Author: OneAngstrom

When working on complex molecular models, it’s easy to feel overwhelmed by the tools available. From deforming structures to generating nanotubes or selecting regions of a model, the number of functionalities can pile up quickly in a molecular modeling interface.…

One of the most common pitfalls in molecular dynamics simulations—particularly involving pulling experiments—is improper box sizing in the direction of pulling. If your molecule gets too close to the edge of the simulation box, periodic boundary conditions can create unwanted…

Communicating molecular insights often requires more than just static images. When presenting dynamic processes like conformational changes, reaction mechanisms, or structural rearrangements, fine control over visibility can convey meaning more effectively. A common issue for molecular modelers is how to…

Have you ever wrestled with clarity while recording molecular animations? Whether you’re creating a presentation for a research talk or designing educational material, sometimes the challenge is simply: how do I make parts of a molecular structure disappear at the…

When working on complex molecular modeling projects, it’s easy to feel overwhelmed by the growing number of molecular structures, edits, and simulation elements. Proteins, ligands, solvents, surfaces, cameras, animations—everything piles up, and soon you’re asking: where did I put this…

When preparing molecular animations, one of the most common frustrations is discovering that your camera angle — the precise view you’ve carefully adjusted — has unexpectedly shifted later in the animation. This often happens because while you’re editing molecular motions,…

For many scientists working on molecular modeling, the first hurdle is often the software itself. Despite being powerful, complex modeling environments like SAMSON can feel overwhelming for newcomers. What should you click? Where are the tools? How do you actually…

Molecular modelers often rely on multiple specialized tools during structure preparation, simulation setup, or analysis stages. If you’re using SAMSON, you’ve probably noticed that the platform includes a feature-rich environment where ‘editors’ allow direct manipulation of molecular models in the…

When setting up molecular dynamics simulations, a common obstacle for many molecular modelers is ensuring that simulation inputs are correct and properly referenced. This becomes particularly crucial during the equilibration phase, where one wrong file can cost time and resources.…

When constructing molecular systems, a frequent challenge faced by researchers is correctly orienting molecular fragments before and after placement. Improper orientations can lead to overlapping atoms, energetically unfavorable structures, and ultimately incorrect simulation results downstream. SAMSON provides several integrated tools…