Carbon nanotubes (CNTs) are a cornerstone of modern nanotechnology, with applications ranging from creating nanodevices and sensors to simulations of material properties or drug delivery systems. However, building accurate models of single-walled or multi-walled CNTs can be a time-consuming challenge…

Visualizing molecular models often comes with the challenge of conveying depth and focus effectively. For molecular modelers, it can sometimes be hard to highlight specific regions of interest when the entire model is displayed in full clarity. This is where…

Understanding the motion of molecules is a critical challenge for molecular modelers. Whether you’re analyzing ligand unbinding, conformation changes in large proteins, or tracking atomic displacement, visualization tools can offer invaluable insights. One such tool in the SAMSON molecular design…

Aligning protein sequences and structures is critical for molecular modelers aiming to understand functional similarities, evolutionary relationships, or to design novel molecules. However, the process can be time-consuming, especially when working with multiple chains or complex models. Fortunately, SAMSON’s Protein…

For researchers delving into protein conformational transitions, ensuring an accurate energy evaluation framework is critical. By aligning computational tools with the physical accuracy needed for molecular modeling, users can unlock more reliable results. This guide focuses on setting up energy…

Molecular modelers often face the challenge of tracking specific atoms or groups of atoms while they move during simulations. This process can feel cumbersome, especially when you need to consistently adjust your camera to keep up with the movements of…

Equilibration is a crucial step in molecular dynamics simulations, preparing your system for accurate and meaningful production runs. Two major phases of equilibration—constant volume (NVT) and constant pressure (NPT)—are widely utilized by molecular modelers. Yet, understanding their purposes and how…

Managing complex cloud computations in molecular modeling can be a daunting task. With a range of tools like AlphaFold, NVIDIA BioNeMo Services, and GROMACS at your disposal, keeping track of jobs, their results, and sharing insights efficiently is critical for…