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All-atom simulations have become increasingly popular to study conformationaland dynamical properties of nucleic acids as they are accurate and provide highspatial and time resolutions. This high resolution however comes at a heavycomputational cost and within the time scales of simulations nucleic acidsweakly fluctuate around their ideal structure exploring a limited set ofconformations. We introduce the RBB-NA algorithm which is capable ofcontrolling rigid base parameters in all-atom simulations of Nucleic Acids.With suitable biasing potentials this algorithm can "force" a DNA or RNAmolecule 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 ofadvanced sampling techniques to probe the structure and dynamics of locallystrongly deformed Nucleic Acids. We illustrate its performance showing someexamples in which DNA is strongly twisted, bent or locally buckled. In theseexamples RBB-NA reproduces well the unconstrained simulations data and otherknown features of DNA mechanics, but it also allows one to explore theanharmonic behavior characterizing the mechanics of nucleic acids in the highdeformation regime.

Rigid Base Biasing in Molecular Dynamics enables enhanced sampling of DNA conformations