Most molecular modeling begins with the ideal. Perfect lattices, flawless symmetry, and pristine atomic arrangements. But real-world materials are rarely so tidy. Defects — like vacancies, substitutions, and distortions — play a crucial role in defining the physical and chemical…

When presenting complex molecular systems, timing matters. Animations that move too quickly from one state to another can overwhelm viewers, especially when trying to highlight an important molecular interaction or structural change. If you’re creating a molecular animation in SAMSON…

Running molecular dynamics simulations across a large number of protein structures—whether they are variants, mutants, or alternative binding poses—can quickly become overwhelming. Repeating the same MD preparation steps for each conformation or each structure wastes time, increases chances of human…

Creating clear, engaging molecular animations can be a challenge, especially when you want to highlight key transitions without overwhelming your audience with too much happening on screen. One common issue faced by molecular modelers and presenters is how to make…

Molecular modelers often face an underappreciated challenge: keeping track of numerous molecules, scripts, conformations, and structure files within a growing project. As the complexity of a molecular simulation increases, so does the burden of managing its components. A cluttered workspace…

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…