Figure 1.

Model RNA sequences and initial structures used in regular and umbrella sampling MD simulations. For illustrative purposes, the hydrogen atoms of the water molecules are not shown. The oxygen atoms of water molecules are represented with red dots. Blue and cyan spheres represent Na⁺ and Cl^– ions, respectively. RNA structures are shown in the “new ribbons” format.⁶⁵ The opaque region of C represents the unit cell, while transparent regions represent the neighboring cells to illustrate the design of the infinitely long RNA system. Residue numbers described for each system are used in the analyses.