The simulator settings dialog is not yet implemented (#13412)
XMegaB1, UC3 except UC3A and UC3L series, and some tinyAVR® and megaAVR® devices are not yet supported in Atmel Studio. See Supported Devices for more information on device support.
AT90CAN*/ATmega*C*, AT90USB*/ATmega*U*, AT90PWM*, and ATtiny87/167 devices will never be supported by simulator models.
External memory is not supported by simulator (#7570, #9442)
When writing to I/O PORT registers and the port is configured as output, the change may show up immediately in the PIN register, not one cycle delayed as on the real chip (#7188). This only affects the Atmel Studio I/O view, not the execution of programs.
The AVR32 Studio instruction set simulator still not implemented in Atmel Studio 7.0 (#11557).
If the simulated device is put to sleep, single-stepping will not promote the program counter. Like a real device, this state will remain until something wakes it up from sleep. The reason for this behavior is that the CPU is not executing code when asleep, the alternative would be having the single step hang until the device wakes up, which would hang the entire Atmel Studio until that happens (maybe never).
Setting fuses in the code of the simulated program may interfere with the operation of the simulator. Especially the OCDEN fuse and the SUT fuse may cause the simulator to abort the session. This is caused by a timeout in the simulator that counts the amount of clock ticks it takes to get the chip out of reset. If this timeout is exceeded, the simulator will fail the session.