Figure 5.

Illustration of the HSMD reconstruction process of conformation i of a peptide consisting of three glycine residues. At each step the transition probability (TP) of a dihedral angle and the successive bond angle is determined and the related atoms are then fixed in their positions in i. The figure describes step 4 where the dihedral and bond angles considered are φ₂ (of the second residue) and the successive θ, respectively; these coordinates are also denoted α₇ and α₈, respectively (see text). In this process the already reconstructed part (the past) is depicted with solid lines and solid spheres (atoms); for simplicity the oxygens and most of the hydrogens are discarded. The TP is obtained by carrying out an MD simulation of the as yet unreconstructed part of the peptide (the future) which is depicted with dashed lines and empty spheres. In this simulation the “past” atoms remain fixed at their positions in i while the conformations of the future part should remain within the limits of the microstate; future-past interactions are taken into account. Small bins δφ₂and δθ are centered at the values of φ₂ and θ in i. The TP is calculated from the number of simultaneous visits of the future part to δφ₂ and δθ during the simulation (see equation (42)). After TP(4) has been determined the coordinates of the two hydrogen atoms of C^α (2) and those of C’(2) are fixed at their positions in i and the process continues.