Averaged configurations from molecular dynamics simulations

Abstract

One of the challenges in the large scale simulations required for biomolecular system is the recording, monitoring and visualization of configurational information from molecular dynamics trajectories. A detailed record of instantaneous configuration along the full trajectory can quickly become unmanageable. In this paper we will describe an alternative approach where configurations averaged over trajectory segments are used to follow the detailed molecular behaviour of a system over multiple-nanosecond simulations. We will then discuss the successful application of this approach to molecular dynamics simulations of crystal growth. © Springer-Verlag Berlin Heidelberg 2007.