Infrared-induced conformational isomerization of N-acetyl-tryptophan methyl amide is studied theoretically using a microcanonical Rice-Ramsperger-Kassel-Marcus description of the rates on potential energy surfaces calculated using the AMBER and OPLS-AA force fields. The results are compared with the experimental data from Dian in the preceding paper [J. Chem. Phys. 120, 133 (2004)]. An exhaustive search of the potential energy surfaces locates all minima and transition states on these surfaces. A simple model is proposed for the vibrational cooling, and an appropriate cooling rate is chosen as the standard conditions for the master equation simulations by comparison with experiment. The two potential energy surfaces differ in the relative energies of minima and the heights of key transition states, leading to differences in the dominant pathways and rates of conformational isomerization. The predicted quantum yields depend sensitively on the cooling rate, varying from the slow cooling limit in which equilibrium populations are achieved to the fast quenching limit in which conformational isomerization is shut off. The excitation energy is varied from 5 to 20 kcal mol(-1). At the lowest energies, isomerization is completely quenched, while at the highest energies, equilibrium conditions are achieved. In between these extremes, the quantum yields are sensitive to the excitation energy, and can be used to locate the rate-limiting barriers to isomerization. (C) 2004 American Institute of Physics.