Physics:
Statistical Mechanics, by Donald A. McQuarrie.
Statistical Mechanics, Entropy, Order Parameters, and Complexity, by James P. Sethna. [PDF]
Statistical Mechanics, by R. K. Pathria & Paul D. Beale.
Nonequilibrium Statistical Mechanics, by Robert Zwanzig.
Theoretical Concepts in Physics: An Alternative View of Theoretical Reasoning in Physics, by Malcolm S. Longair.
Capillarity and Wetting Phenomena by Pierre-Gilles de Gennes et al.
Soft Mater Physics, by Maso Doi.
Physical Chemistry:
Molecular Driving Forces, by Ken A. Dill and Sarina Bromberg.
Statistical Physics of Biomolecules, by Daneil M. Zuckerman.
Protein Physics, by Alexei V. Finkelstein and Oleg B. Ptitsyn.
The Theory of Intermolecular Forces, by Anthony Stone.
Intermolecular and Surface Forces, by Jacob N. Israelachvili.
Polymer:
Polymer Physics, by Micheal Rubinstein and Ralph H. Colby.
Physics of Charged Macromolecules, by Murugapphan Muthukumar.
Polymer Chemistry, by Paul C. Hiemenz and Timothy P. Lodge.
Scaling Concepts in Polymer Physics, by Pierre-Gilles de Gennes.
Liquid theory:
Molecular theory of solutions, by Arieh Ben-Naim.
Theory of Simple Liquids with Applications to Soft Matter, by Jean-Pierre Hansen and Ian R. McDonald.
Chemistry:
Introduction to computational chemistry, by Frank Jensen.
Physical Chemistry: Thermodynamic, Structure and Change, by Peter Atkins and Julio de Paula.
Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, by Attila Szabo and Neil S. Ostlund.
Molecular Orbitals and Organic Chemical Reactions, by Ian Fleming.
MD & MC:
Computer Simulations of Liquids, by Michael P. Allen & Dominic J. Tildesley.
Understanding Molecular Simulation: From Algorithms to Applications, by Berend Smit and Daan Frenkel.
A Guide to Monte Carlo Simulations in Statistical Physics, by David P. Landau and Kurt Binder.
Free Energy Calculations: Theory and Applications in Chemistry and Biology, Editors: Ch. Chipot and A. Pohorille.
Markov State Models:
An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation, Editors: Gregory R. Bowman, Vijay S. Pande and Frank Noé.
Biology:
Molecular Biology of the Cell, by Alberts, Johnson, Lewis, Morgan Raff, Boberts and Walter.
Cell Biology by Pollard, Earnshaw, Lippincott-Schwartz and Johnson.
Pricinples of Biochemistry, by David L. Nelson and Michael M. Cox.
Misc:
Virial Expansion – A Brief Introduction, by Frank Schreiber, Fabio Zanini & Felix Roosen-Runge.
[To be updated]