Membrane permeability is a crucial factor in drug design. Traditionally, Molecular Dynamics (MD) was utilized to simulate drug trajectories across the membrane. However, this method was time-consuming and required extensive computational resources to observe drug permeation through the membrane. To overcome this challenge, we employed the Parallel Cascade Selection Molecular Dynamics (PaCS-MD) method, an approach that offers greater efficiency. We successfully simulated the entire drug permeation trajectories using PaCS-MD and confirmed its accuracy and reproducibility. Moreover, we used the Markov State Model (MSM) to predict drug membrane permeation, calculating the potential of mean force (PMF) from these trajectory data.