VMD-L Mailing List

From: Taco de Wolff (tacodewolff_at_gmail.com)
Date: Thu Mar 10 2011 - 10:46:09 CST

On Thu, Mar 10, 2011 at 4:44 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> 2011/3/10 Olaf Lenz <olenz_at_icp.uni-stuttgart.de>:
> > Hi!
> >
> > On 03/10/2011 01:36 PM, Taco de Wolff wrote:
> >> ITEM: BOX BOUNDS xy xz yz 0 6 0 0 6 3 0 6 0
> >
> >> Does _not_ show to be triclinic, eventhough by specification it
> >> should (shouldn't it?).
> >
> > I do not know the lammpstrj format, but the above values look fishy.
>
> olaf,
>
> the box description in lammps is a bit unusual.
> on top of that, they are boundaries and tilt "factors",
> this all doesn't translate easily into vectors and matrices.
> there is a bit of math needed to convert those.
>
> this is a tilted box which boundaries are a cubic 6 angstrom cell,
> but it is tilted by 3 angstrom in the y direction, i.e. has a
> 45 degrees beta angle.
>
> the notation is xlo, xhi, x-tilt, ylo, yhi, ytilt, xlo, zhi, ztilt.
>
> > Depending on whether they are denoted as column or row vectors, you
> > either have two parallel axes (0 6 0 occurs twice), or one of them is
> > the zero vector (0 0 0). None of this looks useful as unitcell vectors.
> > So my guess is that the error handling of the file reader plugin is not
> > perfect, as it does not complain, but that mainly your box vectors are
> > wrong.
>
> the issue is that the trajectory format was extended not so long ago to
> cover this case and the box boundaries are still read correctly and can
> be displayed, but of course that doesn't give you the correct unitcell.
> there is an explanation that this notation would make it easier for
> visualization programs, but i personally don't see where, and then again,
> the simulation world is full of arbitrarily designed and strange ad hoc
> file formats. ;)
>
> cheers,
>     axel.
>
> > Olaf
> >
> > --
> > Dr. rer. nat. Olaf Lenz
> > Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
> > Phone: +49-711-685-63607
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.

 Hey Alex,

 Thank you for your support. Our computer support guy is currently
installing 1.9, so that should be fine :)

 I did find a nice way to simulate the box though. I added eight atoms
at the corners of the box, and connected them through the PSF file.
 Setting those atoms to a different type you can display them as
lines, while the actual atoms can be displayed as whatever you want.
 Looks about just as good ;). Extrapolation of PBC boxes doesn't work
properly anyways.

 And yes, the choice of tilt factors seems arbitrary, luckily
explained well here:
http://lammps.sandia.gov/doc/Section_howto.html#4_12
 But I find the choice of using lower and upper bounds slightly
awkward too. Best IMO would be to define the a, b, c vectors (aka.
transformation matrix).

 Thanks for the answer,
 Taco

PS: sorry Alex, forgot to Send to All...