Stochastic dynamics simulations of the alanine dipeptide using a solvent-modified potential energy surface

Langevin dynamics on a potential of mean force energy surface is used to model the effects of aqueous solvent on the structure and dynamics of the alanine dipeptide. Conformational transition rates obtained by correlation function analysis and hazard plots from several simulations are compared. In particular, averages obtained over three 25-ns runs are compared with a single run of 100 ns. Rate constants for selected conformational transitions are also examined. For the conformational processes considered here (α to β and the reverse), we observe two rates, one of which is only significant for simulations of more than 25 ns. On further decomposition of the rate process, it is shown that the two observed rates correspond to the individual rates for rotation around the φ and ψ dihedrals. It is also shown that, for the conformational transitions investigated here, the transition process corresponds to an essentially uncorrelated motion of the two dihedral angles.