Books:

1. Molecular Modelling: Principles and Applications by Andrew Leach
2. Understanding Molecular Simulation, Second Edition: From Algorithms to Applications by Frenkel and Smit

These two are enough I'd say to understand what's going on in a MD simulation and programs. They do not deal with a few recent advances, but the basic math and ideas are all there.

Historical Papers:

• Levitt M, Lifson S (1969) Refinement of protein conformations using a macromolecular energy minimization procedure. J Mol Biol 46:269–279. (First energy minimization of a protein structure) [ [PDF][3] ]
• Levitt M, Warshel A (1975) Computer simulation of protein folding. Nature 253:694–698. (Folding simulation, pre-MD) [ [PDF][4] ]
• McCammon J, Gelin B, Karplus M (1977) Dynamics of folded proteins. Nature 267:585–590. (First MD simulation) [ [Nature][5] ]
• Levitt M, Sharon R (1988) Accurate simulation of protein dynamics in solution. Proc Natl Acad Sci USA 85:7557. (First MD simulation in water) [ [PDF][6] ]

Other Papers:

• Shaw DE et al. (2010) Atomic-level characterization of the structural dynamics of proteins. Science 330:341–346. (1st millisecond simulation) [ [PDF][7] ]

Reviews:

• Scheraga HA, Khalili M, Liwo A (2007) Protein-folding dynamics: overview of molecular simulation techniques. Annu Rev Phys Chem 58:57–83. [ [PDF][8] ]
• Guvench O, MacKerell A (2008) Comparison of protein force fields for molecular dynamics simulations. METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA- 443:63. [ [Pubmed][9] ]
• Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S, Xiao X (2011) Biomolecular modeling and simulation: a field coming of age. Quarterly Reviews of Biophysics 44:191–228. [ [PDF][10] ]