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1. computer simulation of liquid

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7. Molecular Modelling Principles and Applications

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This book provides a detailed description of the techniques employed in molecular modelling and computational chemistry. The first part of the book covers the two major methods used to describe the interactions within a system (quantum mechanics and molecular mechanics). The second part then deals with techniques that use such energy models, including energy minimisation, molecular dynamics, Monte Carlo simulations and conformational analysis. The author also discusses the use of more advanced modelling techniques such as the calculation of free energies and the simulation of chemical reactions. In addition he considers aspects of both chemoinformatics and bioinformatics and techniques that can be used to design new molecules with specific properties. Many of the topics are treated in considerable depth but the reader is assumed to have but a basic knowledge of the relevant physical and chemical principles.
Most of the theoretical sections are accompanied by simple calculations together with examples drawn from the literature. The book is well illustrated and a colour plate section highlights the impact of computer molecular graphics. The book will prove a valuable text for postgraduate students and professionals and many sections will be useful to final-year undergraduates taking courses in molecular modelling or computational chemistry.


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2. The Art of Molecular Dynamics Simulation

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¡¾×÷Õß¡¿Dennis C Rapaport

¡¾³ö°æÕß¡¿Cambridge University Press

¡¾³ö°æÈÕÆÚ¡¿1995

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     This book describes the extremely powerful technique of molecular dynamics simulation, which involves solving the classical many-body problem in contexts relevant to the study of matter at the atomic level. The method allows the prediction of the static and dynamic properties of substances directly from the underlying interactions between the molecules. Because there is no alternative approach capable of handling such a broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This volume will be of value to advanced students and researchers in physics, chemistry, polymer science and materials science in universities and industrial laboratories.

Contents
Preface

1 Introduction

2 Basic MD approach
soft-disk fluid, methodology, programming, equilibration, sample results.

3 Simulating simple systems
equations of motion, potential functions, interaction computations, integration methods, initial state, efficiency, trajectory sensitivity.

4 Equilibrium properties of simple fluids
thermodynamics, structure, Voronoi polyhedra, clusters.

5 Dynamical properties of simple fluids
transport coefficients, space-time correlation functions.

6 Alternative ensembles
feedback and constraint methods for constant temperature and pressure.

7 Nonequilibrium dynamics
homogeneous and inhomogeneous systems, sheared flow, heat transport.

8 Rigid molecules
dynamics, molecular construction, water, properties, hydrogen bonds.

9 Flexible molecules
polymer chains, properties.

10 Geometrically constrained molecules
solving the constraint problem, internal forces, alkane chains, properties.

11 Other interactions
long-range forces, three-body potentials, dipole fluid, liquid silicon.

12 Step potentials
computational scheme, events, results, generalizations.

13 Time-dependent phenomena
open systems, thermal convection, obstructed flow.

14 Algorithms for supercomputers
MD algorithms for distributed- and vector-processing computers.

15 The future

Appendices
data management, organizing extensive computations, utility functions, list of variables.

Bibliography

Indices
function index, subject index.

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4. Understanding Molecular Simulation From Algorithms to Applications

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ISBN: 0122673700
Title: Understanding Molecular Simulation: From Algorithms to Applications 1996-08
Author: Daan Frenkel, Berend Smit
Publisher: Academic Press
Publication Date: 1996-08
Number Of Pages: 443
Average Amazon Rating: 4.5
Summary:
Computer simulation techniques have become almost essential in the study of the macro-molecular phenomena and phase behavior on the molecular level. As these techniques become increasingly important, it is necessaryto realize that they are useful tools, but are not the goals of research. With this important distinction in mind, Understanding Molecular Simulation describes simulation techniques along with the physics behind the phenomena that these techniques simulate.
Each chapter is comprised of three components: the general theoretical basis, an outline of the necessary computer code, and a few applications which illustrate the use of the technique demonstrated. The chapters also include examples of the typical practical problems that could be solved using each technique.

Key Features
* Gives a unified presentation of computational tools used to study molecular systems in the equilibrium state
* Describes simulation techniques and physics behind the phenomena simulated
* Emphasizes important topics of phase behavior and computer simulation of macro-molecular (polymer-type) substances
* Includes references to the authors home page where additional information from the authors can be found


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