Molecular dynamics simulations of RNA systems: Importance of the initial conditions

Abstract

Several factors can lead to the generation of accurate and informative molecular dynamics simulations. Among them, the choice of an appropriate starting structure is primordial. Unfortunately, experimental structures are not void of inaccuracies and errors. The aim of this review is to provide practical guidelines for detecting and correcting such inaccuracies in order to start molecular dynamics simulations of nucleic acid systems under the best possible conditions. © 2006 Springer.