Preparing a molecular system for simulation often involves tedious geometry optimization. Many modelers still use steepest descent by default, even though it’s not always the most time-efficient approach, especially with larger systems or flexible molecules. If you’ve ever waited too…

Running molecular dynamics (MD) simulations may sound routine, but if you’ve ever seen unstable temperatures, crashing systems, or hours of lost compute time, you know how crucial getting equilibration right is. One often overlooked challenge is setting up the NVT…

For many molecular modelers, managing simulation workflows can become complex when switching between tools, environments, and machines. If you’re using GROMACS for molecular dynamics, you probably know the challenges involved with setting up simulations locally: installation and compilation, environment configuration,…

When working with complex molecular models and simulations, keeping everything organized is not a luxury—it’s a necessity. Whether you’re comparing different ligands, running multiple simulations, or collaborating with others, your data needs to be structured and accessible. This becomes trickier…

When preparing molecular presentations for collaborators, conferences, or students, one common challenge is how to make complex models appear naturally and clearly during animations. Too often, researchers resort to tweaking transparency or manually toggling visibility, which feels clunky and disrupts…

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…