A versatile coupled three-dimensional (3D) computational model for real-time simulation of the automatic process of filling a complex shaped container with assorted powder granules from an arbitrary moving outer tank is proposed. Interactive tool for both visualization and physically accurate modelling of the dynamic behaviour of a wide range of granular materials is developed. The model combines molecular dynamics technique with detailed description of the 3D kinematics of a container with non-trivial geometry. The model of interparticle interactions and model of interactions between the particles and the 3D complex shaped moving wall are suggested. The virtual interactive environment enables to specify the number, size distribution and properties of particles, the configuration and law of time-dependent movement of the containers. The computational efficiency and real-time simulation capabilities of the method are demonstrated. An experimental verification of the model is performed. (C) 2020 Elsevier B.V. All rights reserved.