun 11, 2012 at 7:05 PM, Edward Lyman <edward.lyman_at_gmail.com>
> wrote:
> >> 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
> >>
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>