Author: OneAngstrom

When working on molecular models in SAMSON, you may have noticed that only one editor can be active at any time. This might appear limiting at first glance, especially to new users. Yet, it’s actually a design choice that simplifies…

One of the frequent challenges in molecular modeling is generating clean, structured data for reaction coordinate analysis. Whether you’re conducting free energy calculations or preparing enhanced sampling inputs, extracting the atomic positions of a ligand along a transition path is…

Running molecular dynamics simulations on a single system is already a complex task, but what happens when you want to simulate a whole set of conformations? For example, you might have generated different poses from a docking study, explored normal…

For many molecular modelers, scripting is both a blessing and a hurdle. Python unleashes the full potential of advanced modeling workflows, but coding from scratch—especially for simple, repetitive tasks—can slow down everyday work. Wouldn’t it be great to just describe…

Accurately visualizing molecular and nanoscale systems can be a challenge, especially when trying to distinguish between different chains, residues or fields in a dense model. This is a common pain point for molecular modelers who need to both inspect and…

When working with molecular simulations, it’s common to want to track how specific parts of a system—like a ligand—move along a predefined path. This is especially important for tasks like reaction coordinate generation or free energy calculations. However, extracting only…

Selecting the right input files when moving from one molecular dynamics step to another can feel repetitive and error-prone. If you’ve spent time scrolling through directories, trying to remember the difference between several similar GRO files, you’re not alone. That’s…

Animations can play a crucial role in molecular design when you’re trying to communicate complex behaviors or structural transitions. But if you’ve ever found yourself trying to make parts of your molecular model appear at the right moment in an…