Increasing the Time Step and Efficiency of Molecular Dynamics Simulations: Optimal Solutions for Equilibrium Simulations or Structure Refinement of Large Biomolecules

Abstract

In biomolecular simulation, the different force field terms determine the motional frequencies found in a particular simulation. By eliminating the high frequencies, longer time steps can be achieved in equilibrium and refinement (non-equilibrium) simulations, sometimes at the expense of decreasing physical correctness of the simulated system. The different force field terms used in molecular simulations can be constrained or softened leading to a maximum time step of 5 fs for a simulation, in which static equilibrium properties are not affected by the changes in the force field parameters introduced, but dynamical quantities are. Using a very smoothed, soft interaction function and increased hydrogen masses, a time step of 14 fs can be reached. However, it should only be used in refinement simulations, in which the unphysical properties of the force field and dynamics are of minor importance.

Keywords:

• Molecular Dynamics Simulation
• Constraints
• Time Step
• Equations Of Motion
• Biomolecules