Running umbrella sampling simulations is a key method for exploring complex molecular processes and reaction coordinates—whether you’re studying ligand unbinding, ion transport, or protein conformational changes. But analysis can be tricky: how do you go from multiple biased simulations to…

For molecular modelers, one of the biggest obstacles to using a new platform is the time it takes to learn the interface and features. Whether you’re switching from another tool or starting your journey in molecular modeling, figuring out how…

If you’ve ever set up a molecular dynamics simulation, chances are you’ve spent time choosing the right periodic boundary conditions. But one decision that often gets overlooked — and can significantly affect simulation efficiency — is the shape of the…

When modeling molecular systems, it’s not uncommon to need to optimize the geometry of only a part of a molecule — for example, tweaking a binding site while preserving the framework of a protein. However, many molecular modeling platforms default…

When modeling large biological assemblies like viral capsids, it’s common to encounter more than one possible symmetry group. For molecular modelers, this raises an important question: how do you choose the most meaningful symmetry group for your system? Incorrect or…

Molecular modelers often juggle multiple structures, data sources, and editing operations all within a single session. As projects grow in size and complexity—especially in fields like drug discovery, protein engineering, or materials science—managing the structure and content of your workspace…

Carbon nanotubes (CNTs) are central to research in nanotechnology, materials science, and molecular modeling. But for many scientists, creating accurate single-walled or multi-walled CNTs in 3D can still be a frustrating experience — either due to lack of tools or…

Creating custom crystal structures is a valuable skill for anyone working in materials science, solid-state chemistry, or molecular modeling. Whether you’re studying lattice strain, dopant behavior, or crystalline defects, simulating accurate, made-to-measure crystal models is essential. Fortunately, SAMSON’s Crystal Creator…

If you’ve ever spent hours building a complex molecular model only to realize that a few clicks wrecked it — you’re not alone. One of the recurring challenges in molecular modeling is the risk of losing work due to unintended…