Periodic Boundary Conditions and Solvent

Isolated gas phase molecules are the simplest to treat computationally. Much, if not most, chemistry takes place in the liquid or solid state, however. To treat these condensed phases, you must simulate continuous, constant density, macroscopic conditions. The usual approach is to invoke periodic boundary conditions. These simulate a large system (order of 10 molecules) as a continuous replication in all directions of a small box. Only the molecules in the single small box are simulated and the other boxes are just copies of the single box. 

HyperChem allows solvation of arbitrary solutes (including no solute) in water, to simulate aqueous systems. HyperChem uses only rectangular boxes and applies periodic boundary conditions to the central box to simulate a constant-density large system. The solvent water molecules come from a pre-equilibrated box of water. The solute is properly immersed and aligned in the box and then water molecules closer than some prescribed distance are omitted. You can also put a group of non-aqueous molecules into a periodic box. 

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