The intergalactic medium (IGM) in the vicinity of galaxy protoclusters are interesting testbeds to study complex baryonic effects such as gravitational shocks and feedback. Here, we utilize hydrodynamical simulations from the SIMBA and The Three Hundred suites to study the mechanisms influencing large-scale Lyman-$\alpha$ transmission in 2Comment: 12 pages, 4 figures, submitted to MNRAS