Author: OneAngstrom

One frequently overlooked step in molecular docking workflows is the minimization of ligands. If you’ve ever run docking experiments and noticed implausible poses or unexpectedly high binding energies, it might be due to poorly configured ligand structures. Let’s explore when…

One common challenge in molecular modeling is presenting structural features that span vertically over large systems, such as membrane-spanning proteins, nanotubes, or layered materials. When trying to communicate the depth of a system in presentations or videos, a smooth vertical…

Presenting molecular systems often involves more than just accurate modeling. Whether you’re preparing a scientific talk, recording a video tutorial, or simply exploring different stages of a simulation, visual clarity is essential. As complexity increases, showing every fragment in your…

When creating presentations or educational content about molecular structures, researchers and educators face a recurring challenge: how to progressively guide the viewer’s focus without overwhelming them visually. Showing every part of a molecule at once—especially complex biomolecules like proteins or…

When presenting molecular models, the way you move the camera can deeply impact how clearly your message gets across. In SAMSON, the Orbit camera animation can help you create smooth, circular camera movements around molecular structures. This is particularly useful…

When working on molecular simulations, it’s common to reach the Energy Minimization (EM) phase and wonder: did it actually work? While tools like SAMSON’s GROMACS Wizard streamline Energy Minimization, interpreting the outcome is still a step many modelers find ambiguous.…

Running molecular simulations in the cloud can save time and unlock access to high-performance computing hardware. But once a job is launched, how do you keep an eye on progress, review results, or even just organize your projects? That’s where…

Visualizing molecular trajectories is a key aspect of understanding conformational changes, reaction mechanisms, docking paths, and other molecular phenomena. However, presenting trajectory data in a clear and synchronized manner can be time-consuming, especially when working with complex molecular systems. SAMSON,…

When working on molecular design, seeing is more than believing — it’s sometimes the only way to fully grasp what’s happening inside nanosystems. But for many researchers and students, figuring out how to effectively visualize structural components can be time-consuming…

One of the surprisingly frustrating moments in molecular modeling comes when you’re trying to intuitively edit a geometry — say, nudge an atom — and your software either resists or breaks the whole system. Traditional modeling tools often require repeated…