title: Molecular modeling of nucleic acid structure: setup and analysis.
abstract: 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.
authors.affiliation: University of Utah, Salt Lake City, Utah, USA.
authors.forename: T E
authors.initials: TE
authors.lastname: Cheatham
authors.forename: B R
authors.initials: BR
authors.lastname: Brooks
authors.forename: P A
authors.initials: PA
authors.lastname: Kollman
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009696:Nucleic Acids