Backbone torsion angles molecular dynamics

Figure 2 Radius of convergence of different refinement methods applied to test refinements with realistic errors added to the initial model. Backbone atom r.m.s. coordinate deviations after refinement are plotted against the starting backbone atom r.m.s. coordinate deviation. The thin dashed line corresponds to refinement by conjugate gradient minimization, the thin solid line corresponds to refinement by slow-cooling simulated annealing using Cartesian molecular dynamics. The thick dot-dashed line corresponds to the average result from ten constant temperature torsion angle molecular dynamics refinements the thick solid line corresponds to the best result from each series of ten refinements...

Figure 110. Six hexose dihedral angles of the homo-DNA backbone and the base—hexose torsion as predicted for a linear conformation (actual values determined by NMR and molecular dynamics techniques). For models A and B, values indicate the lower and upper limits of the dihedral angles observed.

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