Questions and problems?
Periodic Boundary Conditions: translation across boundaries
During the initialization of MD of a solvent in a box of water
I have recognized in some cases that a water molecule has slipped
out of the box and was lying outside the box. I have detected this
from the restart files which was written at the end of each run.
Although the water molecule has moved not very far across
the z-border of the box I'm wondering if I can go on with this
or if there is something serious wrong. From theory I would expect that
a molecule can never cross the border because it would be simultaniously
inserted back into the box at the opposite side.
The routine that translates molecules back into the "box" is called
at the beginning of each MD step. The restart file is written at the
end of an MD step. If a molecule passes the box boundary on the step
just prior to an restart write, you can find molecules that are (slightly)
outside the box.
There is nothing wrong with your simulation, nor is there any problem
with using the restart coordinates for a subsequent run. In fact, the
imaging process used in Amber is such that it doesn't really matter if
molecules appear anywhere in any of the image boxes adjacent to the central
box. But in any case, if you read this restart file into Amber, the
molecules will be re-translated into the central box before the first
MD step.
Web Masters <webadmin@www.amber.ucsf.edu>
Last modified: Tue Nov 15 18:50:24 1994