Tiny　mass　attached　to　the　surface　of　carbon　nanotubes　(CNTs)　would　induce　its　intrinsic　frequency　shift.　Due　to　their　remarkable　mechanical　properties,　such　as　exceptional　high　elastic　modulus　and　low　weight,　CNTs　hold　significant　potential　as　functional　materials　for　the　development　of　mass　sensors　and　biosensors　with　atomic　mass　resolution.　The　effect　of　the　structure　of　molecule　covalently　bonded　to　the　surface　of　CNTs　on　its　intrinsic　frequency　shift　was　investigated　with　full-atom　molecular　dynamics　simulation　(FAMDs),　which　explored　the　REBO　potential　and　Lennard-Jones　potential　to　represent　the　interatomic　interaction.　CNTs　were　constrained　by　the　clamped-clamped　boundary　condition　and　the　fixed-free　boundary　condition,　respectively.　In　order　to　highlight　the　effect　of　molecular　structure　on　the　fundamental　frequency　of　CNTs,　the　simulated　results　via　the　FAMDs　were　compared　with　those　of　additional　mass　molecular　dynamics　simulation　(AMMDs),　in　which　the　mass　of　the　attached　molecule　is　lumped　to　the　bonded　carbon　atom　of　CNTs.　Results　indicate　that　the　structure　of　the　covalently　bonded　molecular　is　strong　enough　to　take　effect　on　the　frequency　response　of　the　CNT　resonator.　©　2013　IEEE.