VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Wed Aug 06 2003 - 18:04:39 CDT

Hi,

On Wed, Aug 06, 2003 at 03:33:45PM -0700, Ioana Cozmuta wrote:
> Hi,
>
> I am trying to vizualize a trajectory where a particle crosses the cell
> boundary several times. I am setting the PBC on the first cell and show
> the periodic copies on the zZ axis.
>
> However when I load the trajectory there is just the original cell left
> and the animation does not show the particle crossing the periodic
> boundary into the next cell but only moving in the original cell.
>
> I did try to load the .xst file on top of the trajectory but this seems
> not to be an accepted file type yet. I did try to set again the unit cell
> parameters for the other frames but this does not seem to work either.
>
> Is this possible at all? Please advise.

NAMD wraps the atom coordinates before writing them to the trajectory
file, so there is no way for VMD to know that that atom crossed a unit
cell boundary. You can turn this wrapping behavior off in NAMD by
specifying "wrapWater off" in the config file.

Specifying "dcdUnitCell on" in the NAMD config file makes NAMD write unit
cell information to the dcd file, which will then be read in by VMD so
that you don't have to specify the unit cell data by hand for each frame.

Justin

>
> Thank you,
> Ioana 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys