Molecular Modeling and Simulation: An Interdisciplinary Guide (Interdisciplinary Applied Mathematics) Review

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(More customer reviews)I am a computer science professional with around 10 years of experience. I got this book to get my self started with molecular simulation for real world practical applications. although this book is titled molecular modeling and simulation, it starts with protein folding. I found reading this book extremely painful due to few reasons.
1) Author just states what she knows, but does not seem to explain them. Rather than starting from a simple scale and gradually building up, the information is presented in ad-hoc manner. The manner in which this information is presented in not in tutorial style and not even in a style that can be used for reference.
2) lots of unnecessary information - author seem to write about every thing that comes to her mind. For some one who has been in this field for long, this is acceptable, but for some one who is just starting like me, this is bit of an overload. Reader might not know what to read and what to skip.
3) The chapters are cyclic dependent. (there are references to later chapters from earlier chapters, but to read later chapters you first need to read earlier chapters). Author herself ask the reader to read some early chapters after reading later ones. This is very confusing at least for me.
For me, this book was a total waste. I am thinking of re-starting with "Molecular Modelling: Principles and Applications" by A.R Leach. Although this book is bit old, it should be enough for me to get started.


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Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

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Molecular Modeling and Simulation Review

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(More customer reviews)... not only to molecular modeling, but to some of the subtleties of DNA and protein behavior and geometry, too.
This book's focus is generally on interactions with large molecules, DNA and proteins, although it does discuss small molecules (drugs, a few dozen to a few hundred atoms) too. That means that it skips most of the quantum mechanical modeling of more advanced computational chemistry texts.
Nothing is lost, because Schlick covers her chosen topic (molecular modeling and dynamics) in such detail. She starts with a very clear discussion of the structure of large biomolecules, with emphasis on the features that need quantitative description for modeling. That covers protein structure at ever level. It also covers DNA/RNA structure in the best detail I've ever seen. The double-helix is the just the starting point. There are alternative helix forms, non-standard binding between nucleotides, and asymmetries caused by nucleotide composition. The next chapters describe the geometric model and, briefly, the forces acting between atoms.
The second half of the book gets down to the nuts and bolts of modeling. This includes numerical techniques, minimization, sampling and Monte Carlo techniques, and the start of dynamics. Schlick attacks some of the nasty points of the calculations, such as modeling of forces that act on very different time scales. As with the simpler material, the development is clear, descriptive, and free of pointless theorems. The meticulous reader should come away able to implement most or all of the techniques described. The level of presentation is consistent and approachable. I think freshman physics should be enough preparation for most students to get most of the value out of the discussion.
The book is written with clarity as a top priority. The glossary is in the front, making sure that the reader knows it's a first-class part of the text. After that, every chapter starts with a list of the mathematical symbols and variables used and a one-line description of each. These are small things, but they increase the book's readability immensely. The illustrations are generally informative enough. On the whole, though, they don't seem quite up to the level of the textual and mathematical presentations.
I needed a crash course in the mathematical techniques used for describing molecular structure and behavior. I should have read this book first - its clarity and thoroughness would have saved me a lot of time. After this one, I can now go back and reread the more complex texts with more hops of understanding. Do yourself a favor and read this one first.

Click Here to see more reviews about: Molecular Modeling and Simulation

Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

Click here for more information about Molecular Modeling and Simulation

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