Author: OneAngstrom

Visualizing motion in molecular systems can be hard, especially when you’re preparing presentations or teaching materials. Rotating molecular groups helps with spatial perception, symmetry analysis, and drawing attention to specific structural features. But creating smooth and precise rotational animations often…

Protein modeling often runs into a simple yet nagging issue: some residues don’t conform to expected backbone geometries. These structural outliers can affect downstream simulations or reduce the quality of homology models—especially when small deviations escape plain sight. Fortunately, there’s…

For molecular modelers working with complex systems in GROMACS, organization and reproducibility can become a challenge—especially when the same custom selections need to be defined across multiple stages or subprojects. Whether you are preparing simulations or running batch workflows, manually…

When designing polymers for simulations or material property prediction, it’s often essential to define precise patterns of monomers: not just their identity but the way they connect. This is particularly true if you’re modeling complex materials, conjugated compounds, or drug-polymer…

If you’ve ever presented molecular models and found the transitions between slides or states too abrupt, you’re not alone. A typical challenge in molecular modeling presentations is maintaining visual continuity. This is especially true when you’re demonstrating conformational changes, structural…

When working with large biomolecular structures, one of the most frequent—and often frustrating—tasks is precisely selecting specific residues or residue ranges. Whether you’re defining regions for simulation, modifying part of a protein, or analyzing interactions, doing this in the 3D…

Running molecular dynamics simulations on multiple conformations of the same molecule—whether to sample different initial states or to conduct techniques like Umbrella Sampling—can be necessary but very repetitive. If you’ve ever found yourself manually preparing each structure, adjusting box sizes,…