One of the crucial but often overlooked steps in molecular simulations with GROMACS is deciding which water molecules to include and which to remove from your system. While it might be tempting to wipe them all and let GROMACS solvate…

One common pain point in molecular modeling is the need to automate repetitive or complex tasks—whether it’s transforming molecular structures, computing properties, or creating simple graphical interfaces for custom workflows. Writing Python scripts can make this process much easier, but…

Creating high-quality molecular visualizations can often feel like a time-consuming and repetitive process. Whether you’re prepping figures for a publication or crafting an animation for a presentation, tweaking rendering settings and applying consistent visuals across structures can quickly become a…

When preparing molecular presentations or educational materials, you’ll likely encounter moments when you want specific components of your model to gradually disappear—either to focus attention elsewhere or to visually communicate molecular dynamics. The Disappear animation in SAMSON solves this by…

Designing synthetic polymers and molecular scaffolds often involves repetitive molecular units that don’t exist in standard libraries. In such cases, molecular modelers are faced with an important question: How can I register a new, custom monomer and reuse it efficiently…

When working with molecular models, one recurring challenge is efficiently selecting specific atoms based on their positions or properties. Whether slicing a geometry, isolating substructures, or modifying subsets of atoms, manual atom selection is often tedious and error-prone—especially in larger…

Studying molecular transitions—the steps a molecule takes between two states—is key to understanding biological processes, designing drugs, and optimizing materials. Transition path sampling and optimization methods, like the Parallel Nudged Elastic Band (P-NEB) approach in SAMSON, help researchers explore these…

Transferring data between different tools and formats is one of the most common pain points in molecular modeling workflows. Whether you’re importing a complex structure from a crystallography database, exporting atomic trajectories after a long simulation, or working with DNA…