Books on simulation methods

Molecular dynamics simulations:
- Computer simulation of liquids, M. P. Allen and D. J. Tildesley
- Understanding Molecular Simulation: From Algorithms to Applications, Berend Smit and Daan Frenkel
- Introduction to Molecular Dynamics Simulation Michael P. Allen, Computational Soft Matter: From Synthetic Polymers to Proteins,2004 pdf
Monte Carlo simulations:
- A Guide to Monte Carlo Simulations in Statistical Physics, David P. Landau, Kurt Binder
Non-equilibrium simulations:
- Nonequilibrium Molecular Dynamics,Theory, Algorithms and Applications, Billy D. Todd and Peter J. Daivis
Thermostat Algorithms for Molecular Dynamics Simulations, Advanced Computer Simulation pp 105-149, Philippe H. Hünenberger,link
The journal Living Journal of Computational Molecular Science is worth checking out
Best Practices for Foundations in Molecular Simulations

Books on statistical mechanics & thermodynamics

Glass Transition Thermodynamics and Kinetics, Frank H. Stillinger and Pablo G. Debenedetti link
Glass and Jamming Transitions, Gulio Biroli link
Particle dynamics modeling methods for colloid suspensions, Dan S. Bolintineanu,Gary S. Grest,Jeremy B. Lechman,Flint Pierce,Steven J. Plimpton,P. Randall Schunk, Comp. Part. Mech. (2014) link
Crystallization kinetics of colloidal model suspensions: recent achievements and new perspectives, Thomas Palberg,J Phys Condens Matter, 2014 link
A Review on Polymer Crystallization Theories, Michael C. Zhang, Bao-Hua Guo and Jun Xu, Cystals, 2014 link
A review of polymer simulation/theory multi-scale methods: Challenges in Multiscale Modeling of Polymer Dynamics,Ying Li,Brendan C. Abberton,Martin Kröger, and Wing Kam Liu,Polymers, 2013 link
Polymer Conformation—A Pedagogical Review, Zhen-Gang Wang, Macromolecules, 2017, 50, 23, 9073–9114 link
Modeling and Simulations of Polymers: A Roadmap, Thomas E. Gartner III and Arthi Jayaraman, Macromolecules 2019, 52, 3, 755–786 link