Net electroneutrality

Tar—Tar system (Chen et al., 2009) are shown in Fig. 20.2. Panels A and B of Fig. 20.2 show the RNA phosphate-counter-/coion RDFs using simulation data based on 80 and 120 A simulation cells, each containing 236 and 792 excess ion pairs, respectively. In the 120 A box, both RDFs decay to unity (within 1%) as the edge of the central simulation cell is approached. This indicates the presence of a clear local-bulk partition and the presence of a bulk-like reservoir with which ions can be exchanged. The phosphate-counterion and phosphate-coion RDFs differ by a few percent in this regime, but these differences are due to the fact that there are always 30 additional neutralizing counterions present to ensure net electroneutrality of the Tar—Tar system. Conversely, at the boundary of the 80 A box, the coion density exceeds unity by 15%. This artifact is the result of the... 

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