Author: OneAngstrom

One of the key challenges in molecular modeling is ensuring that the geometry of your structure is physically realistic. Whether you’re assembling custom molecules or importing existing ones, minimizing structural strain is essential to avoid artificially high energies and forces.…

When analyzing molecular simulations, one of the recurring challenges is maintaining visual focus on a specific group of atoms during animation. Whether you’re tracking how a ligand moves inside a binding pocket or examining the structural flexibility of a protein…

If you've ever tried analyzing or running custom simulations in GROMACS, you've probably faced this: you need a specific group of atoms that isn’t covered by default index groups like Protein, Water, or Ion. Maybe you want to pull on…

If you’ve ever tried to build a carbon nanotube (CNT) manually in a molecular modeling software, you understand how tedious and error-prone it can be. Aligning rings, ensuring bond continuity, and managing overlapping atoms across copies is often a time-consuming…

When working on molecular analogs, one of the recurring pain points is figuring out where to introduce chemical modifications. These modifications need to be both chemically justified and relevant for exploring structure-activity relationships. Traditionally, this step requires careful visual inspection…

When visualizing molecular dynamics, it can be frustrating to lose sight of the area you’re most interested in. As the system evolves over time, atoms move, interactions change, and key regions may drift out of view—even if you had carefully…

One common challenge in molecular modeling is presenting how a ligand exits a binding pocket or how molecular components detach over time. Whether for a presentation, a publication, or to explain a concept to collaborators, animating these motions clearly can…

When working on complex molecular systems, even small time savings can improve focus and productivity. If you’re navigating through menus repeatedly in SAMSON, there’s a quicker way to access your assistant: keyboard shortcuts. SAMSON AI, the intelligent assistant powered by…

If you’ve ever worked with large biomolecular systems, you know the frustration of trying to select a specific type of residues, atoms, or structural groups in a sea of data. Manually clicking or scrolling through complex molecular hierarchies isn’t just…