Before revision:  In analogy with the adiabatic Born-Oppenheimer approximation in which the nuclear dynamics are governed by the energy of the instantaneously-equilibrated electronic degrees of freedom , the protein backbone dynamics are simulated as preceding according to the dictates of the free energy of an instantaneously-equilibrated side chain potential.
After revision:  In analogy with the adiabatic Born-Oppenheimer approximation for electronic structure , the protein backbone dynamics are simulated as preceding according to the dictates of the free energy of an instantaneously-equilibrated side chain potential.