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I thought TIP4P/EW potential would take care of the charges as the atom type was defined.
You need to define the charges explicitly. pair_style lj/cut/tip4p/long only uses the defined charges for its Coulomb interactions; it does not assign charges for you.
I didn’t define the charges in my water box file.
Yes you did: the 4th column are the charges.
Do I need to do that in the molecular file?
Yes, note the warning after your fix deposit command:
fix up_scattering all deposit 1 0 10 8749 region up mol H2O shake water_shake
WARNING: Molecule attributes do not match system attributes (…/molecule.cpp:1350)
The velocity of the deposited molecular was set with velocity command.
That is just a thermal vibration, not a proper incident velocity and certainly would not make your additional H2O to “flying toward the vacuum-water interface”.
Hope this helps.