If you’ve ever performed Potential of Mean Force (PMF) calculations using GROMACS, you probably remember the long list of scripts and careful file organization required to properly apply the Weighted Histogram Analysis Method (WHAM). Piecing together dozens of outputs from…

When working on molecular modeling projects, keeping track of all relevant files—input data, Python scripts, images, papers, notes—can become challenging. Files are often scattered across folders or hard drives, shared by email, or lost in different versions. Wouldn’t it be…

Defects in crystals are not just imperfections—they are the key to understanding and designing materials with advanced properties. If you’re working with molecular models and wondering how to explore atomic-scale imperfections in diamond—one of the most iconic crystals—this post offers…

One common frustration among molecular modelers is managing all the files that come with a single project: molecular structures, datasets, reference PDFs, scripts, and more. Moving your project to another computer or sharing it with collaborators can quickly become messy…

If you’ve ever struggled to create smooth, meaningful camera motion around your molecular system for a presentation or video, you’re not alone. Researchers and educators often need to show complex structures from different angles, but manual camera work can be…

When working with molecular systems, tracking precise physical quantities such as bond lengths and angles is essential—especially during conformational changes, docking, or real-time energy minimization. But manually updating those values as atoms move? That’s time-consuming and difficult to follow visually.…

Running complex simulations like protein folding predictions with AlphaFold or molecular dynamics in GROMACS is increasingly accessible thanks to cloud computing. Yet, managing cloud-based jobs efficiently is still a challenge for many molecular modelers: Where did that protein structure prediction…

Molecular modelers often navigate through complex structures, switching back and forth between ligands, receptors, solvent regions, or specific structural motifs. This back-and-forth process can slow down exploration, analysis, and design workflows. SAMSON offers a feature called Quick Groups that addresses…