We performed molecular dynamics simulations to study the character of hydrophobic interaction between two nanoscale particles in water. For a systematic study of water density fluctuations induced by the hydrophobic interaction, we prepared a graphene plate and also other model plates made of “carbon” atoms that had different interaction strength with water. We calculated the interaction between two identical “carbon” plates immersed in water, and calculated the fluctuations in the number of water molecules in the confined space between two plates. The result showed that fluctuations in some cases are strongly enhanced compared to the fluctuations observed next to a single plate. If the character of water fluctuations in the confined space determines the character of hydrophobic interactions, then it is possible to conclude that the interaction between graphene plates in water is hydrophobic. In another study, we investigated the effect of roughness on hydrophobic interaction (the rough hydrophobic surface was created by attaching non-polar headgroups to the graphene plates). Our study demonstrated that roughness enhances hydrophobic interactions. As a result of this enhancement, we observed a dewetting transition between two rough hydrophobic surfaces, which would not occur between the corresponding particles with smooth surfaces.