An improved emulation system having an improved trigger mechanism is disclosed. During the compilation of the circuit design, a portion of the emulation resources are reserved for dynamic netlists. The dynamic netlists allows a user to create arbitrary trigger circuits that can be based on any signal generated by the device under test during run time, including signals that were optimized out of the design during the compilation process. The dynamic netlists can be loaded and used in the emulator without having to recompile the entire design, which could take many hours. This enables a user to quickly and efficiently debug circuit designs.