Thanks

Molecular dynamics (MD) is the solution of the classical equations of motion for atoms and molecules to obtain time evolution of a system. Since this is many-particle problem, one must use numerical methods and computers (often a parallel supercomputer) to solve it.

MD simulation is a powerful technique to look at time evolution of a system in atomistic details. However, the system must be provided with a set of parameters (often derived empirically from experimental observations or ab-initio calculations) for some mathematical functions that describe the molecular behaviour in the system. Collectively, these sets of mathematical functions are called the force field of the molecular system.

Since one must be able to track the fastest motion of the molecular system such as the vibrational modes of atoms, the timescale of interest are usually confine to the order of nano-seconds.

I agree about what is MD from previous answer. 

On the side about how to study it, I would recommend you some basic lecture about the principles. You can read some in my Ph.D thesis: 

https://www.researchgate.net/publication/316285796_Local_Ordering_and_dynamics_of_plastic_crystals

Chapter 2 contains some basics and you can also check some examples of applications throughout the thesis.

You should also read the book by Frenkel. Understanding Molecular Simulation.

And there are several engines open source such as GroMacs, Namd, Lammps, charmm that you can install and start practicing with.

Wish you the bests in this great world that is MD.

Thesis Local Ordering and dynamics of plastic crystals

Read as many articles as you can to get a better understanding of dynamics.

https://www.nature.com/nsmb/journal/v9/n9/pdf/nsb0902-646.pdf

https://udel.edu/~arthij/MD.pdf

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981647/pdf/nihms243078.pdf

https://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-9-71

By so called transient cavitations mechanism. 

www.fracturae.com/index.php/MST/article/download/1136/1088

Best regards

Thanks Somayeh

Hope this can be helpful:

http://www.compadre.org/osp/items/detail.cfm?ID=12750

Regards

Thanks Dear Fernando

Thanks Dear Anu Manhas

Try it yourself!

Doiwnload Gromacs (free). Or even easier, get a copy of Yasara which has Amber built into it. You can easily set up and start your own MD runs.