We formulate a generalized periodic boundary condition as a limit of the standard twist-and-shift parallel boundary condition that is suitable for simulations of plasmas with low magnetic shear. This is done by applying a phase shift in the binormal direction when crossing the parallel boundary. While this phase shift can be set to zero without loss of generality in the local flux-tube limit when employing the twist-and-shift boundary condition, we show that this is not the most general case when employing periodic parallel boundaries, and may not even be the most desirable. A non-zero phase shift can be used to avoid the convective cells that plague simulations of the three-dimensional Hasegawa–Wakatani system, and is shown to have measurable effects in periodic low-magnetic-shear gyrokinetic simulations. We propose a numerical program where a sampling of periodic simulations at random pseudo-irrational flux surfaces are used to determine physical observables in a statistical sense. This approach can serve as an alternative to applying the twist-and-shift boundary condition to low-magnetic-shear scenarios, which, while more straightforward, can be computationally demanding.