Author: OneAngstrom

Precisely positioning atoms, molecules, or custom structures in 3D space is a common task in molecular modeling. But anyone who has tried to reposition a molecule just right—whether to match experimental data, prepare for simulations, or maintain symmetry—knows it’s a…

A common challenge faced by molecular modelers — especially those preparing visuals for presentations or publications — is how to provide dynamic, smooth, and clear overviews of complex molecular structures. Static viewpoints often fail to capture the full spatial arrangement…

When modeling complex molecular systems, small adjustments to atomic properties — such as positions, element types, or custom user-defined attributes — can have a significant impact on stability, interactions, or simulation outcomes. For both beginners and experienced molecular designers, there’s…

Many molecular modelers working with GROMACS face a recurring challenge when preparing Umbrella Sampling simulations: extracting and organizing suitable initial conformations from a trajectory. While this may seem like a straightforward preprocessing step, doing it repeatedly — and correctly —…

Creating clear and compelling visualizations is one of the ongoing challenges in molecular modeling. Whether you’re preparing a molecular animation for a publication, a presentation, or for educational purposes, making it easier for your audience to follow structural transformations step-by-step…

One challenge that often arises in molecular modeling is how to effectively visualize complex nanosystems. Whether it’s a protein with hundreds of residues, or a molecular assembly involving several interacting species, understanding structure, function, and interactions becomes far easier when…

Visualizing complex molecular systems can be overwhelming, especially when trying to guide your audience’s attention or highlight dynamic elements in your presentation. Whether you’re preparing a research talk, teaching a class, or sharing insights with colleagues, animations can help make…

Creating engaging molecular animations is often essential when preparing scientific presentations, tutorials, or visualizations for molecular modeling projects. One recurring challenge is how to briefly yet clearly showcase the appearance and disappearance of molecular components—without overwhelming the viewer with effects…