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. 2016 Jul 13;12(8):4138–4145. doi: 10.1021/acs.jctc.6b00536

Figure 3.

Figure 3

Algorithmic steps of the SWINGER algorithm. The snapshots represent the state of the system before and after each stage of the algorithm. Before the algorithm is applied the region C contains water molecules (blue) and water clusters (red). After the first stage (I) of the algorithm the clusters are disassembled, and primary (blue) and buffer (gray) lists are constructed. In the second stage (II), initial grouping is performed, where all molecules in the primary list are assigned to a given cluster. In the third stage (III), the clustering is optimized with simulated annealing MC. In the last stage (IV), only the clusters in region C are preserved, whereas other clusters are rejected.