title: Computer simulations of macromolecular dynamics: models for vibrational spectroscopy and X-ray refinement.
abstract: The use of computer simulations to study the internal dynamics of globular proteins and nucleic acids has attracted a great deal of attention in recent years. These simulations constitute the most detailed theoretical approach available for studying internal motions and structural flexibility of biological macromolecules. In this paper we review recent work concerned with the use of computer simulations for the interpretation of, and comparison with, experimental probes of molecular dynamics. New methods for calculating vibrational spectroscopic lineshapes from computer simulations are discussed. A quasiharmonic approximation is described by which classical computer simulations on multidimensional potential surfaces can be used to estimate the effects of anharmonicity on vibrational spectra. A novel aspect of the method is the use of normal-mode eigenvectors as the independent coordinates for Monte Carlo sampling. Results for isolated small molecules and liquid water are reviewed. The construction of vibrational lineshapes from quantum computer simulations using path integral methods with new (quasiharmonic and variable quadratic) reference systems are discussed. Results for small model systems are presented and extension of the methods to large molecules is discussed. The recent use of molecular dynamics simulations to analyze X-ray refinement models for proteins and nucleic acids is also reviewed.
authors.forename: R M
authors.initials: RM
authors.lastname: Levy
mesh_terms: D001704:Biopolymers; D003198:Computer Simulation; D004247:DNA; D046911:Macromolecular Substances; D008954:Models, Biological; D008968:Molecular Conformation; D011506:Proteins; D013057:Spectrum Analysis / Q000379:methods; D014732:Vibration
chemical_list: D001704:Biopolymers; D046911:Macromolecular Substances; D011506:Proteins; D004247:DNA