Molecular dynamics (MD) simulations are performed to model an electrospray thruster for the ionic liquid (IL) EMIM−BF4 using two coarse-grained (CG) potentials. The MD simulations provide insight into the atomistic modeling of a capillary-tip-extractor system, the basic elements of an electrospray thruster. A one-dimensional electric field showed an improvement in a model when compared to the use of a constant electric field. Then, the MD software was coupled to a Poisson solver derived from a Particle-In-Cell (PIC) code. A transient three-dimensional electric field was used at each timestep, taking into account the induced electric field due to space charge repulsion. It was found that the role of inho-mogeneities in the electric field as well as that of the IL space-charge improved agreement between modeling and experiment. The model 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. The influence of parameters such as grid size, diameter of the extraction ring, extraction potential and applied mass flow was studied.