When working on complex molecular modeling projects, it’s not uncommon to have dozens of associated files: scripts, simulation results, plots, PDFs, datasets and perhaps even documentation. These extra files can quickly become difficult to manage, especially when transferring projects between…

One of the common challenges in molecular modeling is presenting protein-ligand interactions in a way that’s both visually engaging and scientifically meaningful. You might find yourself struggling to explain how a ligand fits into a binding site — or more…

As a molecular modeler, your workflow is often enhanced by specialized tools—automated docking assistants, visual analysis aids, simulation bridges, and more. But managing all these tools—knowing what’s installed, trying new features, dealing with limitations based on your current plan—can sometimes…

When running molecular dynamics simulations using GROMACS, one of the most common sources of frustration for modelers is incorrect or inconsistent input structure paths. These mistakes can easily interrupt workflows—especially during the equilibration steps, where continuity of structure and parameters…

When visualizing complex molecular models, clarity matters. Whether you are analyzing molecular surfaces, electrostatic potentials, or volumetric maps, color palettes are not just cosmetic—they’re critical tools that can make or break your interpretation of a structure. But selecting a good…

Finding reliable transition pathways between molecular conformations is a central task in computational chemistry and molecular modeling—whether for studying protein-ligand binding, enzymatic mechanisms, or conformational changes. The Nudged Elastic Band (NEB) method helps compute minimum energy paths (MEPs) between known…

If you’re a molecular modeler creating animations of complex molecular systems, you’ve likely run into this challenge: too many elements vying for attention in your scenes. Whether you’re showing conformational changes, reaction mechanisms, or protein-ligand interactions, excess visual clutter can…

When working with large protein complexes or viral capsids, understanding and leveraging their symmetry can significantly simplify your structural analysis and simulations. The Symmetry Detection extension in SAMSON automatically identifies possible symmetry groups in biological assemblies — but what happens…

If you’ve ever built coarse-grained (CG) models using the MARTINI force field and hit a frustrating error during topology generation, you’re not alone. One common cause? Non-unique residue and chain identifiers in systems that include multiple replicas. Fortunately, SAMSON makes…