Author: OneAngstrom

Choosing the right initial conformations is a crucial step when preparing an umbrella sampling simulation with GROMACS. But what if there was a way to automate this process, visualize it in real time, and avoid manual frame selection from a…

In molecular modeling presentations, showing how atoms move from one place to another can be just as important as the final result. Whether you’re simulating docking, rearranging atoms manually, or animating structural changes, being able to capture these transitions can…

If you’ve ever found yourself watching a molecule slowly crawl towards equilibrium during a simulation, you’re not alone. Many molecular modelers start with raw or predicted structures and need to refine them before simulation. Geometry optimization is essential to remove…

When creating molecular animations, one recurring challenge is controlling when specific parts of a structure appear or disappear. Whether you’re preparing a presentation or clarifying complex structural changes for a publication, timing the visibility of selected molecules or components can…

Molecular modelers often need to communicate complex information through presentations. Whether you’re presenting at a conference, teaching a class, or preparing materials for collaborators, clarity and visual impact matter. But switching between different molecular scenes can be visually jarring. A…

One common challenge faced by molecular modelers is juggling multiple specialized tools—often standalone or with limited interoperability. Researchers may rely on external executables, web services, or legacy codebases without an easy way to incorporate these within an interactive modeling environment.…

When modeling protein interactions or designing molecular assemblies, understanding symmetry isn’t just aesthetic—it’s functional. Whether you’re reconstructing biological assemblies or exploring interface contacts, sometimes protein crystal structures only show part of the picture. That’s where symmetry mates come in. In…

When working with complex molecular systems, visual clarity can be the difference between insight and confusion. Yet, customizing molecular representations for each project can become time-consuming — especially when switching between different systems or presentation styles. This is where Visual…