We study the structures of the Hras-GTP complex and the Hras-GDP complex in water to investigate the mechanism of GTP hydrolysis of the Hras-GTP complex. We performed molecular dynamics simulations of these complexes to investigate the structures of these complexes using the potential parameters of AMBER ff03 and our potential parameters around Mg2+. Our simulations show that the averaged structure differences between the Hras-GTP complex and Hras-GDP complex are found in the switch I and II regions. In particular, in the switch II region, the α2-helix of Hras-GDP is shorter than the α2-helix of Hras-GTP. The averaged number of water molecules in the first hydration sphere in Hras-GDP complex is larger than that in Hras-GTP complex. The occurrence ratio of the duration time of waters in the first hydration sphere of PA has long tail both in Hras-GTP and in Hras-GDP. In Hras-GDP complex, β-phosphate is hard to be hydrolyzed, while the number of waters in the first hydration sphere is larger than those in Hras-GTP. This suggests that there is a special direction for the hydrolysis. © 2013 Wiley Periodicals, Inc.