title: Molecular modeling of nucleic Acid structure: setup and analysis.
abstract: The last in a set of units by the same authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. The unit 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: Vanderbilt University; Rega Institute for Medical Research; Hokkaido University; Rasayan Inc.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Galindo-Murillo
authors.forename: Christina
authors.initials: C
authors.lastname: Bergonzo
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Cheatham
mesh_terms: D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*
chemical_list: D009696:Nucleic Acids
keywords: force field review; nucleic acid chemistry; nucleic acid structure and folding; sampling methods; simulation protocols; simulation setup and analysis