Dynamic disorder in proteins, as demonstrated by variations in single-molecule electron transfer rates, is investigated by molecular dynamics simulations. The potential of mean force for the fluctuating donor-acceptor distance is calculated for the NAD( P) H: flavin oxidoreductase ( Fre) complex with flavin adenine dinucleotide ( FAD) and is found to be in agreement with that estimated from electron transfer experiments. The calculated autocorrelation function of the distance fluctuations has a simple exponential behavior at low temperatures and stretched exponential behavior at higher temperatures on femtosecond to nanosecond time scales. This indicates that the calculated dynamic disorder arises from a wide range of trapping times in potential wells on the protein energy landscape and suggests a corresponding origin for the stretched exponential behavior observed experimentally on longer time scales.