Author: OneAngstrom

One common frustration among molecular modelers is the time-consuming process of creating repetitive molecular structures, whether you’re stacking rings for a nanotube, arranging proteins in symmetric assemblies, or generating repeating motifs in nanomaterials. Precise alignment, duplication, and spatial control over…

Animating molecular scenes can help communicate complex ideas clearly—but presenting *everything* at once can create overwhelming visuals. This is a common challenge in molecular modeling, especially when presenting structures to students, collaborators, or during publication preparation. One useful technique to…

Sharing molecular models and research assets can quickly become complicated, especially across different operating systems, devices, or institutions. Have you ever found yourself emailing multiple files, trying to ensure your collaborator opens the correct version with the right parameters? Or…

When working on complex molecular systems, every click counts. Being able to access the right tool at the right moment without breaking your workflow makes a significant difference, especially during long simulation or modeling sessions. But for many molecular modelers,…

Designing carbon nanotubes (CNTs) manually can be a time-consuming and error-prone process for molecular modelers. SAMSON offers a solution that makes this task more visual, interactive, and reproducible by leveraging pattern creation tools. In this post, we’ll walk through how…

When modeling the flexibility of biomolecules, it’s common to analyze and generate alternative conformations that represent plausible intermediate or functional states. However, there’s often a challenge that arises: once you’ve arrived at an interesting conformation or motion through computational tools,…

One common challenge molecular modelers face when performing umbrella sampling simulations is the post-processing step: extracting the Potential of Mean Force (PMF) from a set of umbrella windows. Setting up the right environment, finding coordinated inputs from multiple simulations, and…

When studying molecular interactions, especially those involving binding or unbinding events, researchers often need access to atomic coordinates along well-defined paths. These trajectories are useful for reaction coordinate analysis, free energy calculations, or simply visualizing how a ligand travels through…

Crystalline materials in the real world often deviate from their ideal structures. Imperfections such as vacancies, substitutions, or interstitials—collectively known as defects—can dramatically influence material properties like conductivity, strength, and optical behavior. Simulating these defects realistically is essential for researchers…