How could I download my hex file to the sam3x8e?

I have tried to download my hex file to the sam3x8e MCU. But don't know how with arduino IDE. I found that the OpenJumper could only download to the atmega MCU but not SAM3X8E? Am I right. My MCU could download the arduino generated file with a serial2usb wire , however i want to use MDK to compile my project and download it with the same wire. What should I do?Is it the USBasp way?