Anti-viral treatment has made a dramatic increase in the survival of AIDS patients; however, the success of conventional long-treatment therapies has been limited due to the emergence of drug-resistant mutants of HIV-1. Therefore, complete understanding of the structure and molecular dynamics associated with the conformational changes of HIV-1 protease is crucial in rational design of more effective treatment regimes. The flap regions of the protease, which exhibit much higher flexibility than other regions in apo HIV-1 protease, are believed to control the access to the active site; therefore a prime target of anti-AIDS drugs. In this work, one microsecond, unrestrained, all-atom molecular dynamics simulations with an explicit solvent model were performed on a wild type HIV-1 protease using the Amberff99SB force field. The flaps showed complex dynamics and various flap conformations (closed, semi-open, open and curled) during the simulations. Significantly, we observed not only multiple conversions among different states of the flaps, but also well reproduced the two major crystallographic forms of HIV-protease with flap Root-mean-square deviations (RMSD) less than 2� from two crystal structures. The global dynamics obtained from these explicit solvent MD simulations agree very well with those from X-ray and NMR observations and our previous implicit solvent simulations. Our simulations gain insights into the flap conformational changes that are associated with the function of this enzyme. We propose that the rearrangement of intra- and inter- monomer hydrophobic clusters triggers the transition of the flap conformations.