Setting up a production molecular dynamics (MD) simulation isn’t just about parameters and resources — it often begins with a critical, deceptively simple question: Which input file do I use? If you’ve ever felt unsure about which structure to load…

If you’ve ever created a scientific animation only to realize your audience isn’t keeping up, you’re not alone. Molecular modelers and scientific presenters know that timing is everything. Whether you’re explaining a complex protein interaction or zooming in on a…

Molecular modelers often face a common challenge: integrating their domain-specific algorithms into user-friendly visual platforms that others can easily access and use. Whether it’s a new force field, simulation algorithm, or structural editor, turning a script or prototype into a…

Have you ever looked at your molecular models and felt like something was missing? Even with high-resolution molecular visualizations, it can be difficult to perceive depth clearly—especially when working with intricate structures. This lack of visual depth may make it…

When creating molecular animations, especially for reports or presentations, it’s common to want to move the camera to show structures from different angles without disorienting the viewer. A frequent challenge is how to pan the view vertically while keeping the…

When launching molecular simulations, especially for systems with flexible conformations, many researchers face a common bottleneck: how to prepare multiple initial states for batch simulations efficiently without duplication of effort. Whether the goal is to explore conformational diversity or sample…

Working on molecular modeling projects often involves more than just simulations and structures — it’s also about sharing, collaborating, and managing contributions across institutions and teams. Scientists, educators, and developers frequently hit roadblocks when trying to organize access to shared…

One common challenge in molecular modeling is organizing all the supporting files around a project. Not just the molecular structures, but also your Python scripts, graphs, notebooks, papers, and other reference materials. Keeping these files in one place—especially when switching…

Watching a molecular trajectory unfold can be both a critical part of your work and an informative way to communicate dynamic processes. But setting up such animations can often be tedious — especially when trying to synchronize structural transitions or…

When working with molecular simulations, visualizing motion is essential to understand molecular mechanisms, reaction pathways, or conformational changes. Molecular modelers often run simulations that yield extensive trajectories—collections of molecular conformations over time. But how do you convert raw trajectory data…