Molecular Dynamics in Systems with Multiple Time Scales: Reference System Propagator Algorithms

Abstract

Systems with multiple time scales, and with forces which can be subdivided into long and short range components are frequently encountered in computational chemistry. In recent years, new, powerful and efficient methods have been developed to reduce the computational overhead in treating these problems in molecular dynamics simulations. Numerical reversible integrators for dealing with these problems called r-RESPA (Reversible Reference System Propagator Algorithms) are reviewed in this article. r-RESPA leads to considerable speedups in generating molecular dynamics trajectories with no loss of accuracy. When combined with the Hybrid Monte Carlo (HMC) method and used in the Jump-Walking and the Smart-Walking algorithms, r-RESPA is very useful for the enhanced sampling of rough energy landscapes in biomolecules.KeywordsMonte CarloSmall Time StepMultiple Time ScaleRange ForceFast Multipole MethodThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.