Periodic boundary conditions
The classical way to minimize edge effects in a finite system is to apply periodic boundary conditions.
The atoms of the sistem to be simulated are put into a space-filling box, which is surrounded by translated copies of itself.
Thus there are no boundaries of the system. The artifact caused by unwanted boundaries is an isolated cluster is now replaced by the artifact of periodic conditions.
If the system is crystalline, such boundary conditions are desired.
If one wishes to simulate non-periodic systems, such as liquids or solutions, the periodicity by itself causes errors.
There are several possible shapes for space-filling unit cells. Some, like the rhombic dodecahedron and the truncated octahedron are closer to being a sphere than a cube is, and are therefore better suited to the study of an approximately spherical macromolecule in solution, since fewer solvent molecules are require to fill the box given a minimum distance between macromolecular images.
For example GROMACS a software for MD simulations use periodic boundary conditions, combined with the minimum image convention: only one, the nearest image of each particle is considered for short range non bonded interaction terms.