Author: OneAngstrom

If you’re a structural biologist or molecular modeler, chances are you’ve needed to visualize the conformational transition between two known protein states. Think of an important molecular mechanism—like a spike protein switching from a down to an up conformation. You…

A common frustration in molecular modeling is thinking you’ve completed an energy minimization — only to discover later that steric clashes or unrealistic geometries persist. To make the most of your GROMACS runs, it’s crucial to verify that the system…

Whether you’re docking ligands, analyzing interactions, or visualizing complex biomolecular systems, you’re likely using a variety of software tools. That means juggling multiple installs, figuring out compatibility issues, and jumping between separate interfaces. It’s time-consuming—especially when all you want to…

When setting up molecular dynamics simulations with periodic boundary conditions, one of the first choices you’ll face is the shape of the simulation box. For many molecular modelers, especially when working with approximately spherical molecules in solution (like proteins or…

When creating molecular presentations, static visuals can limit how well we convey structural dynamics or draw attention to key features. A common challenge for molecular modelers is how to illustrate subtle but important motions—like minor side-chain shifts or protein flexibility—without…

If you’ve ever tried to prepare multiple protein structures for simulations or drug screening, you already know the struggle: inconsistent files, missing atoms, alternate locations, unwanted water molecules and ligands. Doing this manually for each structure is both tedious and…

When working with complex molecular systems, selecting specific parts of a structure can quickly become tedious—especially when using traditional selection tools or manual inspection. Whether you’re preparing a simulation, cleaning a structure, or analyzing binding sites, precise and efficient selection…

Preparing and running molecular dynamics (MD) simulations locally often requires significant setup: installing packages, managing dependencies, compiling code, setting up GPUs and CPUs, and more. For many molecular modelers, this overhead is frustrating—especially when it takes more time to set…

When working on complex molecular models, one recurring challenge is managing the visual navigation across different regions of interest. Whether you’re alternating between atomic-scale details and global structure overviews, or inspecting interactions from different angles, jumping around in 3D space…