SIRAH Tools GUI: An Intuitive Interface for the Analysis of CG Simulations

Abstract

The increasing complexity and scale of molecular systems pose significant challenges for all-atom molecular dynamics (MD) simulations, leading to the growing adoption of coarse-grained (CG) models. However, visualization and analysis of CG simulations remain challenging, particularly for new users, due to limitations in existing tools designed primarily for atomic-level representations. To address these challenges, we present SIRAH Tools GUI, a graphical user interface that integrates with VMD and extends the capabilities of our previous package, SIRAH Tools, for analyzing molecular simulations performed with the SIRAH force field. SIRAH Tools GUI features an intuitive interface with specialized tabs that encompass several analyses to extract data from CG trajectories. In this work, we introduce the functionalities of SIRAH Tools GUI through two case studies employing SIRAH MD simulations of a nucleosome core particle (NCP) and a membrane bilayer. By providing a user-friendly platform, SIRAH Tools GUI significantly facilitates CG simulation analysis while expanding the analytical capabilities available to the MD community. The source code for SIRAH Tools GUI is freely available at https://github.com/SIRAHFF/SIRAH-Tools-GUI.