Is there a way to turn off the WDOG for just one motor?   We have some motors that have magnetic coupling shafts.  when the motor stops, there is some oscillation because shaft is bouncing between the two poles of the magnet and the motor is trying to correct.  turning the WDOG off solves it but other motors may still be running at the same time.  

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Yes, leave the WDOG ON and set these axis parameters.

AXIS_ENABLE AXIS(1) = OFF

AXIS_ENABLE AXIS(2) = OFF

It will set the EtherCAT enable bits in the control word to OFF.

Also works for the MC508 axes which have 8 WDOG outputs and MC405/MC403 which have independent Enable outputs for stepper motors.