Author: OneAngstrom

Molecular dynamics simulations often require finer control over system components for applying specific actions like restraints, pulling, or analysis. In GROMACS, this is handled through index groups. While GROMACS automatically creates standard groups (like protein, water, ions), there are many…

When you’re exploring structure-activity relationships or looking to modify chemical structures to improve binding affinity, identifying reactive or modifiable sites is often one of the first steps. But this task—searching and highlighting specific substructures—can be repetitive and error-prone, especially when…

Visualizing complex molecular systems requires precision, clarity, and often, multiple points of view. If you’ve ever struggled with navigating different scenes or perspectives within the same molecular model, you’re not alone. Many researchers and modelers face the challenge of switching…

One of the most frequent and frustrating roadblocks in molecular dynamics simulations is getting the input right. Whether you’re a graduate student running your first simulation or a seasoned researcher working on a complex biomolecular system, mistakes in selecting input…

Running molecular dynamics (MD) simulations can often be a resource-intensive task. For molecular modelers working on large systems or simulations that need to run for extended periods of time, local computational resources quickly become a bottleneck. But what if launching…

Molecular modelers frequently prepare visual presentations to communicate structural or dynamic insights. But one common challenge when moving between slides or animation segments is preserving visual coherence and engagement—especially when transitioning between different molecular contexts, experimental conditions, or conceptual stages.…

When working with complex molecular systems, one of the most common frustrations is switching between different parts of your model—ligands, receptors, water molecules, ions—especially when selections involve many atoms or residues. Navigating large molecular structures efficiently is essential, especially during…

When presenting a molecular model—whether it’s for a publication, class, or collaboration—clarity matters. Sometimes, even the most detailed model can feel static and hard to read. This is especially true when discussing structural differences, ligand binding, or shape complementarity. Molecular…