Molecular dynamics (MD) simulations are performed to model an electrospray thruster for the ionic liquid (IL) EMIM-BE4 using two coarse-grained (CG) potentials. Different equilibrium properties were obtained for the two potentials and then both were used to study the electrical extrusion of the IL for different electric field strengths and mass flow rates. The MD simulations provide the first insight into the atomistic modeling of a capillary-tip-extractor system, the basic elements of an electrospray thruster. One of the CG potentials was found to predict the formation of the Taylor cone, the cone-jet, and other extrusion modes for similar electric fields and mass flow rates observed in experiments of a IL fed capillary-tip-extractor system. Current distributions and anion and cation behavior were characterized and estimates of thrust and specific impulse are presented and compare reasonably well with measurements. Moreover, the role of inhomogeneities in the electric field as well as that of the IL space-charge most likely will improve agreement between modeling and experiment.