Here are two textbooks for beginners in MD. These are also great if you know some about it, but need help with optimization or best practices when coding it.

These are the textbooks I used when I took the graduate class. They go through MD simulations in Fortran, but you can apply the authors' techniques in any language (I used python in the class). If you are also looking for a decent visualizer that is free, JMOL works great and all you need is a .xyz file output from your code to make it work.

(Monographs in Physical Chemistry) J. M. Haile - Molecular dynamics simulation_ elementary methods-Wiley-Interscience (1992)

(Computational science series 1) Daan Frenkel, Berend Smit - Understanding molecular simulation_ from algorithms to applications-Academic Press (2002)