Stochastic dynamics simulations in a new generalized ensemble

Abstract

We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the methods are tested with an energy function for a protein system. Simulations in this generalized ensemble by the three methods are performed for a penta peptide, Met-enkephalin. For each algorithm, it is shown that from only one simulation run one can not only find the global-minimum-energy conformation but also obtain probability distributions in canonical ensemble at any temperature, which allows the calculation of any thermodynamic quantity as a function of temperature.