Abstract First-principles molecular dynamics simulations are performed to sample the behavior of linear hydrocarbons within the acid zeolite gmelinite at high temperature. The analysis of the trajectories, the time-development of the bond lengths, and simulated IR spectra are presented for both neutral and protonated molecules. The acid proton shows no affinity toward paraffin and slightly increased affinity toward the double bond of the olefin. No spontaneous protonation of the olefin is observed. The simulation of the protonated linear C6H13+ molecule shows that the protonated species is stabilized within the zeolite framework, and no collapse to the neutral molecule occurs. No cracking or isomerization event is observed. The protonated molecule shows rather high mobility accompanied by a series of hydride transfers along the chain of the molecule. The transfer of the H atom leads to a relocation of the positive charge. The relocation is correlated to the position of the Al site in the zeolite framework. In the simulated IR spectra we observe no distinctive feature evidencing the existence of the protonated species.