Understanding Molecular Simulation,
Edition 3 From Algorithms to Applications
By Daan Frenkel and Berend Smit

Publication Date: 18 Jul 2023

Understanding Molecular Simulation explains molecular simulation from a chemical-physics and statistical-mechanics perspective. It highlights how physical concepts are used to develop better algorithms and expand the range of applicability of simulations. Understanding Molecular Simulation is equally relevant for those who develop new code and those who use existing packages. Both groups are continuously confronted with the question of which computational technique best suits a given application. Understanding Molecular Simulation provides readers with the foundational knowledge they need to learn about, select and apply the most appropriate of these tools to their own work. The implementation of simulation methods is illustrated in pseudocodes, and their practical use is shown via case studies presented throughout the text.

Since the second edition’s publication, the simulation world has expanded significantly: existing techniques have continued to develop, and new ones have emerged, opening up novel application areas. This new edition aims to describe these new developments without becoming exhaustive; examples are included that highlight current uses, and several new examples have been added to illustrate recent applications. Examples, case studies, questions, and downloadable algorithms are also included to support learning. No prior knowledge of computer simulation is assumed.

Key Features

  • Fully updated guide to both the current state and latest developments in the field of molecular simulation, including added and expanded information on such topics as molecular dynamics and statistical assessment of simulation results
  • Gives a rounded overview by showing fundamental background information in practice via new examples in a range of key fields
  • Provides online access to new data, algorithms and tutorial slides to support and encourage practice and learning
About the author
By Daan Frenkel, FOM Institute for Atomic and Molecular Physics, The Netherlands and Berend Smit, Professor at the Department of Chemical Engineering of the Faculty of Science, University of Amsterdam
Table of Contents

1. Introduction

Part I: Basics

2. Thermodynamics and Statistical Mechanics

3. Monte Carlo Simulations

4. Molecular Dynamics Simulations

5. Computer Experiments

Part II: Ensembles

6. Monte Carlo Simulations in Various Ensembles

7. Molecular Dynamics in Various Ensembles

Part III: Free -Energy Calculations

8. Free Energy Calculations

9. Free Energies of Solids

10. Free Energy of Chain Molecules

Part IV: Advanced Techniques

11. Long-Ranged Interactions

12. Configurational Bias Monte Carlo

13. Accelerating Monte Carlo Sampling

14. Time-Scale-separation Problems in MD

15. Rare Events

16. Mesoscopic Fluid Models

Part V: Appendices

A: Lagrangian and Hamiltonian

B: Non-Hamiltonian Dynamics

C: Non-equilibrium Thermodynamics

D: Smoothed Dissipative Particle Dynamics

E: Committor for 1-D diffusive barrier crossing

F: Linear Response Theory: examples

G: Statistical Errors

H: Integration Schemes

I: Saving CPU Time

J: Reference States

K: Statistical Mechanics of the Gibbs "Ensemble"

L: Overlapping Distribution for Polymers

M: Some General Purpose Algorithms

Book details
ISBN: 9780323902922
Page Count: 679
Retail Price : £91.95

Graduate students in computational chemistry, physics and materials science departments studying molecular simulation techniques, scientists in the fields of polymers, materials science, and applied physics