Using molecular dynamics (MD) simulations, a porous graphene membrane was exposed to external electric fields to separate positive and negative ions from salt-water and to produce fresh water. It was observed that, by increasing the strength of the applied electric field, ion separation improved noticeably. In addition, to obtain fresh water, the designed system included two graphene membranes, which are exposed to two external electric fields in opposite directions. Ion rejection was found to be greater than 93% for the electric field of 10 mV/Å and higher. This atomic-level simulation increases the understanding of electric field effects on desalination using multilayer graphene membranes and can be helpful in designing more efficient membranes.