Several types of collision processes (such as stripping of negative ions and neutrals and ionization of gas molecules and atoms by negative ions) have been introduced in a simulation code of the extraction, acceleration, and transport of negative ions. The energy spectra of neutral atoms formed in the accelerator, for various values of the pressure in the transport region, have been computed. It will be shown that most of the neutrals are formed in the neighborhood of the thick extraction electrode. The effect of these neutrals on the charge‐state distribution in the beam and the effect of the positive ion formation in the transport region on the ion trajectories will be discussed.