SageMD is the software package for the molecular dynamic simulation and a powerful, user friendly molecular visualization tool. Graphical User Interface (GUI) simplifies user interaction with the MD code and provides for setup of initial data via intuitive and easy to operate dialogues and menus. Initial data, results, parameters, MD cell, and crystal lattice can be inspected on the computer screen. User-friendly GUI also allows for analysis of results with a variety of graphs and tools. SAGE MD code can be used to model properties of materials at constant temperature and/or constant pressure, to study behavior of the crystal lattice under expansion or compression, to calculate Radial Distribution Function (RDF), and to derive atomic diffusion coefficients. The user can choose different boundary conditions, namely: periodical boundary conditions, free surfaces, and movable walls. In addition, the QEq approach for interatomic energy calculation, which takes into account atomic charge distribution, has been incorporated into SAGE MD code for modeling the properties of materials with covalent chemical bonds. For derivation of atomic charges and other parameters of force fields used in SAGE MD, quantum chemical programs (e.g. GAUSSIAN, ABINIT) have been used.