Wind farm-induced atmospheric gravity waves are getting some attention lately as they can impact wind farm performance. Pressure variations associated to gravity waves can contribute to the global blockage effect and wind farm wake recovery. Therefore, accurately numerically simulating flow fields, including wind-farm-induced gravity waves, is important. Few main considerations in such simulations are the overall domain size, the use of Rayleigh damping near domain boundaries to dampen gravity wave reflections, and advection damping to constrain spurious waves at the inlet. Often these considerations are treated ad hoc rather than systematically. This work aims to find the correct length scale to set the domain size and damping layer size, and the time scale to configure the damping coefficient. The importance of compressibility in simulating gravity waves is also addressed. Large eddy simulations of flow over a 2D hill and through a wind farm canopy are performed under conventionally neutral boundary layer conditions. Background atmospheric parameters, such as Froude number, inversion height , and inversion layer Froude number control most of the atmospheric gravity wave characteristics. We observe that the effective wavelengths of the gravity waves is the correct length scale to configure the domain size and damping layer thickness. Likewise, the optimum damping coefficient relates to the buoyancy frequency in the free atmosphere. Besides a Rayleigh damping layer, an advection damping layer is critical to restrict spurious waves at the inlet with inflow/outflow, and a fringe layer is required for periodic boundary conditions.