  All-atom simulations have become increasingly popular to study conformational
and dynamical properties of nucleic acids as they are accurate and provide high
spatial and time resolutions. This high resolution however comes at a heavy
computational cost and within the time scales of simulations nucleic acids
weakly fluctuate around their ideal structure exploring a limited set of
conformations. We introduce the RBB-NA algorithm which is capable of
controlling rigid base parameters in all-atom simulations of Nucleic Acids.
With suitable biasing potentials this algorithm can "force" a DNA or RNA
molecule to assume specific values of the six rotational (tilt, roll, twist,
buckle, propeller, opening) and/or the six translational parameters (shift,
slide, rise, shear, stretch, stagger). The algorithm enables the use of
advanced sampling techniques to probe the structure and dynamics of locally
strongly deformed Nucleic Acids. We illustrate its performance showing some
examples in which DNA is strongly twisted, bent or locally buckled. In these
examples RBB-NA reproduces well the unconstrained simulations data and other
known features of DNA mechanics, but it also allows one to explore the
anharmonic behavior characterizing the mechanics of nucleic acids in the high
deformation regime.
