Continuing advances in development of multi-core CPUs, GPUs, and low-cost six-degree-of-freedom virtual reality input devices have created an unprecedented opportunity for broader use of interactive molecular modeling and immersive visualization of large molecular complexes. We describe the design and implementation of VMD, a popular molecular visualization and modeling tool that supports both desktop and immersive virtual reality environments, and includes support for a variety of multi-modal user interaction mechanisms. A number of unique challenges arise in supporting immersive visualization and advanced input devices within software that is used by a broad community of scientists that often have little background in the use or administration of these technologies. We share our experiences in supporting VMD on existing and upcoming low-cost virtual reality hardware platforms, and we give our perspective on how these technologies can be improved and employed to enable next-generation interactive molecular simulation tools for broader use by the molecular modeling community.