One of the recurring challenges when setting up molecular dynamics (MD) simulations with GROMACS is defining custom index groups. These groups provide more control during analysis and simulation by letting you specify exactly which atoms or residues you want to…

Designing and modeling DNA origami structures involves multiple tools and file formats, which can make managing and sharing your designs a bit challenging. If you work in DNA nanotechnology and are looking for a more integrated approach, SAMSON may help…

When you’re trying to optimize the properties of a lead compound, exploring small chemical changes at specific sites can be a powerful strategy. Medicinal chemists often want to tweak one part of a molecule and see how it affects activity…

When setting up molecular dynamics simulations with periodic boundary conditions in GROMACS, a common challenge is: how to choose the right simulation box shape. Many users default to cubic cells, but there are smarter options available — especially if you’re…

When presenting molecular models, motion can be a powerful tool to enhance understanding and communication. A static image may capture a single perspective, but animating a molecule—particularly by rotating it—can highlight spatial features, reveal internal organization, and simply make your…

Many computational modelers rely on custom or third-party Python packages for tasks ranging from data analysis to deep learning. But integrating these packages into modeling platforms can be frustrating—especially when the environment doesn’t support pip or editing installations. If you’re…

When presenting molecular systems—whether you’re communicating a molecular interaction mechanism, showcasing a conformation change, or simply creating a smooth visual flythrough for a talk—camera movements can make or break the experience. One common pain point in molecular animations is using…

When designing complex molecular systems, positioning fragments in three dimensions can be both critical and challenging. Whether you’re assembling ligands, placing functionalized rings, or orienting biomolecular components for docking simulations or visualization, precise and flexible control over fragment orientation can…