Molecular dynamics overview

Palmer, A.G. Ill (2001) NMR probes of molecular dynamics overview and comparison with other techniques Ann. Rev. Biophys. Biomolec. Struct. 30, 129-155. 

The study of quautum effects associated with nuclear motion is a distinct field of chemistry, known as quantum molecular dynamics. This section gives an overview of the methodology of the field for fiirtlier reading, consult [1, 2, 3, 4 and 5,]. 

To have an overview of the algorithms and basic concepts used to perform molecular dynamics simulations... 

A variety of techniques have been introduced to increase the time step in molecular dynamics simulations in an attempt to surmount the strict time step limits in MD simulations so that long time scale simulations can be routinely undertaken. One such technique is to solve the equations of motion in the internal degree of freedom, so that bond stretching and angle bending can be treated as rigid. This technique is discussed in Chapter 6 of this book. Herein, a brief overview is presented of two approaches, constrained dynamics and multiple time step dynamics. 

IV. MOLECULAR DYNAMICS IN MEMBRANES A. Overview of Dynamic Processes in Membranes... 

This chapter has given an overview of the structure and dynamics of lipid and water molecules in membrane systems, viewed with atomic resolution by molecular dynamics simulations of fully hydrated phospholipid bilayers. The calculations have permitted a detailed picture of the solvation of the lipid polar groups to be developed, and this picture has been used to elucidate the molecular origins of the dipole potential. The solvation structure has been discussed in terms of a somewhat arbitrary, but useful, definition of bound and bulk water molecules. 

In this article we have tried to present a general, although somewhat limited overview of molecular dynamics simulations of gas-surface reactions as they pertain to technologically important processes. In the course of this review we have undoubtedly left out a great deal of very important work. We hope. 

The modeling of carbohydrates is undergoing rapid development. For example, the first comprehensive conformational mappings of disaccharides with flexible residues and the first molecular dynamics studies of carbohydrates have only recently been published. At the same time, interest in carbohydrates has been increasing dramatically, and there is a need for a publication that gently introduces the uninitiated and provides an overview of current research in the area. We feel that Computer Modeling ( Carbohydrate Molecules meets these needs. 

Onufriev, A. Implicit solvent models in molecular dynamics simulations a brief overview. In Annual Reports in Computational Chemistry (eds R.A. Wheeler and D.C. Spellmeyer), Vol. 4, Elsevier, Amsterdam, 2008, pp. 125-37. 

An overview of the approaches that have been taken to linking different theoretical and computational modeling descriptions is also provided in Fig. 2 The first principles (QC) descriptions are based on the Schrodinger equation and the Bom Oppenheimer approximation as realized in most chemical applications by density functional [14] or Hartree-Fock [15] methods. Molecular dynamics (MD) methods [16], based on classical Newtonian me-... 

The method presented in this chapter serves as a link between molecular properties (e.g., cavities and their occupants as measured by diffraction and spectroscopy) and macroscopic properties (e.g., pressure, temperature, and density as measured by pressure guages, thermocouples, etc.) As such Section 5.3 includes a brief overview of molecular simulation [molecular dynamics (MD) and Monte Carlo (MC)] methods which enable calculation of macroscopic properties from microscopic parameters. Chapter 2 indicated some results of such methods for structural properties. In Section 5.3 molecular simulation is shown to predict qualitative trends (and in a few cases quantitative trends) in thermodynamic properties. Quantitative simulation of kinetic phenomena such as nucleation, while tenable in principle, is prevented by the capacity and speed of current computers however, trends may be observed. 

A description of the method of molecular dynamics simulations and its applications to energetic materials research is provided. We present an overview of the development of both reactive and non-reactive interaction potentials used to describe the energetic materials in different phases. Limitations as well as performances of the current models are indicated, including recent advances in reactive model development. Applications of the method to both gas and condensed phases of energetic materials are given to illustrate current capabilities. 

For the past several years we have been developing and applying quantum dynamics (QD) and quantum-classical molecular dynamics (QCMD) methods, which are based on the explicitly time-dependent Schroedinger equation. For an overview of the models and simulation results see e.g.4 and the references cited... 

In the following, an overview of the methodical framework of molecular dynamics (MD) simulations will be given, which - in contrast to MC simulations - also deliver dynamical data including rovibrational spectra. Quality, capability and limitations of the methods will then be illustrated by a number of representative examples. 

Among the numerous theoretical approaches applied to the zeolite reactivity problem, we focus our attention mainly on calculations, which use recently developed ab initio molecular dynamics techniques. After a very brief overview of the main features of this methodology, we discuss some applications taken from the modeling of zeolite chemistry the characterization of the catalytic sites, the protonation of a water molecule and the mechanism of the protolytic reactions of alkanes. 

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