VMD-L Mailing List

From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Wed May 09 2007 - 08:52:55 CDT

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Hi!

Joshua D. Moore wrote:
> I have been using DL_POLY version 3 to create trajectories. When I
> visualize, it appears that all of the coordinates are wrapped with the
> periodic boundary conditions. So the coordinates of some atoms are not
> kept
> with the molecule (as pbcwrap does with NAMD dcd files). So when bonds are
> drawn they are somtimes extended across the box! Is there a way to unwrap
> these coordinates? I tried using pbcunwrap from below, but I didn't have
> much luck.

- From your description, it's not easy to understand your problem. You'll
find documentation on the pbctools in:

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

The problems should not depend on the file format you're using, but on
the simulation type. If I'm not mistaken, DL_POLY does standard MD
simulations, so the pbctools should be able to cope with it.

If I understand it right, DL_POLY writes the trajectiory such, that the
coordinates are already wrapped into the central image. In that case,
you will probably want to unwrap the coordinates, to make the
coordinates continuous over the different frames of the trajectory,
avoiding the jumps caused by the wrapping. To do that, you can use the
function "pbc unwrap". If that doesn't solve your problem, then please
try to specify your problem more precisely.

Best regards
        Olaf
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