Water structure network formation simulation

In the active-site simulations of lysozyme108 (this chapter, Sect. B.2 above) similar water networks that stabilize charged groups have been observed. To illustrate the dynamics of the formation of such networks, a sequence of stereo plots showing the formation and evolution of a stable pair of positively charged residues is displayed in Fig. 56. The pair consists of (NH2)+ moieties of Arg-61 and Arg-73. The solvated structure evolved from a conformation obtained in a vacuum simulation of lysozyme.108,192 The sequence of plots shows the formation of the water-bridged pair over a time period from t = 0 ps to t 8 ps, which followed dynamical equilibration of the solvent around the fixed vacuum structure of the protein. After 8 ps, the ion-pair structure is stable, but fluctuations in the pattern of hydrogen bonds do occur typical... 

As we have discussed earlier, because of the presence of the HB network structure water has an enormous number of stable or quasi-stable energy states (reflected in its high heat capacity). This is also reflected in the difficulty of ice formation in computer simulations. The system needs to search for a long time to find the global minimum for ice structure. The system explores the potential-energy landscape for a considerable amount of time before the start of the ice formation. This scenario agrees well with the nucleation picture discussed earlier in this chapter. 

Formation of a sparming network of hydration water at the DNA surface upon hydration was studied by computer simulations [200,621] using the water drop methods [622, 623]. Simulations were carried out for a rigid dodecamer fragment of double-helical DNA. The structures of the canonical B-DNA and A-DNA [624] were fixed in space. The system involved 24 bases and 22 phosphate groups in two DNA strands surrounded by a mobile hydration shell of 22 Na ions and 24F water molecules. Evolution of the cluster size distribution ns on the surface of B-DNA upon increasing hydration is shown in Fig. 104. At low hydrations (F = 12, 13, and 14), ns shows deviations upward from the power law (19) at the intermediate cluster sizes S. At high hydrations (F = 17, 18, 19, and... 

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