When setting up molecular dynamics (MD) simulations using coarse-grained (CG) models, one recurring issue modelers face is improper solvation: water molecules overlapping with solute atoms or each other. This can happen easily when using default settings that are not tailored…

When creating molecular animations, one frequent challenge is controlling when specific components appear during your presentation. Whether you’re highlighting a ligand binding to a protein or the formation of a molecular assembly, the timing of element visibility is essential to…

When working with proteins, even a single poorly-placed residue can make the difference between a stable simulation and a failed model. For molecular modelers, quickly identifying and fixing conformational outliers is more than just helpful – it’s essential. But in…

Molecular modelers often struggle with one recurring challenge: visual clarity. Whether you’re preparing figures for a publication, a presentation, or simply trying to interpret complex systems more clearly, the way molecules are rendered can have a huge impact on your…

Visualizing molecular transitions is a fundamental part of molecular modeling. Whether you’re tracking a conformational change, reviewing a reaction pathway, or simply cycling between states, being able to loop animations smoothly—and sometimes in reverse—can make a big difference. In SAMSON,…

When modeling molecular interactions, demonstrating a ligand binding to a receptor is essential. But what about the reverse process? Undocking animations are just as important, especially when preparing presentations, educational content, or investigating energy release during the unbinding stage. In…

Whether you’re analyzing protein-ligand interactions or checking geometry optimization results, measuring precise atomic distances is a routine—but vital—task in molecular modeling. Yet, for many users, keeping track of those measurements or quickly accessing the most relevant ones can be frustrating…

One of the recurring challenges in modeling protein conformational transitions is obtaining realistic motion pathways without having to simulate every single atom in the structure. Experienced molecular modelers know that involving too many atoms can be computationally expensive, while ignoring…