Preparing for a ligand unbinding simulation in molecular modeling isn’t just about running an algorithm—it’s about setting up your system correctly so that the underlying method can do its job properly. One of the most important steps, often underestimated, is…

Anyone working with molecular dynamics knows that skipping proper charge neutralization of your system can cause serious artifacts during simulation. From incorrect electrostatics to instabilities during energy minimization, imbalanced systems can quietly sabotage your simulation before it even begins. Thankfully,…

When studying or designing molecules, inspecting and modifying atom-level properties is a common task. Whether you’re analyzing a structure, preparing it for simulation, or refining specific components, you need fast, intuitive access to molecular attributes. In SAMSON, the Inspector is…

Many molecular modelers have faced the challenge of reconstructing complete protein assemblies from asymmetric crystallographic units. Knowing how subunits interact symmetrically is key for understanding biological function, designing protein-based materials, and setting up molecular simulations. But replicating these symmetric arrangements…

One of the recurring challenges in molecular modeling is conveying motion—especially when creating educational or presentation materials about dynamic systems. Whether you’re illustrating a conformational transition, animating a simulation step, or presenting a mechanical movement inside a nanosystem, static images…

Temperature equilibration is a critical step in molecular simulations, especially when preparing systems to reflect physiological or experimental conditions. But if you’ve ever finished an NVT equilibration and noticed your system’s temperature still hasn’t stabilized at the target value—say, 300…

Creating convincing and understandable molecular presentations is often a challenge in computational modeling, especially when navigating complex structures or showing interactions in 3D. Static snapshots can only go so far. When you’re building scientific content—whether for a presentation, paper, or…

For molecular modelers, one recurring bottleneck is the lack of tools tailored exactly to their specific research needs. Whether it’s a custom simulation workflow, a unique visualization method, or a connector to an external computational tool, many scientists end up…

Creating molecular animations isn’t just about making visually engaging presentations. For researchers and designers in molecular science, it’s also a method to understand molecular interactions, spatial changes, and dynamics better. One frequent need during molecular modeling is to rotate a…

Controlling the visual introduction of molecular elements in a scene can make a major difference when presenting complex biomolecular data. Whether you’re making a video to share your results or building an interactive animation to highlight dynamic features of a…