computer modeling in molecular biology.pdf

5 Modelling Nucleic Acids 11 1Figure 5-2. Breakage of aWatson-Crick pair during aMD simulation seen from themajor groove (top) and fromthe minor groove (below). Thestarting conformation is at theleft and the conformationafter 53 ps simulation at theright. Such large deformationsare obtained when the systemis not properly equilibratedbefore starting the simulation.(From Fritsch [64]).Figure 5-3. Two views of a DNA fragment with its associated sodium counterions (blackspheres). At left is shown the starting conformation. The state obtained after 40 ps of MDsimulation is shown at the right. A counterion has been strongly displaced from the DNA andis about to cross the “wall” of the solvation box leading to a halt of the simulation. Again,such situations occur when the whole system is not adequately equilibrated. (From Fritsch~41).