Web-based applications for automated generation of functionalized graphene and carbon nanotube for molecular dynamics simulations and automated three-dimensional analysis of ion flow through nanopores

Abstract

Functionalized graphene and carbon nanotubes (CNTs) are widely recognized for their exceptional physical properties, which make them highly suitable for various applications. Although molecular dynamics (MD) simulations are essential for investigating the atomic-level interactions and transport phenomena in functionalized graphene and CNT systems, setting up these simulations remains complex and time-consuming. To streamline this process, we have developed a novel web application that automates the generation of MD simulation setups of functionalized graphene and CNT systems compatible with AMBER force fields and the Gromacs software. Key features include the creation of nanopores, functionalization with hydrogen, hydroxyl, and/or carboxylate groups, and the application of periodic boundary conditions to effectively simulate infinite structures. To facilitate the MD analysis of transport phenomena through nanopores, our web application offers an automated analysis tool that generates and visualizes three-dimensional local flux fields from MD trajectories. Overall, our web applications significantly enhance the accessibility and efficiency of MD simulations of functionalized graphene systems, particularly for nanopore applications. Our web applications are freely available at https://yoo.skku.edu/apps.