The thesis investigates the process of modeling and simulation of the mobile ad-hoc networks. It provides a overview of the actual state of art together with a literature survey. Basic ideas of both security issues in mobile ad-hoc networks as well as intrusion detection systems are presented. Additionally some new ideas for improvements - like the AGM mobility model - are proposed, and tested during the simulation proces. As an addition a set of applications designer for automating the simulation processes were created.