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…

One of the most common frustrations for molecular modelers working with GROMACS is managing simulation parameters — especially when you want to adjust them frequently across different stages like energy minimization, NVT/NPT equilibration, or production molecular dynamics. Editing raw .mdp…

In molecular modeling, creating and analyzing complex architectures often starts with simple structural units. But when it comes to replicating molecular motifs—be it for nanotubes, molecular crystals, or repeating protein units—the process can be surprisingly tedious. If you’ve ever spent…

Collaborating with colleagues on molecular models can be challenging—especially when everyone is working across different platforms, needs specific extensions, or simply wants to provide feedback efficiently. Rather than relying on mailing large files back and forth, wouldn’t it be easier…

When analyzing molecular dynamics or preparing systems for enhanced sampling methods, it is often unnecessary—or even overwhelming—to export the entire atomic system. Molecular modelers frequently need to extract just specific atoms, like a ligand, or the residues lining a binding…