Author: OneAngstrom

Sharing a molecular model with collaborators often comes with a familiar headache: supplementary scripts are in a separate folder, dependent files are missing, and paths break across systems. As molecular modelers, we frequently juggle multiple files—models, data, Python scripts, results—and…

When you’re working on a molecular model, getting the science right is step one. But communicating it effectively—especially visually—is just as important. A common challenge molecular modelers face is that 3D structures often appear flat and hard to interpret due…

Managing index groups is a regular task for anyone working with molecular dynamics in GROMACS. If you’ve ever had to manually modify an index.ndx file just to track specific atoms or residues across simulations, you know how time-consuming and error-prone…

Many molecular modelers rely on GROMACS for molecular dynamics simulations, and SAMSON’s GROMACS Wizard provides a user-friendly way to perform these simulations locally or in the cloud. But did you know that SAMSON also allows you to use your own…

When analyzing molecular structures, color is more than just a visual aid—it’s a key part of how we identify, compare, and communicate structural properties. Whether highlighting hydrophobic residues in a protein or displaying thermal motion via B-factors, effective color mapping…

When analyzing large macromolecular assemblies, symmetry can be a powerful tool to simplify structure, improve visualizations, and reduce computational cost. However, many biological systems allow for multiple plausible symmetry descriptions. So how do you decide which symmetry group to use?…

When presenting molecular models, clarity is everything. Whether you are communicating with collaborators, students, or writing a publication, the timing and visibility of different components in a scene can dramatically affect understanding. That’s where the “Shown” animation effect from the…

Defects in crystals are a central topic when studying material properties, especially in semiconductors, ionic conductors, and many catalysts. While perfect crystals might be ideal starting models, real materials almost always include imperfections like vacancies and substitutions. But simulating these…

Molecular modelers often spend significant time analyzing the pathways between two conformations of a molecule: from binding and folding events to transitions between states discovered via simulations. While forward trajectories are the norm, playing them in reverse can offer unique…