Reweighted ensemble dynamics simulations: Theory, improvement, and application*
Gong Lin-Chena), Zhou Xinb)†, Ouyang Zhong-Cana),c)
       
RED analysis with the basis functions of dihedral angles and inter-atomic distances. Shown are the results for solvated alanine dipeptide, which is simulated at T = 300 K with the modified force field. (a) The eigenvalues of H matrix calculated with different sets of basis functions, including the full set of inter-atomic distances (squares), 12 inter-atomic distances (upward triangles), first-to-fourth order trigonometrical functions of ϕ and ψ (circles), and first-to-second order trigonometrical functions of ϕ and ψ (stars). (b) The behavior of S 2 is shown either with the inter-atomic distances (distance-angle) at first, or with the trigonometrical functions of ϕ and ψ at first (angle-distance). The values calculated with truncated trajectories (80 percent length) versus the ones calculated with full trajectories are shown. The results are obtained either with the first-to-second order trigonometrical functions of ϕ and ψ (c), or with the inter-atomic distances (d). The arrows label the intersection points between the dashed and dotted lines.