Download or read book Understanding Molecular Simulation written by Daan Frenkel and published by Elsevier. This book was released on 2001-10-19 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on: · Transition path sampling and diffusive barrier crossing to simulaterare events · Dissipative particle dynamic as a course-grained simulation technique · Novel schemes to compute the long-ranged forces · Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations · Multiple-time step algorithms as an alternative for constraints · Defects in solids · The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules · Parallel tempering for glassy Hamiltonians Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.
Download or read book Molecular Simulations written by Saman Alavi and published by John Wiley & Sons. This book was released on 2020-06-29 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides hands-on knowledge enabling students of and researchers in chemistry, biology, and engineering to perform molecular simulations This book introduces the fundamentals of molecular simulations for a broad, practice-oriented audience and presents a thorough overview of the underlying concepts. It covers classical mechanics for many-molecule systems as well as force-field models in classical molecular dynamics; introduces probability concepts and statistical mechanics; and analyzes numerous simulation methods, techniques, and applications. Molecular Simulations: Fundamentals and Practice starts by covering Newton's equations, which form the basis of classical mechanics, then continues on to force-field methods for modelling potential energy surfaces. It gives an account of probability concepts before subsequently introducing readers to statistical and quantum mechanics. In addition to Monte-Carlo methods, which are based on random sampling, the core of the book covers molecular dynamics simulations in detail and shows how to derive critical physical parameters. It finishes by presenting advanced techniques, and gives invaluable advice on how to set up simulations for a diverse range of applications. -Addresses the current need of students of and researchers in chemistry, biology, and engineering to understand and perform their own molecular simulations -Covers the nitty-gritty ? from Newton's equations and classical mechanics over force-field methods, potential energy surfaces, and probability concepts to statistical and quantum mechanics -Introduces physical, chemical, and mathematical background knowledge in direct relation with simulation practice -Highlights deterministic approaches and random sampling (eg: molecular dynamics versus Monte-Carlo methods) -Contains advanced techniques and practical advice for setting up different simulations to prepare readers entering this exciting field Molecular Simulations: Fundamentals and Practice is an excellent book benefitting chemist, biologists, engineers as well as materials scientists and those involved in biotechnology.
Download or read book A Practical Introduction to the Simulation of Molecular Systems written by Martin J. Field and published by Cambridge University Press. This book was released on 2007-07-19 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.
Download or read book Numerical Simulation in Molecular Dynamics written by Michael Griebel and published by Springer Science & Business Media. This book was released on 2007-08-16 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book details the necessary numerical methods, the theoretical background and foundations and the techniques involved in creating computer particle models, including linked-cell method, SPME-method, tree codes, amd multipol technique. It illustrates modeling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. The text offers step-by-step explanations of numerical simulation, providing illustrative code examples. With the description of the algorithms and the presentation of the results of various simulations from fields such as material science, nanotechnology, biochemistry and astrophysics, the reader of this book will learn how to write programs capable of running successful experiments for molecular dynamics.
Download or read book Statistical Mechanics Theory and Molecular Simulation written by Mark Tuckerman and published by OUP Oxford. This book was released on 2010-02-11 with total page 720 pages. Available in PDF, EPUB and Kindle. Book excerpt: Complex systems that bridge the traditional disciplines of physics, chemistry, biology, and materials science can be studied at an unprecedented level of detail using increasingly sophisticated theoretical methodology and high-speed computers. The aim of this book is to prepare burgeoning users and developers to become active participants in this exciting and rapidly advancing research area by uniting for the first time, in one monograph, the basic concepts of equilibrium and time-dependent statistical mechanics with the modern techniques used to solve the complex problems that arise in real-world applications. The book contains a detailed review of classical and quantum mechanics, in-depth discussions of the most commonly used ensembles simultaneously with modern computational techniques such as molecular dynamics and Monte Carlo, and important topics including free-energy calculations, linear-response theory, harmonic baths and the generalized Langevin equation, critical phenomena, and advanced conformational sampling methods. Burgeoning users and developers are thus provided firm grounding to become active participants in this exciting and rapidly advancing research area, while experienced practitioners will find the book to be a useful reference tool for the field.
Download or read book Industrial Applications of Molecular Simulations written by Marc Meunier and published by CRC Press. This book was released on 2016-04-19 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of quantum and molecular simulations has experienced strong growth since the time of the early software packages. A recent study, showed a large increase in the number of people publishing papers based on ab initio methods from about 3,000 in 1991 to roughly 20,000 in 2009, with particularly strong growth in East Asia. Looking to the futu
Download or read book The Art of Molecular Dynamics Simulation written by D. C. Rapaport and published by Cambridge University Press. This book was released on 2004-04 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.
Download or read book Molecular Dynamics Simulation written by Giovanni Ciccotti and published by MDPI. This book was released on 2018-10-08 with total page 627 pages. Available in PDF, EPUB and Kindle. Book excerpt: Printed Edition of the Special Issue Published in Entropy
Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text
Download or read book Molecular Dynamics Simulations in Statistical Physics Theory and Applications written by Hiqmet Kamberaj and published by Springer Nature. This book was released on 2020-03-20 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents computer simulations using molecular dynamics techniques in statistical physics, with a focus on macromolecular systems. The numerical methods are introduced in the form of computer algorithms and can be implemented in computers using any desired computer programming language, such as Fortran 90, C/C++, and others. The book also explains how some of these numerical methods and their algorithms can be implemented in the existing computer programming software of macromolecular systems, such as the CHARMM program. In addition, it examines a number of advanced concepts of computer simulation techniques used in statistical physics as well as biological and physical systems. Discussing the molecular dynamics approach in detail to enhance readers understanding of the use of this method in statistical physics problems, it also describes the equations of motion in various statistical ensembles to mimic real-world experimental conditions. Intended for graduate students and research scientists working in the field of theoretical and computational biophysics, physics and chemistry, the book can also be used by postgraduate students of other disciplines, such as applied mathematics, computer sciences, and bioinformatics. Further, offering insights into fundamental theory, it as a valuable resource for expert practitioners and programmers and those new to the field.
Download or read book Ab Initio Molecular Dynamics written by Dominik Marx and published by Cambridge University Press. This book was released on 2009-04-30 with total page 503 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.
Download or read book Molecular Dynamics Simulation written by Kun Zhou and published by Academic Press. This book was released on 2022-02-10 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Dynamic Simulation: Fundamentals and Applications explains the basic principles of MD simulation and explores its recent developments and roles in advanced modeling approaches. The implementation of MD simulation and its application to various aspects of materials science and engineering including mechanical, thermal, mass transportation, and physical/chemical reaction problems are illustrated. Innovative modeling techniques that apply MD to explore the mechanics of typical nanomaterials and nanostructures and to characterize crystalline, amorphous, and liquid systems are also presented. The rich research experience of the authors in MD simulation will ensure that the readers are provided with both an in-depth understanding of MD simulation and clear technical guidance. Provides a comprehensive overview of the underlying theories of molecular dynamics (MD) simulation Presents application-based examples pertaining to a broad range of mechanical, thermal, and mass transport problems Explores innovative modeling techniques for simulating typical nanomaterials and nanostructures and for characterizing crystalline, amorphous, and liquid systems
Download or read book Computer Simulation of Liquids written by M. P. Allen and published by Oxford University Press. This book was released on 1989 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer simulation is an essential tool in studying the chemistry and physics of liquids. Simulations allow us to develop models and to test them against experimental data. This book is an introduction and practical guide to the molecular dynamics and Monte Carlo methods.
Download or read book Molecular Dynamics Simulation written by J. M. Haile and published by Wiley-Interscience. This book was released on 1997-03-14 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Provides a lot of reading pleasure and many new insights." -Journal of Molecular Structure "This is the most entertaining, stimulating and useful book which can be thoroughly recommended to anyone with an interest in computer simulation." -Contemporary Physics "A very useful introduction . . . more interesting to read than the often dry equation-based texts." -Journal of the American Chemical Society Written especially for the novice, Molecular Dynamics Simulation demonstrates how molecular dynamics simulations work and how to perform them, focusing on how to devise a model for specific molecules and then how to simulate their movements using a computer. This book provides a collection of methods that until now have been scattered through the literature of the last 25 years. It reviews elements of sampling theory and discusses how modern notions of chaos and nonlinear dynamics explain the workings of molecular dynamics. Stresses easy-to-use molecules * Provides sample calculations and figures * Includes four complete FORTRAN codes
Download or read book Molecular Dynamics Simulations written by Maria Emilova Velinova and published by Delve Publishing. This book was released on 2017-11 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular dynamics method is a numerical statistical mechanics technique for integration of the equations of motion for a many-particle system. The particle-particle interactions and the energy are quantified using the potentials and parameter sets of molecular-mechanics force fields. The resulting trajectories can then be used to evaluate various time-dependent structural, transport and thermodynamic properties of the system.In this book, Molecular Dynamics Simulations, it is presented the state-of-the-art in the field, from both a methodological and application perspective. The book begins with a brief introduction of the molecular dynamics simulations formalism. Important definitions and terminology, used later in the book, have been explained. For example, terms as integrators, SHAKE (or LINCS) algorithm, periodical boundary conditions, cutoff, ensemble and many others are considered in the introduction.Molecular dynamics simulations are suitable for describing of systems with extensive number of degrees of freedom such as the biologically relevant targets. The next parts contain collection of articles, which illustrate the computer experiments using molecular dynamics simulations in the studies of synthetic and biological macromolecules. The topics covered of this book include: molecular dynamics simulations of biological membranes, proteins, polymers, peptides, and nanotubes.
Download or read book Computational Molecular Dynamics Challenges Methods Ideas written by Peter Deuflhard and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.
Download or read book Biomolecular Simulations written by Massimiliano Bonomi and published by Humana. This book was released on 2020-08-14 with total page 581 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.
