Table 1. Summary of MD Simulations Performed in This Work.

starting RNA structure	ions added	nomenclature	figure
Rerefinement
1TBK models 2–11	20 Na+, 4 Cl–	rerefined MgFree ensemble	Figure 2b
Long MD Simulations −10 × 250 ns Simulations for Each System
1TBK model 1	20 Na+, 4 Cl–	n/a	Supporting Figure 2
rerefined 1TBK, all 10 models	20 Na+, 4 Cl–	MgFree + 50 mM NaCl	Figure 2b; Figure 3c,g; Figure 4, blue; Figure 6, red
1YN2 model 1	20 Na+, 4 Cl–	MgBound + 50 mM NaCl	Figure 3a,e
1YN2 model 1	12 Mg2+, 4 Cl–	MgBound + 40 mM MgCl2	Figure 3b,f; Figure 4, black and red; Figure 6, black
rerefined 1TBK, all 10 models	12 Mg2+, 4 Cl–	MgFree + 40 mM MgCl2	Figure 3d,h
Replica Exchange Simulation: 48 replicas × 1.2 μs per Replica
rerefined 1TBK, model 1	20 K+, 4 Cl–	MgFree + 50 mM KCl	Figure 6, blue