(iii) Choice of collective variables. To facilitate the free energy calculations for both studies above, we have defined the collective variables based on an intuitive way of understanding the process and also based on reported studies on similar RNA motifs, as these choices are heuristic. Since the goal of the present study is to understand the folding-unfolding thermodynamics in the presence of amino acids, our choice was governed by the need to observe the conformational change in the RNA (e.g., the stem distance, radius of gyration, contacts, ermsd ). Also, we studied binding free energy of a particular stereoisomer to the folded RNA using another set of CVs (binding distance, angvec). The CVs are discussed in more detail below.