Understanding Molecular Simulation: From Algorithms to Applications (Google eBook)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 coursegrained simulation technique · Novel schemes to compute the longranged forces · Hamiltonian and nonHamiltonian dynamics in the context constanttemperature and constantpressure molecular dynamics simulations · Multipletime step algorithms as an alternative for constraints · Defects in solids · The prunedenriched Rosenbluth sampling, recoilgrowth, 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. 
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Review: Understanding Molecular Simulation: From Algorithms to Applications
User Review  Andrey Kirilchyuk  GoodreadsIt is a comprehensive guide on molecular dynamics and Monte Carlo simulations. This book is oriented more on physicists and material scientists than chemists. Despite of difficult maths, the concepts ... Read full review
Review: Understanding Molecular Simulation: From Algorithms to Applications
User Review  Andrey Kirilchyuk  GoodreadsIt is a comprehensive guide on molecular dynamics and Monte Carlo simulations. This book is oriented more on physicists and material scientists than chemists. Despite of difficult maths, the concepts ... Read full review
Contents
1  
7  
Ensembles  109 
Free Energies and Phase Equilibria  165 
Advanced Techniques  289 
Appendices  479 
589  
619  
628  
Common terms and phrases
¹ ½ ½¼ ¼µ acc´Ó Òµ acceptance rule Æ ½ algorithm atoms Boltzmann bond calculation canonical ensemble CBMC center of mass chemical potential coefficient coexistence computer simulation configuration conformation consider constant constraints coordinates crystal denote density derive detailed balance distribution enddo ensemble simulation equations of motion equilibrium Ewald summation example Figure free energy Gibbs ensemble given grandcanonical Hamiltonian hard spheres Hence ideal gas integration interactions intermolecular Ìµ Lagrangian lattice LennardJones fluid liquid method Molecular Dynamics Molecular Dynamics simulations monomer Monte Carlo method Monte Carlo scheme Monte Carlo simulations Nos´eHoover number of particles Øµ parallel tempering partition function phase space Phys polymer potential energy pressure probability random Rosenbluth factor sampling segment statistical step subroutine technique temperature thermodynamic tion total energy total number trajectory trial move trial orientations trial position velocity Verlet algorithm Verlet list