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Numerical Simulation In Molecular Dynamics
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Book Synopsis Numerical Simulation in Molecular Dynamics by : Michael Griebel
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 476 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.
Book Synopsis Numerical Simulation in Molecular Dynamics by : Michael Griebel
Download or read book Numerical Simulation in Molecular Dynamics written by Michael Griebel and published by Springer. This book was released on 2010-11-30 with total page 476 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.
Book Synopsis Numerical Simulation in Molecular Dynamics by : Michael Griebel
Download or read book Numerical Simulation in Molecular Dynamics written by Michael Griebel and published by Springer. This book was released on 2007-08-09 with total page 476 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.
Book Synopsis Molecular Dynamics Simulation by : Giovanni Ciccotti
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
Book Synopsis Understanding Molecular Simulation by : Daan Frenkel
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.
Book Synopsis Molecular Simulation and Industrial Applications by : Keith E. Gubbins
Download or read book Molecular Simulation and Industrial Applications written by Keith E. Gubbins and published by Taylor & Francis. This book was released on 1996 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: First published in 2004. Routledge is an imprint of Taylor & Francis, an informa company.
Book Synopsis Molecular Dynamics by : Ben Leimkuhler
Download or read book Molecular Dynamics written by Ben Leimkuhler and published by Springer. This book was released on 2015-05-18 with total page 443 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method.
Book Synopsis Molecular Dynamics Simulations in Statistical Physics: Theory and Applications by : Hiqmet Kamberaj
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.
Book Synopsis Computer Simulations Of Molecules And Condensed Matter: From Electronic Structures To Molecular Dynamics by : Wang Enge
Download or read book Computer Simulations Of Molecules And Condensed Matter: From Electronic Structures To Molecular Dynamics written by Wang Enge and published by World Scientific. This book was released on 2018-01-17 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a relatively complete introduction to the methods used in computational condensed matter. A wide range of electronic structure theories are introduced, including traditional quantum chemistry methods, density functional theory, many-body perturbation theory, and more. Molecular dynamics simulations are also discussed, with extensions to enhanced sampling and free-energy calculation techniques including umbrella sampling, meta-dynamics, integrated tempering sampling, etc. As a further extension beyond the standard Born-Oppenheimer molecular dynamics, some simulation techniques for the description of quantum nuclear effects are also covered, based on Feynman's path-integral representation of quantum mechanics. The book aims to help beginning graduate students to set up a framework of the concepts they should know before tackling the physical/chemical problems they will face in their research. Contents: Introduction to Computer Simulations of Molecules and Condensed MatterQuantum Chemistry Methods and Density-Functional TheoryPseudopotentials, Full Potential, and Basis SetsMany-Body Green's Function Theory and the GW ApproximationMolecular DynamicsExtension of Molecular Dynamics, Enhanced Sampling and the Free-Energy CalculationsQuantum Nuclear EffectsAppendices: Useful Mathematical RelationsExpansion of a Non-Local FunctionThe Brillouin-Zone IntegrationThe Frequency IntegrationReferencesAcknowledgements Readership: Researchers in computational condensed matter physics. Keywords: Electronic Structures;First-Principle;Molecular Dynamics;Path-IntegralReview: Key Features: Elaboration on a framework of concepts based on the authors' research experiencesIllustrations of methods ranging from electronic structures to molecular dynamicsDetailed explanation of the path-integral method
Book Synopsis Molecular Dynamics Simulations by : Maria Emilova Velinova
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.
Book Synopsis Molecular Simulations by : Saman Alavi
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.
Book Synopsis Supercomputing for Molecular Dynamics Simulations by : Alexander Heinecke
Download or read book Supercomputing for Molecular Dynamics Simulations written by Alexander Heinecke and published by Springer. This book was released on 2015-03-30 with total page 76 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work presents modern implementations of relevant molecular dynamics algorithms using ls1 mardyn, a simulation program for engineering applications. The text focuses strictly on HPC-related aspects, covering implementation on HPC architectures, taking Intel Xeon and Intel Xeon Phi clusters as representatives of current platforms. The work describes distributed and shared-memory parallelization on these platforms, including load balancing, with a particular focus on the efficient implementation of the compute kernels. The text also discusses the software-architecture of the resulting code.
Book Synopsis New Algorithms for Macromolecular Simulation by : Benedict Leimkuhler
Download or read book New Algorithms for Macromolecular Simulation written by Benedict Leimkuhler and published by Springer Science & Business Media. This book was released on 2006-03-22 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.
Book Synopsis Molecular Dynamics Simulations in Statistical Physics by : Hiqmet Kamberaj
Download or read book Molecular Dynamics Simulations in Statistical Physics written by Hiqmet Kamberaj and published by . This book was released on 2020 with total page 470 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. .
Book Synopsis Monte Carlo and Molecular Dynamics Simulations in Polymer Science by : Kurt Binder
Download or read book Monte Carlo and Molecular Dynamics Simulations in Polymer Science written by Kurt Binder and published by Oxford University Press, USA. This book was released on 1995 with total page 602 pages. Available in PDF, EPUB and Kindle. Book excerpt: Talks about various computer simulation techniques used for macromolecular materials. This book describes how to use simulation to explain experimental data and gain insight into structure and dynamic properties of polymeric structures. Explanations are given on how to overcome challenges posed by large size and slow relaxation polymer coils.
Book Synopsis Computer Simulation in Chemical Physics by : M.P. Allen
Download or read book Computer Simulation in Chemical Physics written by M.P. Allen and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer Simulation in Chemical Physics contains the proceedings of a NATO Advanced Study Institute held at CORISA, Alghero, Sardinia, in September 1992. In the five years that have elapsed since the field was last summarized there have been a number of remarkable advances which have significantly expanded the scope of the methods. Good examples are the Car--Parrinello method, which allows the study of materials with itinerant electrons; the Gibbs technique for the direct simulation of liquid--vapor phase equilibria; the transfer of scaling concepts from simulations of spin models to more complex systems; and the development of the configurational--biased Monte-Carlo methods for studying dense polymers. The field has also been stimulated by an enormous increase in available computing power and the provision of new software. All these exciting developments, an more, are discussed in an accessible way here, making the book indispensable reading for graduate students and research scientists in both academic and industrial settings.
