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 inhomogeneities 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.