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. Author manuscript; available in PMC: 2022 Mar 11.
Published in final edited form as: J Chem Theory Comput. 2010 Nov 9;6(12):3836–3849. doi: 10.1021/ct100481h

Figure 6.

Figure 6.

Typical progression of GNRA tetraloop AMBER simulations. Left: simulations without the χ correction or with Ode et al.’s correction illustrated by a 25 ns GAGA_bsc0 simulation. Right: simulations with χOL-DFT, χOL, and χYIL variants illustrated by a 1 μs GAGA_bsc0χOL simulation. The upper graphs present a time evolution of the β(GL3) torsion (black line), γ(GL3) torsion (red line), and mean χ torsion averaged over either stem nucleobases (green line) or the GNRA tetraloop (blue line). The middle graph shows the GL1/AL4 buckle, and the lower graph presents the GNRA tetraloop signature H-bonds: GL1(N2)•••AL4(N7), GL1(N2)•••AL4(pro-Rp), and GL1(O2′)•••GL3(N7) in black, red, and green, respectively.