FIG. 3.

Theory-experiment comparisons of the folding free energy for (a) the BWYV and (b) the T2 pseudoknots. In the theoretical predictions, we use the same temperature and ionic solution condition as the experiment. Here the folding free energy is defined as the free energy difference between the folded state (pseudoknot) and the folding intermediate (hairpin). The red filled stars denote the experimental data for BWYV¹¹ and T2,⁶⁰ respectively. For each case, we select five sets of hairpin conformational ensembles, each with 3600 conformations generated from MD simulations. The conformations are randomly selected from the conformations generated from MD trajectories. For each set of the conformational ensemble, the ensemble-averaged result for the folding free energy is marked with an open symbol. In each figure, the pink solid line shows the average value of the five sets of the results. The x-axis denotes the ion concentration in units of M.