Author: OneAngstrom

When working with complex biomolecular structures, selecting the right atoms, residues, or fragments can feel like searching for a needle in a haystack. Scrolling through long lists or manually clicking in the Document view becomes inefficient as models grow in…

Have you ever added labels to atoms or molecules in a molecular model and then wondered why they mysteriously disappear when you zoom out? It’s a common experience for many scientists and researchers using visualization platforms. In SAMSON, this behavior…

If you’ve ever tried to build repetitive molecular structures manually — nanotubes, rings, or arrays — you know how tedious it can be to duplicate, rotate, and align atoms correctly. This is especially painful when working at the nanoscale level…

When setting up molecular dynamics simulations, one of the often overlooked decisions is the choice of the unit cell shape used for periodic boundary conditions. Yet, this decision can have a significant impact on simulation efficiency and accuracy—especially when dealing…

When modeling protein conformational transitions, choosing the right atoms to guide your simulations can make a big difference. In SAMSON’s Protein Path Finder app, using the ARAP (As-Rigid-As-Possible) method requires identifying specific active atoms—those that drive structural changes and influence…

When running molecular dynamics simulations using GROMACS, selecting the right input for each step is more than a technicality—it influences the reliability of your results and the ease of your workflow. If you’re using the GROMACS Wizard Extension in SAMSON,…

If you’ve ever needed to move a molecular modeling project from one system to another, collaborate seamlessly with a colleague, or archive an entire workflow for reproducibility, you may have run into the challenge of keeping everything organized and intact.…

When setting up coarse-grained (CG) simulations in GROMACS, preparing the system correctly is essential—and solvent addition is a step that is often glossed over, or improperly configured. If you’re working with MARTINI-based CG models, especially those generated by Martinize2, there’s…

When preparing a biomolecular system for simulation, one common step is removing unnecessary water molecules. But not all waters are created equal. Active-site waters, often tightly bound and functionally important, should typically be preserved. So how can you remove only…