A microtubule gliding assay is a biological experiment observing the dynamics of microtubules driven by motor proteins fixed on a glass surface. When appropriate microtubule interactions are set up on gliding assay experiments, microtubules often organize and create higher-level dynamics such as ring and bundle structures. In order to reproduce such higher-level dynamics in silico, we have been focusing on making a real-time 3D microtubule simulation. This real-time 3D microtubule simulation enables us to gain more knowledge on microtubule dynamics and their swarm movements by means of adjusting simulation parameters in a real-time fashion. One of technical challenges when creating a real-time 3D simulation is balancing the 3D rendering and the computing performance. GPU programming plays an essential role in balancing the millions of tasks, and makes this real-time 3D simulation possible. By the use of GPGPU programming we are able to run the simulation in a massively parallel fashion, even when dealing with more complex interactions between microtubules such as overriding and snuggling.