Running molecular simulations with GROMACS requires precision, but it also demands patience—especially when you’re waiting for a system to equilibrate. One of the common challenges researchers face is tracking their simulations while continuing other work. If you’ve ever found yourself…
When working with force fields in molecular modeling, one common challenge is handling systems where automatic perception of atom types and bond orders fails. This can happen during the modeling of new compounds, structures with unconventional bonding, or even systems…
Visualizing molecular systems isn’t just about making things look good. It’s about clarity, insight, and helping you make the right decisions for your research. If you’ve used tools where atoms and bonds are shown as 3D sticks and spheres by…
When working on complex DNA nanostructures, molecular modelers often need to reuse specific design elements across multiple projects. Rebuilding frequently used motifs from scratch wastes time and increases the risk of error. Adenita, the DNA nanostructure editor in SAMSON, provides…
Designing nanostructures from atomic rings can be a time-consuming process if done purely manually, especially when building repeated patterns such as carbon nanotubes. Molecular modelers often need to carefully position and rotate molecules using fine controls, which can be tedious…
When comparing protein structures, sometimes the focus isn’t on the whole protein — but rather on a specific region: an active site, a conserved domain, or just a few residues that differ between species. In these cases, global alignment can…
One of the challenges molecular modelers frequently face is how to visually simulate the departure of a ligand or component from a molecular complex. Whether you’re preparing a presentation, investigating structural hypotheses, or producing educational material, animating this process in…
When working with complex molecular systems, clarity matters. But as your structures grow, so does the risk of visual clutter — especially if labels start overlapping or hide critical parts of your model. Labels in SAMSON are crucial for annotating…
Creating attractive and informative molecular visualizations can take time—especially when you need to tweak multiple settings like visual models, color schemes, and rendering styles. If you’ve ever felt like this slows down your workflow or makes it harder to focus…
Anyone who has spent long evenings fine-tuning molecular models knows the eyestrain that comes with prolonged exposure to bright interfaces. It’s not just about aesthetics—high screen brightness in low-light environments can cause discomfort, fatigue, and reduce focus. That’s where Dark…
