Timescales for convergence in all-atom molecular dynamics simulations of hydrated amorphous xylan

Abstract

Atomistic molecular dynamics simulation is an important complement to experimental techniques for investigating properties of hydrated carbohydrate polymers at the molecular scale. A critical problem is to determine whether or not a simulation has converged to thermal equilibrium before data collection can begin. In this work, simulations of xylan oligomers starting from random configurations at different levels of hydration are performed. The simulations show clear evidence of phase separation into water-rich and polymer-rich phases at higher hydration, in spite of standard indicators of equilibrium, such as density and energy, remaining constant. Using instead a set of parameters that are coupled to the structural and dynamical heterogeneity of the system, it is shown that simulation times on the order of one microsecond are needed to reach an equilibrated state. Moreover, qualitative similarities in the temporal evolution of these parameters suggest significant interplay between the structure and both polymer and water dynamics.