  Ion-induced DNA damage is an important effect underlying ion-beam cancer
therapy. This paper introduces the methodology of modeling DNA damage induced
by a shock wave caused by a projectile ion. Specifically, it is demonstrated
how single- and double-strand breaks in a DNA molecule could be described by
the reactive CHARMM (rCHARMM) force field implemented in the program MBN
Explorer. The entire workflow of performing the shock wave simulations,
including obtaining the crucial simulation parameters, is described in seven
steps. Two exemplary analyses are provided for a case study simulation serving
to (i) quantify the shock wave propagation and (ii) describe the dynamics of
the formation of DNA breaks. The paper concludes by discussing the
computational cost of the simulations and revealing the possible maximal
computational time for different simulation setups.
