Author: OneAngstrom

When setting up molecular dynamics simulations, small frustrations can have a big impact—especially when it comes to defining groups of atoms for analysis or pulling simulations. By default, GROMACS defines standard index groups such as proteins, water, and ions. But…

One of the most common and time-consuming tasks in molecular modeling is generating accurate 3D molecular structures from SMILES (Simplified Molecular Input Line Entry System) strings. Whether you’re preparing datasets for simulations, virtual screening, or property prediction, the process often…

Creating clear, communicative visualizations of molecular systems is often a crucial—but time-consuming—part of working in molecular modeling. Whether you’re demoing an interaction site to collaborators or preparing a presentation for a larger audience, the camera movement in your animations can…

When exploring complex molecular systems, visuals often speak louder than numbers. Whether you’re showcasing structural transitions, highlighting reaction pathways, or simply presenting a model to colleagues, how you move the camera during a molecular animation can significantly affect how your…

When presenting large molecular assemblies, it’s easy for your audience to get lost in the complexity. Whether you’re showcasing a protein-ligand complex, a multi-domain macromolecule, or a supramolecular structure, your viewers may struggle to understand how each part fits into…

In molecular modeling, clarity is often more valuable than completeness. When preparing scientific presentations or instructional materials using complex biomolecular structures, showing every atom at once can be overwhelming—and, more importantly, unnecessary. Sometimes, emphasizing certain atoms and hiding others can…

Tracking dynamic molecular behavior during a simulation is a challenge many molecular modelers face. When atoms move across a system, the default camera often stays put—forcing users to constantly adjust their view just to follow what matters. This can interrupt…

When working with large biological assemblies—whether viral capsids, multimeric proteins, or supramolecular complexes—understanding the underlying symmetry is more than a theoretical curiosity. It can unlock practical efficiencies in molecular modeling, validation, and simulation setup. But what happens when a structure…

When creating molecular visuals, clarity and realism are key. Whether you’re preparing a presentation, a scientific publication, or an explainer for a broader audience, the way your molecules look can significantly affect how they are perceived and understood. A flat,…

One common challenge in molecular modeling is aligning molecular fragments precisely — especially when assembling large systems. Misoriented fragments can lead to structural clashes and inaccurate simulations. If you’ve ever found yourself frustrated by overlapping atoms or spent too much…