Using molecular dynamics simulations, we show that a designed graphene-charged carbon nanotube (CNT) membrane can act as a nanofilter with the efficiency more than 90%, to separate Na+/Mg+2/Fe+3 and Cl- ions from NaCl, MgCl2 and FeCl3 solutions. It is observed that there are two significant factors in ion separation process: the magnitude of charge density which covers the surface of the CNT and the velocity of the movable wall. The ion separation is improved by increasing the magnitude of surface charge density and decreasing the velocity of the movable wall. Also, it is found that, reducing the positive surface charge of the CNT will increase the percentage of passed water molecules through the CNT. (C) 2015 Elsevier B.V. All rights reserved.