When creating animations of molecular systems, clarity and precision play a crucial role in effectively communicating scientific insights. Have you ever tried to zoom into a specific molecular region, only to realize that adjusting camera positions changed your rendering setup…

If you’ve ever tried preparing more than a handful of PDB files for simulations or docking, you know the pain: cleaning structures one by one, checking for missing atoms, removing waters, renaming residues… It’s a tedious, time-consuming task—and one that’s…

When comparing protein structures, it’s common to find that overall alignment doesn’t always capture biologically relevant differences—or similarities. Sometimes you’re only interested in a specific region, like the active site or an alpha-helix that’s been mutated. Trying to force a…

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…