Author: OneAngstrom

One challenge molecular modelers frequently face is ensuring that their system reaches a stable temperature before proceeding to production molecular dynamics simulations. This step — known as NVT Equilibration — is crucial to achieve meaningful simulation results. It sounds straightforward…

When dealing with large macromolecular assemblies in structural biology, it is common to encounter multiple plausible symmetries within a single structure. Whether you’re simulating a viral capsid or designing symmetric nanomaterials, selecting the correct symmetry group can streamline your workflow…

Understanding protein conformational changes can be both technically challenging and crucial for molecular modelers, especially in the context of drug design and protein-ligand interaction predictions. One such key conformational transformation is the opening movement of the SARS-CoV-2 spike protein—a process…

For molecular and materials modelers, reproducing realistic structural behaviors of crystals is essential for accurate simulations. One recurrent challenge is incorporating and visualizing point defects—like vacancies or substitutions—into periodic crystal models. These small changes can drastically affect the physical and…

When communicating molecular mechanisms, clarity matters. Whether for educational content, journal illustrations, or presentations, effectively showing what appears—and more importantly, what disappears—can help molecular modelers deliver their message without visual noise. If you’ve ever needed to hide specific molecules or…

When modeling molecules, accurate and up-to-date measurements are critical. Whether you’re working on distances, angles, or torsions, being able to capture and revisit your measurements — and share them clearly with colleagues — can save time and reduce ambiguity in…

Whether you’re running simulations, training machine learning models on molecular data, or preparing a paper, molecular modeling projects often involve more than just molecules. You may need Python scripts, research images, datasets, PDFs, and more. Managing all of these scattered…

Creating clean, expressive images of molecular systems often involves a lot of manual adjustments—choosing representations, applying colors, tweaking rendering settings. While this flexibility is essential, it can become tedious when you need consistent visuals or just want to focus on…