Molecular Dynamics Simulations In Statistical Physics Theory And Applications
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Molecular Dynamics Simulations In Statistical Physics Theory And Applications
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Author : Hiqmet Kamberaj
language : en
Publisher: Springer Nature
Release Date : 2020-03-20
Molecular Dynamics Simulations In Statistical Physics Theory And Applications written by Hiqmet Kamberaj and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-20 with Science categories.
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.
Molecular Dynamics Simulations In Statistical Physics
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Author : Hiqmet Kamberaj
language : en
Publisher:
Release Date : 2020
Molecular Dynamics Simulations In Statistical Physics written by Hiqmet Kamberaj and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020 with Statistical physics categories.
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. .
Statistical Mechanics Theory And Molecular Simulation
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Author : Mark Tuckerman
language : en
Publisher: OUP Oxford
Release Date : 2010-02-11
Statistical Mechanics Theory And Molecular Simulation written by Mark Tuckerman and has been published by OUP Oxford this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-02-11 with Science categories.
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.
Understanding Molecular Simulation
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Author : Daan Frenkel
language : en
Publisher: Elsevier
Release Date : 2001-10-19
Understanding Molecular Simulation written by Daan Frenkel and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2001-10-19 with Science categories.
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.
Free Energy Calculations
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Author : Christophe Chipot
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-01-08
Free Energy Calculations written by Christophe Chipot and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-01-08 with Language Arts & Disciplines categories.
Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.
Computer Simulations In Molecular Biology
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Author : Hiqmet Kamberaj
language : en
Publisher: Springer Nature
Release Date : 2023-07-31
Computer Simulations In Molecular Biology written by Hiqmet Kamberaj and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-07-31 with Science categories.
This book covers a range of topics in quantum mechanics and molecular dynamics simulation, including computational modeling and machine learning approaches. The book also provides a Python GUI and tutorials for simulating molecular biological systems and presents case studies of quantum mechanics simulations for predicting electronic properties. Its pedagogical formatting makes it easy for students to understand and follow and has been praised for providing clear and detailed explanations of complex topics. This book is ideal for graduate students and researchers in theoretical and computational biophysics, physics, chemistry, and materials science, as well as postgraduates in applied mathematics, computer science, and bioinformatics.
Molecular Dynamics Simulation
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Author : J. M. Haile
language : en
Publisher: Wiley-Interscience
Release Date : 1992-06-05
Molecular Dynamics Simulation written by J. M. Haile and has been published by Wiley-Interscience this book supported file pdf, txt, epub, kindle and other format this book has been release on 1992-06-05 with Technology & Engineering categories.
"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
Explorations In Computational Physics
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Author : Devang Patil
language : en
Publisher: Educohack Press
Release Date : 2025-02-20
Explorations In Computational Physics written by Devang Patil and has been published by Educohack Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-02-20 with Science categories.
"Explorations in Computational Physics" delves into the intricate world of computational physics, offering a comprehensive guide from fundamental theories to cutting-edge applications. This book serves as an indispensable companion for both novice learners and seasoned researchers. We cover a diverse array of topics, meticulously unfolding layers of computational techniques and their applications in various branches of physics. From classical mechanics simulations elucidating celestial mechanics to quantum mechanics computations unraveling atomic and subatomic realms, the book navigates through the vast landscape of computational methodologies with clarity and precision. Furthermore, we delve into electromagnetic field simulations, statistical mechanics, and thermodynamics, equipping readers with tools to model complex physical phenomena with accuracy and efficiency. High-performance computing techniques, data analysis, and visualization methodologies are elucidated, empowering readers to harness modern computational resources in their research. With lucid explanations, illustrative examples, and insightful discussions on emerging technologies like quantum computing and artificial intelligence, "Explorations in Computational Physics" fosters a deeper understanding of computational methodologies and their transformative impact on physics research.
Amber 2021
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Author : David A. Case
language : en
Publisher: University of California, San Francisco
Release Date : 2021-06-13
Amber 2021 written by David A. Case and has been published by University of California, San Francisco this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-06-13 with Computers categories.
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools21, a collection of freely available programs mostly under the GPL license, and Amber20, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber20 represents a significant change from the most recent previous version, Amber18. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.
Amber 2023
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Author : David A. Case
language : en
Publisher: University of California, San Francisco
Release Date : 2023-04-30
Amber 2023 written by David A. Case and has been published by University of California, San Francisco this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-04-30 with Computers categories.
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.[1, 2] The term Amber is also used to refer to the empirical force fields that are implemented here.[3, 4] It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools23, a collection of freely available programs mostly under the GPL license, and Amber22, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber22 represents a significant change from the most recent previous version, Amber20. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.