Real-time interactive simulation and visualization of organic molecules

Abstract

Three-dimensional visualization of molecular simulations in virtual reality (VR) is an emerging teaching tool in chemical education. This work describes a VR application which can generate a 3D molecular dynamics (MD) simulation from arbitrary molecular structures and renders that MD simulation trajectory on a VR headset in real-time. This system uses the ZeroMQ (ZMQ) message passing framework for multisimulation to multiclient VR visualization of MD simulation. All MD simulations are done in the HOOMD-blue simulation engine, and the graphics for the VR are rendered in Unity3D. The key feature that sets this software apart from previous 3D viewer programs is the real-time simulation and thus the ability to manipulate thermodynamic variables like temperature on the fly. This allows viewers to build an intuitive understanding of the effects of thermodynamics state variables in a hands-on way. This application was used as a pedagogical tool with high school students, and the curriculum used, along with outcomes of the activity, has been presented here. This application can provide an interactive tool for teaching thermodynamics and statistical mechanics, and even as a diagnostic tool for MD simulations for research purposes.