Superbox algorithm

Two macromolecular computational problems are considered (i) the atomistic modeling of bulk condensed polymer phases and their inherent non-vectorizability, and (ii) the determination of the partition coefficient of polymer chains between bulk solution and cylindrical pores. In connection with the atomistic modeling problem, an algorithm is introduced and discussed (Modified Superbox Algorithm) for the efficient determination of significantly interacting atom pairs in systems with spatially periodic boundaries of the shape of a general parallelepiped (triclinic systems). 

Figure 1. A two-dimensional implementation of the Modified Superbox Algorithm.

This algorithm is readily extendable to three (or more) dimensions. The only computationally costly step is (iii.c), which is very rare if the grid has been chosen fine enough. The Modified Superbox Algorithm is not as efficient as the Screening Algorithm (6), but is very attractive for its generality and simplicity. 

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