Molecular dynamics (MD) simulations are performed to model an electrospray thruster for the ionic liquid (IL) EMIM−BF4 using an effective-force coarse-grained (CG) potential. 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 the 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 inhomogeneous electric field as well as that of the IL space-charge improved agreement between modeling and experiment. The influence of numerical parameters such as extraction potential and applied mass flow were studied. Particular emphasis was put on the importance of parameters relative to the grid used to solve Poisson’s equation, such as the grid cell size and the boundary conditions in the vicinity of the capillary tip. The boundary conditions were found to have a substantial impact on the potential and electric field.