The trajectory of folding polyalanine during the NEIMO-Hoover simulaton. The helix first forms at residues 8 to 11. Then the amino terminal half of the polymer forms a helix. Finally, residues 14 to 18 folded starting from the center and propagating up progressively. The times of the conformations are, from left to right, 0 ps, 50 ps, 100 ps, 125 ps, 150 ps, 175 ps, 200 ps, and 225 ps. The initial state has all phi and psi torsional angles equal to 180 degrees.
Formation of the first alpha-helical, i, i+4 hydrogen bond during a molecular dynamics simulation of polyalanine folding. At 103 ps, the carbonyl oxygen of residue eight is strongly bonded to the amino hydrogen of residue ten. By 106 ps, the carbonyl oxygen has formed a hydrogen bond with residue 11. Slowly residue eight walks up the chain, forming hydrogen bonds, until it is strongly bonded with residue 12, the fourth residue away.