Experiments to compare implicit and explicit methods of integration in molecular dynamics simulation

Molecular Dynamics (MD) simulation is a versatile methodology that has found many applications in material science, chemistry and biology. In biology, the models employed range from mixed quantum mechanical and fully atomistic to united atom and continuum mechanical. These systems are evolved in discrete time by solving Newton’s equations of motion at each time step. The numerical methods currently in use limit the step size of a typical all atom simulation to 1 femtosecond. This step size limitation means that many steps need to be taken in order to reach biologically relevant time scales. At each time step, an evaluation of the forces on each atom must be performed resulting in heavy computational loads. We are currently investigating the utility of implicit integration methods for use in MD. Implicit integration methods have been proven superior to their explicit counterparts in classical mechanical simulation, with which MD has many similarities. If longer time steps can be taken then this reduces the number of force evaluations that must be performed and the corresponding computational load