When preparing a molecular presentation or animation, communicating docking—how molecules or fragments fit together—is often more than just showing two structures side by side. A static image of a docked complex may be clear to experienced modelers, but lacks the…

Molecular modelers often create presentations or simulations to clearly convey structural behaviors or dynamics. But sometimes, static images don’t quite capture everything — and even traditional rotations can feel flat. If you’re trying to draw attention to the spatial arrangement…

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…