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The last snapshots of implicit water simulations (a) under AMBER03 force field and (b) PHB model.
Backbone RMSD from the native structure and radius of gyration as a function of simulation time using AMBER03 charge (black) and the PHB (red) model in explicit water. The representative structures and their relative distributions from these two simulations are also plotted (right panels).
Snapshots of intermediate structures of the peptide at different simulation time under PHB model (compared to the NMR structure). The C-terminal is always on the top.
Free energy landscapes at 288 K mapped to RMSD from the native structure and radius of gyration obtained from simulations employing (top) AMBER03 charge and (bottom) PHB model. The representative structures are also shown in the figure.
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