We have simulated the heating process of gold nanorods, elucidating a mechanism by which nanorods alter their aspect ratio at higher temperatures. We also studied the relative stabilities of nanorods by constructing nanorods with varying ratios of {110} to {100} exposed surfaces along the body of the nanorod. The least stable nanorod was found to be the nanorod with the largest {110} surfaces, followed by the nanorod with the largest {100} surfaces, while the nanorod with approximately equal surface areas of {100} and {110} surface was found to be the most stable. It was also found that the addition of surface disorder increased the stability of nanorods with large {110} surfaces, while paradoxically decreasing the stability of nanorods with large {100} surfaces. The reasons for this are elucidated and compared to experimental laser-induced gold nanorod transformation studies.