Fig. 7.

Average number of H-bonds between different groups of molecules (see labels in the plots), determined through the last 100 ns of all the trajectories. The plots containing the CD-CD and CD-Water H-bonds (top row) are normalized by CD molecule, while those containing the CD-REMD and REMD-Water H-bonds (bottom row) are normalized by remdesivir molecule. The plots correspond to simulations with 20 CD molecules and 1 (black), 2 (red), 4 (blue) or 8 (orange) neutral (lined bars) or protonated (solid bars) remdesivir molecules, determined through the last 100 ns of all the trajectories. The numerical values for these plots, including standard deviations, are shown in Table S2. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)