Background Digital twins offer rich potential for exploration in virtual reality (VR). Using interactive molecular simulation approaches, they enable a human operator to access the physical properties of molecular objects and to build, manipulate, and study their assemblies. Integrative modeling and drug design are important applications of this technology. Methods In this study, head-mounted virtual reality displays connected to molecular simulation engines were used to create interactive and immersive digital twins. They were used to perform tasks relevant to specific use cases. Results Three areas were investigated, including model building, rational design, and tangible models. Here, we report several membrane-embedded systems of ion channels, viral components, and artificial water channels. We were able to improve and create molecular designs based on digital twins. Conclusions The molecular application domain offers great opportunities, and most of the technical and technological aspects have been solved. Wider adoption is expected once the onboarding of VR is simplified and the technology gains wider acceptance.