Author: OneAngstrom

Working with complex molecular models often leads to cluttered workspaces full of multiple molecules, scripts, visualizations, and data files. Over time, it becomes harder to keep track of what’s relevant, what belongs together, and how to perform operations on multiple…

When working on complex molecular structures, selecting the right tool for the task is crucial. In SAMSON, one of the key concepts that helps streamline molecular design workflows is the use of Editors. Editors in SAMSON are interactive tools designed…

Creating dynamic molecular presentations can often feel overwhelming—especially for researchers who want to communicate complex transitions in a molecule over time. Whether you’re teaching, presenting a concept, or showcasing a simulation result, having the ability to animate atom positions clearly…

When preparing protein structures for simulation or modeling, one frequent challenge is identifying residues that adopt energetically unfavorable conformations. Even a few outliers in backbone dihedral angles can introduce strain, reduce model quality, or degrade simulation stability. That’s where the…

When studying molecular mechanisms such as ligand unbinding, full atomic trajectories are often unnecessary. Many molecular modelers prefer to focus only on a specific subset of atoms—like a ligand or a binding site—when running free energy calculations, visualizing reaction coordinates,…

Designing compelling molecular animations often becomes a bottleneck in structural biology and molecular modeling—especially when trying to clearly present docking events or compare bound and unbound states. In many cases, modelers want to show how ligands or components fit with…

In molecular modeling, every action—like building a molecule, tweaking a conformation, or applying a force field—can dramatically change your model. This flexibility is essential, but it comes with a risk: a misclick or unwanted operation may send your system into…

When setting up coarse-grained (CG) molecular dynamics simulations, solvation may seem like a straightforward checkbox. However, if you’re using the MARTINI v.3.0.0 force field with coarse-grained beads and GROMACS, there’s a subtle — but impactful — parameter you should not…

Anyone who works with molecular modeling software knows this feeling: you just adjusted a conformation, or deleted a node, or modified a complex interaction… and instantly wish you hadn’t. Modeling mistakes happen to everyone — sometimes it’s a misclick, sometimes…