Here we describe a computational workflow that was used to perform virtual screening based on CaverDock trajectories for 4358 drug molecules and six conformational states of the s-glycoprotein of SARS-CoV-2. This analysis involved a total of 26,148 calculations. Each calculation took a real-time average of 37 minutes to complete on 8 CPUs, making the method sufficiently fast for thorough virtual screening.