Author: OneAngstrom

When working with molecular systems over time—such as when visualizing molecular dynamics simulations—one of the most common frustrations for researchers is losing track of what they’re supposed to be watching. The molecule, or a part of it, moves through space,…

Molecular modelers and simulation scientists often run into the same frustrating bottleneck: long simulation wait times and resource limits on their local machines. Whether it’s for NVT/NPT equilibration or production molecular dynamics runs, the hardware constraint often becomes the biggest…

One of the most common challenges molecular modelers face is knowing when their system is ready for production simulations. After all the time spent preparing molecular systems and minimizing their energy, how can you be confident that your model’s pressure…

When presenting molecular models, the ability to manage visibility dynamically can make a big difference. Whether you’re crafting a video for a presentation, generating educational content, or highlighting specific structural features during a simulation, controlling how objects fade in and…

When setting up a molecular simulation in GROMACS, an important yet often overlooked decision is the shape of the unit cell used to apply periodic boundary conditions. Many researchers default to cubes simply because they’re familiar, but this choice can…

Whether you’re visualizing protein docking, showcasing a molecular simulation, or animating custom atom movements, path recording can drastically enhance molecular presentations. But what happens once the movement is complete? Many molecular modelers face the challenge of capturing and exporting atom…

When building molecular presentations, clarity often depends on more than just content—it depends on pacing and focus. One challenge modelers frequently encounter is how to transition parts of a molecule out of view without causing visual clutter or confusion. Fading…

One of the most frequent sources of friction in molecular modeling happens when you’re deep into a structure refinement or simulation, only to find you need to remove or add a few atoms. For many tools, this means stopping the…