Author: OneAngstrom

One of the most common challenges in molecular modeling is effectively communicating complex molecular structures and interactions. Whether you’re collaborating with a cross-disciplinary team, preparing a presentation, or simply trying to understand your own simulation results, clear and customizable visualizations…

If you’ve ever run a molecular model through a simulation without optimizing its geometry first, you probably know the risks: instability, unrealistic forces, or alignment issues that skew downstream results. Geometry optimization is a fundamental step in molecular modeling—but it’s…

When preparing coarse-grained (CG) molecular systems for simulations in GROMACS, one often focuses heavily on force fields, solvation, and the periodic box—but there’s a crucial final step before minimization that can make or break a simulation: adding ions. 🧪 Adding…

When modeling biomolecular systems, it’s common to compute pathways for ligand binding or unbinding. Whether you’re performing free energy profiling, setting up enhanced sampling simulations, or simply visualizing molecular movement, you often only need the atomic coordinates of a ligand—not…

When visualizing molecular models, color is more than aesthetic—it’s a communication tool. Whether you’re highlighting atom types, representing molecular groups, or differentiating between molecular chains, selecting the right color palette helps make your models intuitive and easier to interpret. But…

Visualizing molecular measurements—like distances, angles, or torsions—plays a vital role when modeling or analyzing molecular structures. Often, you’re examining multiple interactions simultaneously, especially when comparing conformers or tracking structural changes during simulations. But how do you avoid clutter while maintaining…

When presenting molecular models to an audience—whether it’s in a classroom, during a group meeting, or at a conference—how atoms and structures appear can have a surprisingly big impact on clarity. Abrupt visual transitions are jarring, and make it harder…

Setting up a molecular dynamics simulation that involves a reaction coordinate—such as a ligand unbinding pathway—can be time-consuming. One frequently reported pain by molecular modelers is the extraction of atomic coordinates along a pre-defined path for use in free energy…