When preparing a molecular dynamics (MD) simulation, defining the periodic box correctly ensures accuracy and stability in the results. But what happens when you’re not just simulating one structure, but a whole batch of conformations? Should each snapshot have a…
One commonly overlooked yet crucial step in molecular docking studies is ligand preparation. 🧪 Docking algorithms like AutoDock Vina assume that ligands are clean, chemically sensible, and ready to interact with the target. Unfortunately, that’s not always the case —…
In molecular modeling, especially when working with complex systems or animations, user interfaces packed with many nodes can quickly become overwhelming. It’s sometimes surprisingly hard to focus on what really matters—perhaps a specific ligand interaction or a folding mechanism—when multiple…
When preparing a molecular system for simulation, understanding the role of position restraints during the NPT (constant pressure and temperature) equilibration phase can save you time—and help you avoid unexpected behavior in your trajectories. This post walks you through how…
Choosing the right color palette when visualizing molecular structures can have a significant impact on how data is interpreted, especially when dealing with large biomolecules or complex simulation results. With SAMSON, molecular modelers can apply and customize color palettes to…
Molecular modeling workflows often require adjusting structures on the fly—whether to simulate mutations, adjust conformations, or test stability under structural modifications. But in many modeling tools, adding or removing atoms mid-simulation means having to restart the entire setup. This can…
Creating compelling molecular presentations is a challenge many modelers face. Whether you’re explaining a complex conformational change to a colleague or preparing a presentation for a broader scientific audience, showing atoms actually moving—not just flipping between static states—can make all…
When working on complex molecular systems, the ability to quickly access the tools you need — without constantly navigating menus — can make a big difference. Several molecular modelers have expressed that flexibility in interface layout is important, yet difficult…
When exploring complex molecular modeling software, it’s all too easy to run into a wall. Whether you’re a student trying to learn the basics of molecular visualization, or a researcher transitioning from legacy tools, the steep learning curve can be…
When preparing molecular animations, it’s common to focus on what moves — conformational changes, ligand binding, structural transitions. But sometimes, equally important is making sure some parts stay still. That’s where the “Hold atoms” animation in SAMSON becomes very helpful.…
