The particle-particle particle-mesh (PPPM) method is an accurate and computationally efficient method for calculating interactions in molecular simulations. The PPPM method is based on separating the total interaction between particles into the sum of short-range interactions, which are computed by direct particle-particle summation, and long-range interactions, which are calculated by solving Poisson’s equation using periodic boundary conditions (PBCs). For nonperiodic systems there is a concern that use of PBCs may introduce an artificial periodicity into the system. In this article we propose, and test, the use of boundary conditions for the long-range interactions which mimic surrounding the explicit system by high dielectric material such as water.