The effective stress principle is one of the most fundamental concepts in the mechanics of porous materials. Several mathematical expressions have been proposed for this fundamental principle, leading to unsettled debates on the validity and applicability of the principle and its mathematical descriptions. Recent developments in atomistic modeling techniques make it possible to understand multiphase systems at the atomistic scale. In this paper, molecular dynamics simulation is explored as a tool to investigate the stress formulation in porous materials. A molecular dynamics framework, including molecular models of phases, interatomic potentials, initial configuration, and simulation procedure, is presented. Numerical simulations based on the framework preliminarily show the validity of the effective stress principle at the atomistic scale. Furthermore, the effectiveness of typical expressions for the principle is investigated.