Application of a Symplectic-Energy-Momentum Preserving Integrator to Molecular Dynamics

In molecular dynamics simulations, an integrator-induced resonance is observed for conservative molecular system subject to the classical equations of motion when a Verlet integrator or Implicit Midpoint scheme is used. In this report, an existing variational integrator with adaptive timesteps is introduced to handle resonance. This Symplectic-Energy-Momentum (SEM) preserving algorithm is first applied to a diatomic molecule governed by a Morse potential and then it is further applied to a 22-atom model system. Computational experiments indicate that the SEM algorithm can avoid energy resonances and produce more accurate sampling of phase space. Moreover, it can increase the feasible timestep and hence has the potential to improve the simulation times. These are the main advantages over other fixed timestep methods. Its main disadvantage, however, is that the algorithm is computationally more expensive since one needs to solve a complicated nonlinear system of equations during its use.