Author: OneAngstrom

Visualizing molecular systems often feels like a balancing act—switching representations, adjusting colors, highlighting key atoms—before you’ve even started analyzing. For researchers and students dealing with increasingly large biomolecular structures, the time spent configuring these visualizations manually can quickly add up.…

When preparing molecular presentations, one common challenge researchers face is making specific moments stand out. Whether you’re highlighting a protein-ligand interaction or illustrating a crucial conformational change, these scientific storytelling moments need time to register with your audience. Animations move…

When creating molecular animations, many researchers and educators face a common challenge: controlling the visibility of individual atoms without relying on transparency settings, which can lead to cluttered visuals and overlapping structures. Whether you’re preparing a molecular dynamics presentation or…

As a molecular modeler, you might have encountered the following situation: you’re trying to reproduce simulations from a paper, or continue a project started on another machine. But your local GROMACS version doesn’t quite match the one previously used. Differences…

If you’ve ever launched molecular simulations in the cloud—such as protein structure predictions or molecular dynamics simulations—you know that managing these jobs efficiently can quickly become a challenge. You might lose track of which simulations are running, which ones have…

Many molecular modelers spend significant time navigating menus, remembering shortcuts, and writing scripts to perform everyday tasks: visualizing surfaces, modifying representations, or selecting atom groups. While flexibility is appreciated, the friction can add up—especially when switching between modeling tools and…

Switching between different versions of GROMACS isn’t just a technical preference—it’s often a necessity for molecular modelers. Whether for ensuring reproducibility, taking advantage of specific performance improvements, or simply using a cluster’s precompiled GROMACS, being able to control the version…

One of the subtle yet recurring challenges in preparing biomolecular systems for simulations is the question of what to do with crystal waters. These water molecules, often captured in PDB structures, can be either essential to the biological function or…

Preparing molecular animations for presentations often raises the question: how can I make certain components of a model appear and then vanish in sync with narration or key visual moments? Whether you’re explaining reactive sites in a protein or walking…

One of the key challenges in molecular modeling is communicating complex molecular motions clearly. Whether you’re modeling ligand binding, protein folding, or molecular assembly, it’s often difficult to visualize trajectories in a way that’s intuitive to others — or even…