Author: OneAngstrom

When exploring molecular motions, one common challenge for modelers is how to effectively capture and reuse intermediate or final conformations. Whether you’re inspecting how a ligand access channel opens, or evaluating different configurations of a flexible loop, you often find…

When setting up a molecular system for simulation in GROMACS, atom group selections—known as index groups—play an important role in defining regions for restraints, analysis, and advanced sampling techniques like umbrella sampling. While GROMACS automatically generates standard index groups (e.g.,…

Crafting clear, visual molecular presentations often requires more than just beautiful molecules — context is important. If you’ve ever found yourself wishing your molecular animations could flow more smoothly between informational slides or contextual backgrounds, SAMSON’s Set background animation can…

When preparing molecular presentations, one frequent challenge is communicating spatial relationships without overwhelming the viewer with motion or detail. If a complex appears out of nowhere or its components aren’t clearly transitioning into place, the educational value can be diminished.…

One of the most time-consuming and repetitive tasks in molecular modeling is scripting. Whether you want to automate structure manipulation, calculate properties, or build custom GUIs, scripting remains essential—but not always straightforward. For many users, the hurdles range from not…

Running molecular simulations can be incredibly resource-intensive. If you’re working with large systems, you might have faced the frustrating reality: your local machine simply can’t handle it. Or worse, trying to run the simulation slows your entire workflow down. 😓…

As molecular modelers know, working on a single molecule is rarely the whole story. Often, you’re juggling multiple molecular systems, simulations, reference structures, and so on—each of which can quickly flood your workspace and leave you feeling lost. Have you…