Improving the efficiency of BD algorithms for biological systems simulations

摘要

In this work, an error analysis methodology is applied to the study of various integration schemes used in Brownian Dynamics simulations of ion channels. Three algorithms have been compared for the integration of the full Langevin Equation. A first-order Euler scheme, the Verlet-like algorithm proposed by [3], and a novel Predictor/Corrector (PC) scheme have been implemented and analyzed using our assessment methodology. Our results show that a significant increase in the integration timestep, and a subsequent reduction in computational cost and improvement in efficiency, can be achieved with the second order Verlet-like and PC schemes, while maintaining an excellent accuracy for the description of both structure and dynamics of the electrolyte solution. This work extends the analysis developed in [5] to dynamic properties of the solution as well as structural aspects of inhomogeneous systems such as a lipid membrane.