You can watch the video of the methodolgy used to induce (large) muscle damage
An in vivo rodent model of contraction-induced injury and non-invasive monitoring of recovery. Lovering RM, Roche JA, Goodall MH, Clark BB, McMillan A. J Vis Exp. 2011 May 11;(51). pii: 2782. doi: 10.3791/2782.
I think it depends on the question you're asking. Downhill running is probably the most physiological method to induce injury but direct muscle deformation using a torque motor or linear motor is more controlled to study mechanics. It really depends whether you're asking muscle mechanism questions or exercise questions. Good luck!