Molecular dynamics (MD) simulations are used to determine the agglomeration rates of wet grains (particles coated with a viscous, liquid layer) engaged in simple shear flow under dilute conditions. In this work, a closed-form model derived from the elastohydrodynamic theory describes the normal restitution coefficient for binary collisions. Unlike previous MD studies, the particle deformation is not assumed to depend on a particle “overlap” (penetration), but instead depends on the formal coupling of Hertzian deformation theory with lubrication theory. The initial rate of doublet formation is studied as a function of system properties and the energy input to the system. In addition to the system properties, the distribution of relative velocities in the system is found to be a key factor influencing the initial rates of clustering. A theory based on estimating the collision frequency and the critical velocity below which no rebound is observed—due to viscous dissipation—is found to provide a good approximation of the initial aggregation rate. The rate of aggregation is found to increase with increasing number of particles in the system, increasing solid fraction, decreasing overall Stokes number, and decreasing compliance parameter.