Author: OneAngstrom

For molecular modelers juggling different tools, scripts, and data files, maintaining consistency, reproducibility, and portability across projects often becomes a challenge. Whether you’re working on protein-ligand docking, simulating reaction mechanisms, or analyzing trajectories, your work usually relies on custom scripts,…

When building or modifying molecular models, structure alignment may seem like a small step—but it can have a big impact. Misaligned atoms or molecules can lead to misleading visuals, unnecessary complexity during simulation, or trouble when exporting for publications or…

One of the key challenges in molecular modeling is ensuring that the geometry of your structure is physically realistic. Whether you’re assembling custom molecules or importing existing ones, minimizing structural strain is essential to avoid artificially high energies and forces.…

When analyzing molecular simulations, one of the recurring challenges is maintaining visual focus on a specific group of atoms during animation. Whether you’re tracking how a ligand moves inside a binding pocket or examining the structural flexibility of a protein…

If you've ever tried analyzing or running custom simulations in GROMACS, you've probably faced this: you need a specific group of atoms that isn’t covered by default index groups like Protein, Water, or Ion. Maybe you want to pull on…

If you’ve ever tried to build a carbon nanotube (CNT) manually in a molecular modeling software, you understand how tedious and error-prone it can be. Aligning rings, ensuring bond continuity, and managing overlapping atoms across copies is often a time-consuming…

When working on molecular analogs, one of the recurring pain points is figuring out where to introduce chemical modifications. These modifications need to be both chemically justified and relevant for exploring structure-activity relationships. Traditionally, this step requires careful visual inspection…

When visualizing molecular dynamics, it can be frustrating to lose sight of the area you’re most interested in. As the system evolves over time, atoms move, interactions change, and key regions may drift out of view—even if you had carefully…

One common challenge in molecular modeling is presenting how a ligand exits a binding pocket or how molecular components detach over time. Whether for a presentation, a publication, or to explain a concept to collaborators, animating these motions clearly can…