Visualizing molecular trajectories or conformational transitions is a core need in molecular modeling. Whether you’re tracking a ligand moving through a tunnel, observing backbone flexibility, or reviewing snapshots of a molecular dynamics simulation, being able to animate the path clearly…

When running GROMACS simulations, defining custom selection groups—also known as index groups—can be essential. These groups allow for targeted analysis, pulling configurations, and interaction computations. However, editing GROMACS .ndx files manually is tedious and error-prone, especially when dealing with large…

Designing molecular animations often involves illustrating dynamic structural changes, such as docking and undocking interactions between molecules. When preparing presentations, tutorials, or simulations for teams or publications, manually separating complex molecular interactions frame-by-frame can become repetitive and imprecise. SAMSON’s Undock…

Running molecular dynamics (MD) simulations with GROMACS can be computationally heavy, especially when preparing longer trajectories or simulating large biomolecular systems. Local hardware often becomes a bottleneck — not everyone has access to clusters or high-end GPUs, and even test…

Anyone who has prepared protein systems for molecular dynamics (MD) simulations knows how tricky it can be to clean up your structure without deleting something important. A common pain point: selectively removing crystal waters that are outside of the active…

One of the most common frustrations when visualizing molecular systems is the repetitive and time-consuming process of manually applying visual styles and color schemes. Whether you’re preparing figures for a presentation, teaching structural biology, or analyzing large biomolecular complexes, you’ve…

When working with large molecular systems, one of the most time-consuming tasks for molecular modelers is selecting specific atoms or groups of atoms based on precise geometric or chemical criteria. Manual selections can quickly become unmanageable, especially in dense structures…

When refining a protein model—whether from homology modeling, docking, or simulation—chances are you’ll encounter a few residues out of place. These are often exposed on a Ramachandran plot as positions falling into disallowed regions, indicating strained backbone conformations. How can…

As a molecular modeler, your workflow often depends on integrating the right tools at the right time. SAMSON helps streamline activity through its modular approach using SAMSON Extensions. Learning how to add, try, subscribe to, or remove these extensions can…