SAMSON Blog – Page 195

Avoid Solvent Clashes in Martini Simulations with This One Setting

When working with coarse-grained (CG) systems in GROMACS using the MARTINI force field, one recurring issue for molecular modelers is solvent bead clashes during solvation. These can lead to non-physical behavior during energy minimization or even cause simulations to crash.…

How to Select Atoms by Expression Without Writing Scripts

OneAngstrom

For molecular modelers working with large systems, it’s common to face repetitive and time-consuming tasks like selecting specific atoms based on custom values, geometric patterns, or chemical types. Doing so manually through the interface—especially over thousands of atoms—can become tedious…

Quickly Filter Visible Labels with NSL in SAMSON

OneAngstrom

When working on complex molecular systems in SAMSON, labels can be critical for clarity — but too many of them can clutter your visualization. Molecular modelers often face the challenge of managing these label nodes efficiently, especially when preparing clean…

What Are Node Types in SAMSON (and Why Should You Care?)

OneAngstrom

Anyone working in molecular modeling or structural biology knows that dealing with complex systems often means juggling different layers of information: atomic coordinates, chemical bonds, visual styles, simulation data, annotations, and more. If this sounds familiar, you may be relieved…

Why Only One Editor Can Be Active at a Time in SAMSON

OneAngstrom

When working with complex molecular models, workflows can often become tangled—especially when juggling multiple tools. If you’ve ever wondered why SAMSON, the molecular design platform, allows only one editor to be active at a time, you’re not alone. This design…

Switching to Your Own GROMACS: When and How to Do It in SAMSON

OneAngstrom

If you use GROMACS frequently for molecular dynamics simulations, you’re probably familiar with situations where you need to run simulations with a specific version of GROMACS — for example, for reproducibility in publications, for performance comparisons, or simply because your…

Which Nodes Are Actually Visible in Your Molecular Model? A Quick Guide

OneAngstrom

When working on complex molecular models, it’s common to load or import large systems with many hierarchical components. As your scene builds up, things start to disappear from view—or never appear at all. It’s frustrating to realize that parts of…

Keeping Your Eyes on the Molecules: How to Lock Camera Focus in Molecular Animations

OneAngstrom

When visualizing complex molecular systems, it’s easy to lose track of what matters most. If you’re working on a dynamic simulation—following a ligand binding to a receptor, or tracking a conformational change over time—you often want the camera to stay…

Which Molecular File Formats Can SAMSON Read and Write?

OneAngstrom

Choosing the right platform for molecular modeling can depend heavily on its ability to handle the variety of file formats researchers use daily. For molecular modelers working across simulation packages, crystallography tools, and cheminformatics platforms, file compatibility often becomes a…

Reducing Visual Clutter in Molecular Presentations with the Hide Animation

OneAngstrom

When working on molecular presentations, one common challenge faced by modelers is managing visual complexity. Scenes often involve dozens to hundreds of molecular entities, and many of them are not necessary to show simultaneously. Having too much on screen not…