To help visualize ensembles in molecular dynamics. Molecular dynamics simply studies chemical systems by simulating the systems on a computer. Because it's impossible to computationally study a system in all of its many states, we study ensembles that are representative of the several states of the system. Molecular dynamics is primarily concerned with microscopic behavior of a system which affects the system's bulk properties.
Quite a few simulations are done in cubic boxes. In order to make the simulation behave as if it is an infinite system, a periodic boundary condition PBC is used. This ensures that bulk effects like surface tension are minimized in the system.
|The shaded box is the simulation box. The other boxes are
exact copies of the simulation box. The copies behave exactly
as the simulation box. The atoms move in the same direction, with
the same speed at the same time. As a result the number of atoms
in the simulation box are conserved, because when an atom leaves,
another exactly like it enters the simulation box.
Thanks to MSRI and the organizers for a very productive fortnight.
Thanks to everybody!!