Modified Potential Energy Functions for Constrained Molecular Dynamics
Author: Sebastian Reich
Publisher:
Published: 1997
Total Pages: 16
ISBN-13:
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Numerical Simulation in Molecular Dynamics
Author: Michael Griebel
Publisher: Springer Science & Business Media
Published: 2007-08-16
Total Pages: 472
ISBN-13: 3540680950
DOWNLOAD EBOOKThis 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
Author: Ben Leimkuhler
Publisher: Springer
Published: 2015-05-18
Total Pages: 461
ISBN-13: 3319163752
DOWNLOAD EBOOKThis 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.
Free Energy Calculations
Author: Christophe Chipot
Publisher: Springer Science & Business Media
Published: 2007-01-08
Total Pages: 528
ISBN-13: 3540384472
DOWNLOAD EBOOKFree 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.
Polarizable Potential Energy Functions for Molecular Simulation
Author: Harry Stern
Publisher:
Published: 2001
Total Pages: 368
ISBN-13:
DOWNLOAD EBOOKProteins: Form and Function
Author: R.A. Bradshaw
Publisher: Elsevier
Published: 2012-12-02
Total Pages: 279
ISBN-13: 0080983936
DOWNLOAD EBOOKProteins are of fundamental importance in all aspects of cell structure and function. The study of proteins has always formed a central part of biochemistry, and recent expansion in the range and sophistication of available techniques has provided a wealth of new information. The current methods and approaches used to gain a better understanding of the structure of proteins are described within this book, while other articles focus on the role of proteins within the cell. Most of the articles have appeared previously in the monthly review journal Trends in Biochemical Sciences (TIBS), with a few commissioned specifically for this collection, which should appeal to students, lecturers and researchers interested in the form and function of proteins.
Potential Energy Surfaces and Dynamics Calculations
Author: Donald Truhlar
Publisher: Springer
Published: 1981-08
Total Pages: 878
ISBN-13:
DOWNLOAD EBOOKThe present volume is concerned with two of the central questions of chemical dynamics. What do we know about the energies of interaction of atoms and molecules with each other and with solid surfaces? How can such interaction energies be used to understand and make quantitative predictions about dynamical processes like scattering, energy transfer, and chemical reactions? It is becoming clearly recognized that the computer is leading to rapid progress in answering these questions. The computer allows probing dynamical mechanisms in fine detail and often allows us to answer questions that cannot be addressed with current experimental techniques. As we enter the 1980's, not only are more powerful and faster computers being used, but techniques and methods have been honed to a state where exciting and reliable data are being generated on a variety of systems at an unprecedented pace. The present volume presents a collection of work that illustrates the capabilities and some of the successes of this kind of computer-assisted research. In a 1978 Chemical Society Report, Frey and Walsh pointed out that "it is extremely doubtful if a calculated energy of activation for any unimolecular decomposition can replace an experimental deter mination. " However they also recorded that they "believe[d] that some of the elaborate calculations being performed at present do suggest that we may be approaching a time when a choice between reaction mechanisms will be helped by such [computational] work.
Nonequilibrium Molecular Dynamics
Author: Billy D. Todd
Publisher: Cambridge University Press
Published: 2017-03-10
Total Pages: 371
ISBN-13: 0521190096
DOWNLOAD EBOOKThis coherent collection of theory, algorithms, and illustrative results presents the field of nonequilibrium molecular dynamics in detail.
Understanding Molecular Simulation
Author: Daan Frenkel
Publisher: Elsevier
Published: 2001-10-19
Total Pages: 661
ISBN-13: 0080519989
DOWNLOAD EBOOKUnderstanding 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.
Multiscale Computational Methods in Chemistry and Physics
Author: Achi Brandt
Publisher:
Published: 2001
Total Pages: 384
ISBN-13:
DOWNLOAD EBOOKThis book brings together interdisciplinary contributions ranging from applied mathematics, theoretical physics, quantum chemistry and molecular biology, all addressing various facets of the problem to connect the many different scales that one has to deal with in the computer simulation of many systems of interest in chemistry (e.g. polymeric materials, biological molecules, clusters, surface and interface structure). Particular emphasis is on the "multigrid technique" and its applications, ranging from electronic structure calculations to the statistical mechanics of polymers.
