Molecular Dynamics

This is a demonstration molecular dynamics (MD) simulation of a polymer melt. Each of these colored chains represents a single molecule of polyethylene, a common polyer made up of many repeating CH2 units (and using the united-atom model, these are represented by a single colored point). The simulation starts with the polymers aligned within a box, and the goal of this simulation is to generate physically-reasonable conformations starting from this initial state. The temperature for this simulation is 400K and the timestep is 1 femptosecond. As time progresses, the thermal energy is distributed throughout the system, and the polymers explore various conformational states. By the end of this simulation, the polymers have reached a randomized equilibrium configuration and are ready to be used in an MD run where we can measure their properties.