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Population annealing is a novel generalized-ensemble simulation scheme used in large-scale parallel Monte Carlo simulations of disordered spin systems and similar problems. In a recent publication we proposed a generalization of this method to molecular dynamics simulations of biopolymers. In the present article we review this work and introduce a scheme for automatically choosing the temperature steps based on the observed distribution of potential energies in the population of simulated replica.

We present comparative results from simulations of a lattice and an off-lattice model of a homopolymer, in the context of kinetics of the collapse transition. Scaling laws related to the collapse time, cluster coarsening and aging behavior are compared. Although in both models the cluster growth is independent of temperature, the related exponents turn out to be different. Conversely, the aging and associated scaling properties are found to be universal, with the nonequilibrium autocorrelation exponent obeying a recently derived bound., 6 pages, 3 figures, conference; accepted for publication in J. Phys.: Conf. Ser