Check books referenced and make sure we want to endorse

[davidlmobley]

We list a lot of books without giving full details; we should give full details and citations.

Additionally, we should make sure that one or more of the authors actually knows and would recommend each of these books; we will be essentially endorsing them so I want to be able to say, "Yes, we really do recommend that; authors ABC and DEF are familiar with it and say it's one of the best books on this topic."

Probably to do that I should list every book by topic here and then get people to put their initials by it if they endorse. Objections?

[davidlmobley]

Here are the books referenced; please edit this comment and put your initials next to them if you endorse for the corresponding topic (@samarjeet @hmayes @avisekdas @JIMonroe @justinGilmer @dmzuckerman ) or if for some reason that doesn't work, just comment below and I'll consolidate initials. The goal of this is to make sure we do not point people to books that we don't endorse.

Overall:

• Allen & Tildesley (JBG, DLM, EB)
• Frenkel & Smit, 2nd Edition (JIM, DMZ, DLM, EB)
• Tuckerman (EB though it's more advanced than the other texts and I wouldn't recommend it to the audience that the paper is targeting)

Classical mechanics

• Goldstein, Poole and Safko (removed for now since no one recommended)

Thermodynamics

• Atkins PChem (DLM: Standard but not remarkable?)
• Zemansky and Dittman (no one endorsed, so removing)
• Shell (JIM; not referenced yet, but Ch. 1-15 actually cover thermodynamics, so should)
• McQuarrie & Simon, "Physical Chemistry" which is a great though huge book on QM, stat mech, thermo (DMZ, JBG)
• Dill (DMZ)
• Thermal Physics by Kittel and Kroemer (JBG)

Stat mech

• Reif (DMZ)
• McQuarrie (JIM, DMZ)
• McQuarrie & Simon (DMZ, JBG)
• Dill (DLM)
• Hill (JIM, DMZ)
• Shell (DLM, JIM)
• Zuckerman (DLM)
• Kaznessis (removed since no one endorsed)
• Chandler (added by EB)

Classical electrostatics

• Griffiths (DLM)
• Jackson (DLM with caveats -- graduate-level, math-heavy)

Stochastic dynamics (to be merged with another section)

• McQuarrie
• Zuckerman

Force fields

• Leach (DLM, JIM, DMZ)
• AMBER manual (JIM - see comment in text)
• GROMACS manual (JIM - see comment in text)

Periodic boundary conditions:

• Leach (DLM, JIM)
• Shell (JIM)

Main steps of MD simulation:

• Leach (DLM, JIM)

Several sections following these have no books referenced yet.

@dmzuckerman please feel free to note which of these are well-covered by your book, which I do not have in my hands at the moment. :)

[justinGilmer]

Could not edit, but here are my recommendations:

overall

Allen and Tildesley (JBG)

Stat mech

McQuarrie (JBG)
Thermal Physics by Kittel and Kroemer (JBG)

Thermodynamics

McQuarrie (JBG)
If I recall correctly, McQuarrie also provided a treatment for themo as well. This was the book we used in my undergrad classes.

Thermal Physics by Kittel and Kroemer (JBG)

[davidlmobley]

@JIMonroe @samarjeet any thoughts?

[samarjeet]

I have used this book "Numerical Simulation in Molecular Dynamics : Numerics, Algorithms, Parallelization, Applications" by Michael Griebel, Gerhard Zumbusch, Stephan Knapek. I would definitely endorse it as I have used it heavily in writing my sections.

[davidlmobley]

@hmayes - did you have any input on the book list above?

[hmayes]

The books I see most used (because found helpful) for beginners are:
Molecular Modelling: Principles and Applications (2nd Edition)Apr 9, 2001, by Andrew Leach
Understanding Molecular Simulation: From Algorithms to Applications (Computational Science Series, Vol 1)Nov 7, 2001, by Daan Frenkel and Berend Smit

I don't want to overwhelm folks with the suggestions, but agree that some key books on Stat Mech (e.g. McQuarrie or McQuarrie & Simon) should be listed. I also find myself referencing Shell often.

I'm going to add refs in based on feedback above; feel free to change!

[davidlmobley]

I think we have most of these in already, @hmayes !

[davidlmobley]

Marking this as closed because I think I have people's recommendations above, and I brought all the references in in #44 I believe.