Figure 3
From: Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations
Potential of mean force for kissing-complex formation Potential of mean force (PMF) as a function of the distance between the centers of mass of the L2 and L3 loops. Results for Holo and Apo forms are shown as obtained from two independent umbrella sampling simulations using different protocols to obtain the initial structures (forward, Fwd, and backward, Bwd, see main text for definition). Fwd and Bwd profiles are aligned at the maximum distance.