Using molecular dynamics simulations, fluorescence Stokes shift for the tryptophan in Staphylococcus nuclease was examined using both nonequilibrium calculations and linear response theory. 
molecular dynamics simulations
Using molecular dynamics simulations, fluorescence Stokes shift for the tryptophan in Staphylococcus nuclease was examined using both nonequilibrium calculations and linear response theory.  However, the linear response theory on the unperturbed surface breaks down even in the presence of Gaussian fluctuations. 
linear response theory