If using the option -encoder_type=gnmt, can I still change the number of layers, the recurrent cell (LSTM,GRU), word embeddings, etc? Or Google’s model is used as defined in their paper?

Yes, you can change all of these values.

Thanks for your reply. I guess Google default parameters are used by default?

No. As these options can be configured via command line, it uses the default value of each of these options.