TextBook:
T. Schlick, Molecular Modeling: An Interdisciplinary Guide, Springer-Verlag, NY (2002)
T. Schlick, Molecular Modeling: An Interdisciplinary Guide, Second Edition, Springer-Verlag, NY (2010)
(See website for updates, reviews, etc.)
https://www.biomath.nyu.edu/biomath/index/book/2/book2.html