Book: Understanding Molecular Simulation


Daan Frenkel and Berend Smit


Understanding Molecular Simulation, Second Edition: From Algorithms to Applications (Computational Science Series, Vol 1)

This is a textbook on molecular simulations Daan Frenkel and I wrote in 1996 the first edition and 2002 the second edition. Daan and I were unhappy with the notion that a molecular simulation program is nothing more than a set of recipes. The preface starts “This is not a computer simulation cookbook” Our aim is to explain the physics behind the “recipes” of molecular simulations. The idea is that molecular simulations have a solid foundation in Statistical Thermodynamics and that we need this understanding to fully grasp what an algorithm is doing. This understand is essential to know the limitations of an algorithms and often gives us the hints how to improve it. 

It is pleasure to see that our book is adopted by many groups as a reference in the field. We hope that we can find some time to write a third edition. Our move to Cambride and Berkeley have delayed these plans a little. 

For Daan and me it always a pleasure to teach the Molecular Simulation course each winter in Amsterdam. A traditon we hope to continue for many years. In this context I would like to react on one review about our book on Amazon

” … The authors even offer scientific workshops based on their book (and probably make a lot of money with that). One can only hope that those are better than the coding examples of the exercises. Therefore only 2 stars.  …”  

I do not want to argue about the coding examples, but I would like to comment on “make a lot of money with that.” This remark does hurt, since nor Daan nor I have ever received ANY money for giving this course. This is not the way our community works! In fact, Daan and I with our colleagues in Amsterdam have spent quite some efforts in writting several proposals to the European Committe and to the European Science Foundation so that PhD students from all over the world could attend this course free of charge and that even (part) of their travel and hotel costs were covered by these grants. Unfortunately, these grants have expired and we can now only contribute to the hotel costs. 

Why are we doing this free of charge? And even travel from Cambridge and Berkeley to Amsterdam to teach part of this course. This may sound impressive, but it is in fact a small effort compared to the efforts it costs for someone from the University of Yaounde in Cameron to attend our course. Why we do this? Look at this publication that came out of this course! Or, while working on the third edition there is nothing better than having to discuss an article of which the authors have followed the course in an early stage of their career.