LNB-MDT: An Integrated Python Toolkit for Preparing and Analyzing Lipid Nanobubble Simulations

Molecular dynamics (MD) simulations have become a powerful tool for studying the physical mechanisms of lipid nanobubbles. However, progress in this area has been limited by a lack of specialized tools designed for these systems. To fill this gap, we introduce LNB-MDT (lipid nanobubble-molecular dynamics toolkit), a powerful, fast, and user-friendly software designed to streamline the entire simulation workflow. It supports the generation of presimulation files, performs trajectory analysis, creates 2D plots, and allows for interactive visualization of results with VMD. By offering both a GUI and script-based workflow, LNB-MDT significantly reduces the manual effort and time required for simulation setup and postanalysis. Software is available on GitHub at https://github.com/xinyuren-bio/LNB-MDT.