Molecular dynamics (MD) are based on a algorithm, the figure below shows the basic molecular dynamics steps:
For each MD step (lines 3, 4 and 5), is necessary to integrate the Newton’s motions equation, the Verlet algorithm is widely use for this task. However, there is a important issue to tackle, the Delta T has to be small (on 1 fs order) to minimize the error and result on a correct simulation. To solve this issue is possible to use accelerated molecular dynamics.
Blender is 3D modeling tool, with blender is possible to make games, animations, scenes etc. With some extensions blender can be used for molecular dynamics with Atomic Blender, XYZ importer and PDB importer is possible elaborate amazing scenes for MD. One example produced for one poster, carbon atoms (atom.blend):
The study of material phase is important theme, with this information new materials could be used to a variety of events. However, this study lead to a cost experiments, with Open Phase is possible to simulate the metal phases, materials and others..
One example what OpenPhase can produces (visualization with ParaView)