Biomedical Engineering Reference
In-Depth Information
Modern molecular modelling packages such as HyperChem usually include the option
of a periodic solvent box, often the TIP3P box of 216 water molecules. The example shown
in Figure 23.4 is from a MM optimization using phenylanine in water.
Figure 23.4
Phenylanine in periodic solvent box
The standard box is a cube of side 1870 pm, and it is conventional to choose the appro-
priate box with sides in multiples of this. I should not need to remind you by now of the
significance of the word 'periodic'.
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