computer modeling in molecular biology.pdf

122 E. WesthoL C. Rubin-Carrez, and K FritschFigure 5-11. Illustration of the spine of hydration, i. e. of water molecules bound to N3 and02 atoms in the minor groove of the (dA)-(dT) decamer, along the MD simulation in aquaThe black circles correspond to the water oxygen atom positions. Notice how the periodicityat the end of the thermalization step is slowly broken up during the simulation, although watermolecules still bind systematically in the minor groove up to the end of the production step.(From Fritsch et al. [25]).