When working with protein systems that include multiple replicas—either for crowding simulations, protein-protein interaction analysis, or other ensemble-based studies—generating coarse-grained (CG) models using the MARTINI force field can be challenging if your atoms, chains, or residues aren’t uniquely identified. One…

For many molecular modelers, the initial stages of a simulation can often be frustratingly slow. Before any meaningful analysis can begin, structures must be relaxed and optimized — and this step can become a bottleneck, especially for large or flexible…

When preparing to model protein transitions—such as conformational changes or reaction pathways—many molecular modelers face a frustrating issue: their interpolation algorithm fails to run, or produces unrealistic outputs. A frequent cause? Poorly prepared structures. If you’re using the As-Rigid-As-Possible (ARAP)…

When preparing molecular animations, it’s easy to focus on moving objects—proteins folding, ligands binding, conformational changes. But one often overlooked element is just as important: the virtual camera. If your perspective shifts unexpectedly between frames where no camera path has…

Molecular modeling projects often involve not just atoms and molecules, but hierarchical systems comprising proteins, ligands, solvents, ions, and other components. When working with such complex structures, users frequently struggle with clarity and navigation—especially when tracking changes or analyzing subcomponents.…

Preparing initial conformations for umbrella sampling can be a daunting process for molecular modelers, especially when dealing with long trajectories or custom paths. Selecting appropriate frames that are well-distributed along a reaction coordinate often requires scripting or external processing. Fortunately,…

When modeling complex molecular systems, getting started with a new software platform can be a challenge. You open the application, browse through menus, and might find yourself wondering: Where do I even begin? If you’ve recently installed SAMSON, the integrative…

One of the most overlooked obstacles in molecular modeling is having to work in a cluttered or rigid software interface. As your projects grow in complexity, productivity often takes a hit—not because of a lack of features, but because finding…