If molecular machines actually moved as shown in most videos, they wouldn't work. Don't blame the simulation or the design, though. The problem is that the standard way to render video frames creates a stroboscopic illusion of jerky motion. Atoms typically vibrate hundreds of times per frame, but standard frames capture the position of each atom at a single instant, as if seen by the flash of a stroboscope. This creates the illusion that the atoms all vibrate at the frame rate, which is far too close to the frequency of the machine's moving parts. This gives the false impression that the machine parts are moving at nearly thermal speed, comparable to the speed of sound. At that speed, even if the machine worked, friction would be intolerable.