Author: OneAngstrom

Running molecular dynamics (MD) simulations with GROMACS usually requires not just scientific knowledge, but also technical setup: compiling software, configuring command-line commands, managing dependencies, and securing enough computing resources. This can be a challenge — especially when you just want…

Working with molecular systems often goes beyond analyzing structures on screen. Whether it’s for 3D printing, rendering in external visualization software, or integrating models into larger scenes, exportable 3D geometry is a must for many molecular modelers, educators, and researchers.…

When working with molecular simulations or modeling, one of the most common visualization challenges involves communicating structural dynamics effectively. There are times when entire groups of atoms, residues, or molecules should fade in and out of view to direct attention,…

When you’re trying to build a clear and engaging molecular animation, timing is everything. Whether preparing a conference presentation, an educational video, or just showing an interaction mechanism to colleagues, how and when a molecule appears on screen can significantly…

In polymer design, starting with the right building blocks can make all the difference. If you’re creating custom polymers in SAMSON, one of the first steps is often registering monomers—your fundamental repeat units. But many modelers don’t realize just how…

One of the recurring challenges in molecular modeling is presenting molecular dynamics in a compelling and intuitive way. If you’ve ever tried to create a smooth animation of a ligand moving through a binding pocket or a protein folding over…

One of the recurring challenges faced by molecular modelers is identifying and triggering functionally relevant conformational changes in biomolecules—such as the opening of a binding pocket—without resorting to computationally intensive simulations. Normal mode analysis (NMA) offers a far more efficient…

Molecular modelers working with large structural datasets often face the challenge of visually demonstrating how different biomolecules interact. Whether you’re presenting receptor-ligand binding events, assembling complex biomolecular systems, or simply trying to communicate structural hypotheses, an animation can go a…

When building, comparing, or preparing molecular models for visualization or simulation, one common issue faced by modelers is the orientation and relative positioning of molecular structures. Misaligned molecules can complicate analysis, generate cluttered views, and obstruct accurate measurements or transformations.…