Dear @rx9abc,
If you assign vacuum instead of air to the surrounding space, the 200 keV deuterons have a chance to arrive to your target (instead of being stopped), and some of them even to the water volume further downstream.
The messages you see in the .err file are innocuous (they reflect a very low energy deuteron failing to interact with a target proton). The developers are aware of the verbosity of these messages and will surely moderate them in the upcoming minor release before the end of the year.