Numerical Simulation In Molecular Dynamics

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Numerical Simulation in Molecular Dynamics

Michael Griebel,Stephan Knapek,Gerhard Zumbusch
Numerical Simulation in Molecular Dynamics Book PDF

Author : Michael Griebel,Stephan Knapek,Gerhard Zumbusch
Publisher : Springer Science & Business Media
Page : 472 pages
File Size : 49,9 Mb
Release : 2007-08-16
Category : Science
ISBN : 9783540680956

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Numerical Simulation in Molecular Dynamics by Michael Griebel,Stephan Knapek,Gerhard Zumbusch Pdf

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.

Molecular Dynamics Simulation

Giovanni Ciccotti,Mauro Ferrario,Christof Schuette
Molecular Dynamics Simulation Book PDF

Author : Giovanni Ciccotti,Mauro Ferrario,Christof Schuette
Publisher : MDPI
Page : 627 pages
File Size : 55,8 Mb
Release : 2018-10-08
Category : Electronic book
ISBN : 9783906980652

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Molecular Dynamics Simulation by Giovanni Ciccotti,Mauro Ferrario,Christof Schuette Pdf

Printed Edition of the Special Issue Published in Entropy

Molecular Dynamics Simulations in Statistical Physics: Theory and Applications

Hiqmet Kamberaj
Molecular Dynamics Simulations in Statistical Physics Theory and Applications Book PDF

Author : Hiqmet Kamberaj
Publisher : Springer Nature
Page : 463 pages
File Size : 51,5 Mb
Release : 2020-03-20
Category : Science
ISBN : 9783030357023

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Molecular Dynamics Simulations in Statistical Physics: Theory and Applications by Hiqmet Kamberaj Pdf

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.

The Art of Molecular Dynamics Simulation

D. C. Rapaport
The Art of Molecular Dynamics Simulation Book PDF

Author : D. C. Rapaport
Publisher : Cambridge University Press
Page : 568 pages
File Size : 43,7 Mb
Release : 2004-04
Category : Science
ISBN : 0521825687

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The Art of Molecular Dynamics Simulation by D. C. Rapaport Pdf

First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.

Computer Simulations Of Molecules And Condensed Matter: From Electronic Structures To Molecular Dynamics

Wang Enge,Li Xin-zheng
Computer Simulations Of Molecules And Condensed Matter From Electronic Structures To Molecular Dynamics Book PDF

Author : Wang Enge,Li Xin-zheng
Publisher : World Scientific
Page : 280 pages
File Size : 40,7 Mb
Release : 2018-01-17
Category : Science
ISBN : 9789813230460

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Computer Simulations Of Molecules And Condensed Matter: From Electronic Structures To Molecular Dynamics by Wang Enge,Li Xin-zheng Pdf

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

Molecular Simulation and Industrial Applications

Keith E. Gubbins,Nick Quirke
Molecular Simulation and Industrial Applications Book PDF

Author : Keith E. Gubbins,Nick Quirke
Publisher : Taylor & Francis
Page : 568 pages
File Size : 53,8 Mb
Release : 1996
Category : Molecules
ISBN : 9056990055

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Molecular Simulation and Industrial Applications by Keith E. Gubbins,Nick Quirke Pdf

First published in 2004. Routledge is an imprint of Taylor & Francis, an informa company.

Understanding Molecular Simulation

Daan Frenkel,Berend Smit
Understanding Molecular Simulation Book PDF

Author : Daan Frenkel,Berend Smit
Publisher : Elsevier
Page : 664 pages
File Size : 45,9 Mb
Release : 2001-10-19
Category : Science
ISBN : 0080519989

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Understanding Molecular Simulation by Daan Frenkel,Berend Smit Pdf

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.

Molecular Dynamics

Ben Leimkuhler,Charles Matthews
Molecular Dynamics Book PDF

Author : Ben Leimkuhler,Charles Matthews
Publisher : Springer
Page : 443 pages
File Size : 50,8 Mb
Release : 2015-05-18
Category : Mathematics
ISBN : 9783319163758

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Molecular Dynamics by Ben Leimkuhler,Charles Matthews Pdf

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.

Computer Simulation in Chemical Physics

M.P. Allen,D.J. Tildesley
Computer Simulation in Chemical Physics Book PDF

Author : M.P. Allen,D.J. Tildesley
Publisher : Springer Science & Business Media
Page : 522 pages
File Size : 44,9 Mb
Release : 2012-12-06
Category : Science
ISBN : 9789401116794

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Computer Simulation in Chemical Physics by M.P. Allen,D.J. Tildesley Pdf

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.

Molecular Simulations

Saman Alavi
Molecular Simulations Book PDF

Author : Saman Alavi
Publisher : John Wiley & Sons
Page : 342 pages
File Size : 53,8 Mb
Release : 2020-06-29
Category : Technology & Engineering
ISBN : 9783527341054

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Molecular Simulations by Saman Alavi Pdf

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.

Molecular Dynamics Simulations in Statistical Physics

Hiqmet Kamberaj
Molecular Dynamics Simulations in Statistical Physics Book PDF

Author : Hiqmet Kamberaj
Publisher : Unknown
Page : 470 pages
File Size : 52,9 Mb
Release : 2020
Category : Statistical physics
ISBN : 3030357031

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Molecular Dynamics Simulations in Statistical Physics by Hiqmet Kamberaj Pdf

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. .

Computational Chemistry. Computer Simulation Techniques

Edward Timoshenko
Computational Chemistry Computer Simulation Techniques Book PDF

Author : Edward Timoshenko
Publisher : Edward Timoshenko
Page : 32 pages
File Size : 48,7 Mb
Release : 2021-05-06
Category : Computers
ISBN : 9798749716511

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Computational Chemistry. Computer Simulation Techniques by Edward Timoshenko Pdf

We describe the important role of the in-silico methods in modern Chemistry and Physics of complex systems and overview the major techniques. The Born-Oppenheimer approximation for electronic configurations is introduced. Classical treatment of the motion of nuclei is then considered. Potential energy surfaces, force fields, geometry optimization and energy minimisation methods are discussed. The Newton’s equations of motion and their numerical integration methods are presented with the Euler and Verlet algorithms. Calculation of various observable averages is considered in Molecular Dynamics techniques in the NVE, NVT and NPT ensembles. Brownian stochastic Dynamics and the use of random numbers generators are introduced. Equilibrium simulations based on the Monte Carlo importance sampling methods and the Metropolis algorithm are discussed. The variational approach for the Schrödinger equation and various modern Quantum Chemistry methods for the electronic configurations of atomic and molecular systems are reviewed.

Numerical Modelling and Simulation of Metal Processing

Christof Sommitsch
Numerical Modelling and Simulation of Metal Processing Book PDF

Author : Christof Sommitsch
Publisher : MDPI
Page : 374 pages
File Size : 47,7 Mb
Release : 2021-08-16
Category : Technology & Engineering
ISBN : 9783036510804

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Numerical Modelling and Simulation of Metal Processing by Christof Sommitsch Pdf

This book deals with metal processing and its numerical modelling and simulation. In total, 21 papers from different distinguished authors have been compiled in this area. Various processes are addressed, including solidification, TIG welding, additive manufacturing, hot and cold rolling, deep drawing, pipe deformation, and galvanizing. Material models are developed at different length scales from atomistic simulation to finite element analysis in order to describe the evolution and behavior of materials during thermal and thermomechanical treatment. Materials under consideration are carbon, Q&T, DP, and stainless steels; ductile iron; and aluminum, nickel-based, and titanium alloys. The developed models and simulations shall help to predict structure evolution, damage, and service behavior of advanced materials.

Molecular Dynamics

Ben Leimkuhler,Charles Matthews
Molecular Dynamics Book PDF

Author : Ben Leimkuhler,Charles Matthews
Publisher : Springer
Page : 0 pages
File Size : 45,8 Mb
Release : 2016-10-09
Category : Mathematics
ISBN : 3319353241

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Molecular Dynamics by Ben Leimkuhler,Charles Matthews Pdf

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.

Molecular Simulation of Fluids

Richard J. Sadus
Molecular Simulation of Fluids Book PDF

Author : Richard J. Sadus
Publisher : Elsevier
Page : 617 pages
File Size : 45,9 Mb
Release : 2023-09-16
Category : Science
ISBN : 9780323910552

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Molecular Simulation of Fluids by Richard J. Sadus Pdf

Molecular simulation allows researchers unique insight into the structures and interactions at play in fluids. Since publication of the first edition of Molecular Simulation of Fluids, novel developments in theory, algorithms and computer hardware have generated enormous growth in simulation capabilities. This 2nd edition has been fully updated and expanded to highlight this recent progress, encompassing both Monte Carlo and molecular dynamic techniques, and providing details of theory, algorithms and both serial and parallel implementations. Beginning with a clear introduction and review of theoretical foundations, the book goes on to explore intermolecular potentials before discussing the calculation of molecular interactions in more detail. Monte Carlo simulation and integrators for molecular dynamics are then discussed further, followed by non-equilibrium molecular dynamics and molecular simulation of ensembles and phase equilibria. The use of object-orientation is examined in detail, with working examples coded in C++. Finally, practical parallel simulation algorithms are discussed using both MPI and GPUs, with the latter coded in CUDA. Drawing on the extensive experience of its expert author, Molecular Simulation of Fluids: Theory, Algorithms, Object-Orientation, and Parallel Computing 2nd Edition is a practical, accessible guide to this complex topic for all those currently using, or interested in using, molecular simulation to study fluids. Fully updated and revised to reflect advances in the field, including new chapters on intermolecular potentials and parallel algorithms Covers the application of both MPI and GPU programming to molecular simulation Covers a wide range of simulation topics using both Monte Carlo and molecular dynamics approaches Provides access to downloadable simulation code, including GPU code using CUDA, to encourage practice and support learning