Can anybody recommend a statistical mechanics book that:
1) is suited for self-teaching in an undergrad level
2) includes solved problems
3) includes the math needed for each topic
What I have in mind is something similar to what "Quantum Chemistry" by Ira Levine does to QM: each of the chapters includes an intro explaining all the math you'll need for the chapter subject, considering the reader has only a good calculus background. I'm looking for something similar for statistical mechanics, aimed at those interested in molecular dynamics.
Hello. I would suggest the book "Thermodynamics and Statistical Mechanics", by Walter Greiner, Ludwig Neise and Horst Stoecker. It has a very good level, with detailed explanations and worked examples.
I also like the book by Mark Tuckerman, already oriented to some molecular dynamics simulations, "Statistical mechanics: theory and molecular simulation". It is more comprehensive than Greiner, but a bit more formal and with less examples thoroughly worked out.
Look at "Concepts in Thermal Physics" by Stephen J. Blundell, and Katherine M. Blundell. Its a nice book. It provides a modern introduction to the main principles that are foundational to thermal physics, thermodynamics and statistical mechanics. Each chapter concludes with detailed exercises. Explains the concepts clearly and good number of worked examples were also presented. It even covers Ising model and Monte Carlo methods. Enjoy..!!
I think this book meets all your requirements: http://books.google.com.br/books?id=12DKsFtFTgYC&dq=greiner+statistical+mechanics&hl=pt-BR&sa=X&ei=CU2OU_CrG6ngsASO4YIw&ved=0CCkQ6AEwAA
Try "Fundamentals of Statistical and Thermal Physics" by Federic Reiff. Published long ago by McGraw-Hill
You may want two books, one on statistical mechanics, and one on molecular dynamics calculations. Having written a stat mech book myself, I am prejudiced, but for an introduction to computer simulations you might find Gould and Tobachnik to be of value.
It's not a book, but I have parked my own StatPhys tutorial for second-year students here:
http://homepage.univie.ac.at/franz.vesely/sp_english/sp/sp.html
If you find anything useful in it, feel free to use it.
My suggestion is, Ch. Kittel, Thermal Physics.
http://www.amazon.com/Thermal-Physics-Edition-Charles-Kittel/dp/0716710889
The book "Statistical Mechanics" by Donald A.McQuarrie is very interesting.
There are two Tolman books. The large one (now from Dover) is stuffed with a huge middle section on the newly discovered science of quantum mechanics. The small one is much more plainly written. My won "Elementary Lectures in Statistical Mechanics" Is Stat Mech *only*, no thermo and the like. I try to cover all the math first.
What are you trying to simulate?
There is software available that may help, e.g., GROMACS. As a practical matter you might want to be careful to include electrostatics involving the dielectric constant difference between water and the protein core. See my paper with Sushkin N. Sushkin and G. D. J. Phillies, Charged Dielectric Spheres in Electrolyte Solutions: Induced Dipoles and Counterion Exclusion Effects", Journal of Chemical Physics,103, 4600-4612 (1995)
Induced dipoles are *not* a small effect.
Yes, actually I am using NAMD already - it's just that I don't want to be using such packages as black boxes. My background is in crystallography (I've worked some time with powder diffraction/high resolution XRD then moved to protein crystallography) and I made as many physics courses I could - sadly, stat mech was not one of them. Thanks a lot for the reference, I'll get it now.
Some software packages are at least open source. Having said that, there is also an issue as to which surface groups are charged. There is a series of 1985 papers by F (iirc, it's been 30 years) Gurd and collaborators on calculating which protein groups are charged and by how much as you adjust the pH. Back then this was a heavy computational problem.
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