VMD-L Mailing List

From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Tue Apr 05 2011 - 02:29:57 CDT

Mark,

On 04/04/2011 10:04 PM, Mark M Huntress wrote:
> Am I understanding this correctly? If so, does this accurately
> reflect how the solvent is modeled with periodic boundary
> conditions? Would I be making an error to start a new QMMM trajectory
> with these velocities after re-centering? Thanks.

It sounds to me as though you haven't really grasped the meaning of
periodic boundary conditions. Maybe you should read the following page:

  http://polymer.bu.edu/Wasser/robert/work/node6.html

Yes, of course you can reuse the velocities when the positions have been
translated! That's what I meant with velocities being "translational
invariant". The reason in periodic boundary conditions is that an atom
does not only exist at a single set of coordinates, but that you can
think of it as infinitely many copies of the same atom in the periodic
images. VMD usually only shows a single image of an atom. You can,
however, show periodic images in Menu "Graphics" -> Menu
"Representations" -> Tab "Periodic". If you use that, you will probably
understand why it doesn't matter.

Olaf 

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