Molecular Modeling of Nucleic Acid Structure: Setup and Analysis

The last in a set of units by these authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. It describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and how to analyze molecular dynamics trajectories.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153007/1/cpnc0710.pd