Sampling molecular conformations and dynamics in a multiuser virtual reality framework

Abstract

VR combined with cloud computing enables surgical manipulation of real-time molecular simulations, accelerating 3D research tasks.

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

“…The interaction shown in Video 1, where multiple participants in the same room are able to easily pass a simulated molecule between themselves (or e.g., collaboratively tie a knot in a protein) as if it were a tangible object, represents a class of simulated virtual experience which is simply not possible within the large-scale immersive stereoscopic CAVE environments that have become popular within academic and industrial research institutions. 10 In previous work, 8 we have shown thatwith an good network connection -the Figure 1 MD server can be cloud-mounted, so that remotely located workers can occupy the same virtual space.…”

“…Over the past several years, our laboratory has been carrying out an interdisciplinary research program exploring interactive molecular dynamics (iMD) beyond standard 2d interfaces, designed to enable direct multisensory interaction with molecular simulations. [4][5][6][7][8][9] The recent emergence of robust and affordable virtual reality (VR) technologies has been a key enabler in these efforts, allowing us to develop a framework where scientists can manipulate rigorous real-time simulations of molecular systems, as shown in Figure 1 and Video 1 (vimeo.com/244670465). Figure 1 shows two optically tracked participants (each wearing a VR headmounted display (HMD) and holding in each hand wireless controllers which function as atomic 'tweezers') manipulating the real-time MD of a C60 molecule using interactive molecular dynamics in virtual reality (iMD-VR).…”

“…The observed accelerations become increasingly significant for molecular pathways and structural transitions whose conformational choreographies are intrinsically 3-dimensional. 8 For reactive systems where multiple competing reaction channels are available, we have also recently demonstrated that iMD-VR combined with 'on-the-fly' ab initio quantum chemistry offers an extremely efficient strategy for sampling reactive geometries along the minimum energy path (MEP) which can be used to train neural networks. 13 Figure 1: schematic of the setup for Narupa, our open-source multi-person iMD-VR framework, showing two participants using handheld wireless controllers to manipulate a real-time MD simulation of a C60 molecule.…”

The Exploration of Chemical Reaction Networks

“…They may invoke new hardware (see, for instance, Refs. 114,115,116,117) to intuitively experience these data in order to easily put focus on relevant aspects. Such hardand software also allows for manual interference and control of the otherwise automated exploration process.…”

VRmol: an Integrative Cloud-Based Virtual Reality System to Explore Macromolecular Structure

“…Areas such as engineering, education, arts, entertainment, and biomedical research have started to embrace VR for better visualization, modeling, and simulation [12,13]. Recently, VR systems have been used to facilitate molecular simulation by creating an interactive way to help determine the simulation strategy [14,15]. AltPDB protein-viewer provides an immersive VR environment for viewing and for collaborative studies on complex biological structures.…”