With decreasing clearance between the protrusion of a slider and a disk interface, there is a higher likelihood of contact occurring during shock or vibration experienced by hard disk drives (HDDs), which may induce lubricant depletion. Based on the molecular dynamics (MD) model of perfluoropolyether lubricant with a coarse-grained beads spring approach, we compared the slider configurations’ influence on the lubricant transfer volume quantitatively. By further investigating the parameters of the cylindrical asperities, including the width and depth, as well as considering the asperity amounts of the slider, we successfully observed the lubricant depletion process during slider and disk contact. The results demonstrate that the penetration depth was reduced as the asperity amount increased, mainly owing to the increased contact area between the surfaces. The decreasing depth of the asperity and the increasing width of the asperity helped to reduce the depletion volume. In addition, the utilization of a cylindrical slider configuration can contribute to a reduction in lubricant depletion resulting from contact between the head and disk.