Dynamics of grain boundary (GB) grooving plays an important role in microstructural evolution. Classical theory on GB grooving assumes the solid-solid interface as a homogeneous boundary where details of GB structures are ignored. This assumption clearly requires certain modifications for cases such as low angle GB. The advantage of phase field crystal (PFC) method is its capability to describe materials with atomic resolutions. We investigated how dislocations influence dihedral angle in low angle GB. Furthermore, we used amplitude equations derived from PFC model to describe quantitatively the interplay between stresses, dislocations, and the dihedral angle. While GB grooves, interesting phenomena such as grain rotation and dislocation translation were observed, which provide an alternative way to control grain growth at the nanoscale.