computer modeling in molecular biology.pdf

5 Modelling Nucleic Acids 115With in vacua simulations, the microcanonical ensemble appears preferable; whilein aquo simulations with periodic boundary conditions are better handled in the(A? T)-ensemble (Figures 5-5 and 5-6).Figure 5-6. Root mean squares deviations (in A) versus time (in ps) during the heating, theequilibration, and the production steps for the three types of MD simulations described inFigure 5-5. The deviations are calculated on all atoms between the starting conformation andthe instantaneous one. (From Fritsch et al. [25]).5.8 Choice of Cut-OffsAlthough, ideally, no cut-off limiting inter-particle interactions should be applied,practically, computer limitations impose them especially in case of in aquo simulations.The notion of Debye distance mentioned above sets a cut-off on electrostaticinteractions around 10 A. For in aquo simulations, the cut-off for solute-solvent interactionswas generally chosen around 8 to 9 A, while no cut-off was set for solutesoluteinteractions (i. e. interactions between nucleic acid atoms as well as betweennucleic acid atoms and counterions which are considered in AMBER as belongingto the solute).