Author: OneAngstrom

Creating molecular animations for presentations, papers, or tutorials can be time-consuming — and when the result doesn’t convey your key message clearly, it can be frustrating 😓. If you’ve ever found yourself trying to visualize a docking process or highlight…

Designing and optimizing small molecules is central to many molecular modeling efforts, from drug discovery to materials science. But chemical space grows rapidly, and exploring it effectively is often challenging and time-consuming. One common pain point is identifying how subtle…

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…