VMD-L Mailing List

From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Mon Oct 01 2012 - 06:24:05 CDT

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Hi!

On 10/01/2012 12:56 PM, Steven Neumann wrote:
> Shall I then save those coordinates in pdb and/or psf? - I mean is
> that just a visual effect or when the box is shifted that means my
> system is not in the box so the water will go to the vacuum while
> running simulation?

If you are using periodic boundary conditions (and I trust that you
are), it is purely visual. It doesn't matter where you put the
boundaries, the system is always the same.

Olaf

- --
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
Phone: +49-711-685-63607
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