Molecular Visualization of High Performance Computing Simulations with VTX

Molecular Dynamics Simulations (MD) are widely used in molecular and structural biology and drug discovery to study the structure, properties and dynamics of small and macromolecules.

The size of the simulated systems (up to a billion atoms) and the length of the simulations (from microseconds in 2010 to milliseconds in 2021 in million atom scenes) have dramatically increased following the recent advances in computing hardware (GPU clusters) and storage.

Additionally, with the recent advances in Cryo Electron Microscopy and the arising of AlphaFold many new models of macromolecular structures and complexes are now available for molecular simulation.

Due to their more and more extreme size, the storage, analysis and visualization of the resulting data is becoming problematic: 1. Technically for a usable and efficient processing of the data and 2. Environmentally in terms of storage, bandwith and power comsumption.

Within the ERC ViDOCK project, we created a highly usable, free and open-source high-performance molecular visualization software called VTX.

VTX is optimized to handle the biggest molecular structures and trajectories notably by including cutting-edge molecular graphics with a high performance graphics engine coupled with a video game based minimalistic task-oriented GUI to maximize its usability.The goal of the VTX-HPC project is to improve the performance, usability and sustainability of VTX for the visualization of the High Performance Computing Molecular Dynamics Simulations big data by developing and implementing 1. a highly compact molecular structure and trajectories file format optimized for streaming for increased performances and reduced environmental load. 2. a meshless version of the widely used Solvent Excluded Surface representation for scalability purposes and real-time ray tracing in the rendering engines and 3.

Adapted manipulation and controls for the generation of illustrations and movies of massive dynamic molecular scenes.