When analyzing molecular mechanisms, understanding how a system transitions between two conformations is often just as important as knowing the endpoint structures. But finding realistic, physically meaningful paths between such conformations can be a significant challenge. Molecular modelers face this…

Studying protein conformational changes often means diving into large simulation datasets and sorting through movement trajectories, energy variations, and transition intermediates. For many molecular modelers, a common pain point arises once a path between two protein conformations has been computed:…

When presenting molecular systems to colleagues, students, or collaborators, one of the most common goals is to clearly highlight a region of interest or to steer attention gradually from one part of the system to another. Yet, many molecular modelers…

Many molecular modelers face the same recurring issue: their toolkits almost—but not quite—do everything they need. Maybe it’s a specific simulation engine, a niche file importer, or simply a preferred workflow that doesn’t easily integrate with existing interfaces. When this…

If you’ve spent time setting up molecular dynamics simulations, you know how quickly your workflow can get tangled—especially when navigating multiple input files and output directories. One common friction point in this process is figuring out the correct input structure…

Parsing through molecular systems to select the atoms or residues you need can often feel like finding a needle in a haystack. Whether you’re isolating ligands, identifying backbone atoms, or filtering for residues near an active site, manually selecting nodes…

When creating animations of molecular systems, visual clarity is important not just for aesthetics, but also for scientific communication. One common issue faced by many modelers is the abrupt appearance of structures between frames, especially when transitioning between different stages…

Running a molecular dynamics (MD) production simulation can be a major milestone in the modeling of biomolecular systems. But this important step often becomes a source of confusion, especially when it comes to choosing the right input files and making…