The three-dimensional structures of proteins are obtained through physicochemical processes using the amino acid sequences [1,2].  A lot of effort both experimental and theoretical has been put into the elucidation of the protein folding problem.  At the moment the most widely accepted view of how the protein folding process takes place is based on the energy landscape perspective [3].  In this view the folding to the native state is regarded as a complex process with multiple pathways.  In this theory the energy landscape resembles a funnel with several local minima, which could trap the protein in misfolded states.  Recently molecular dynamics simulations in combination with experimental studies have tried to characterize the denatured and transition state conformations of proteins.  This kind of collaborations will be very important in elucidating the protein folding mechanism.  In this review an overview of the molecular dynamics simulations of protein folding and unfolding will be discussed.