We use ab initio molecular dynamics to investigate the mechanical response and geometric deformation for the capped and stem structures of (5,5) nanotubes, during doping by Cs ions. The favorable doping sites/energies are generally different from those of thicker tubes. After collision with kinetic energy 50 eV, the Cs ion is detached from the short, thin nanotubes; however, the dopants get adsorbed on long ones. At higher energies, partial encapsulation accompanied by local sp3 bondings and bridge-like structures is observed. Our estimates of distortion wave velocity support the observation that armchair nanotubes are less stiff compared to zigzag ones.