Utilizing Averaged Configuations from Molecular Dynamics Simulation Trajectories

Abstract

One of the challenges in the large-scale simulations required for many molecular systems (such as those of biological interested) is the recording, monitoring and visualization of configurational information from molecular dynamics trajectories spanning millions, and sometimes billions, of timesteps. A detailed record of instantaneous configurations along the full trajectory can quickly become unmanageable. In this paper we will describe an alternative approach that utilizes time coarse-graining, where configurations averaged over trajectory segments are used to follow the detailed molecular behaviour of a system over multiple-nanosecond simulations. We will demonstrate that the sensitivity of structural measures (order parameters) can be dramatically enhanced when applied to averaged configurations. We then specifically discuss the successful application of this approach to molecular dynamics simulations of crystal growth.