Molecular dynamics simulations present a powerful approach that may be used to gain insight into many biological systems. In most cases, simulations do not take into account any bond breaking or formation. This is obviously a problem when the behavior that we are wishing to explore requires such changes in the chemistry of the system. For example numerous processes in proteins in general, and membrane transporters in particular are triggered by protonation and deprotonation events. In my lecture I will describe how one can trigger such events in the course of the simulation thereby mimicking the biological functionality. I will focus on two systems: The E. coli Na+/H+ antiporter and the influenza A M2 H+ channel. I will presents the simple ways in which one can perform such triggering and the analysis tools that one may use to analyze the results.