The artifact derives its name from a particularly noticeable manifestation that arises in simulations of particles in vacuum, where the system being simulated acquires high linear momentum and experiences extremely damped internal motions, freezing the system into a single conformation reminiscent of an ice cube or other rigid body flying through space.
The artifact is entirely a consequence of molecular dynamics algorithms and is wholly unphysical, since it violates the principle of equipartition of energy.
[1] The flying ice cube artifact arises from repeated rescalings of the velocities of the particles in the simulation system.
Rescaling to an ensemble that is not invariant under microcanonical molecular dynamics results in a violation of the balance condition that is a requirement of Monte Carlo simulations (molecular dynamics simulations with velocity rescaling thermostats can be thought of as Monte Carlo simulations with molecular dynamics moves and velocity rescaling moves), which is the artifact's underlying reason.
Thus, suggestions were given to avoid the flying ice cube effect under the Berendsen thermostat, such as periodically removing the center-of-mass motions and using a longer temperature coupling time.