One of the most frequent frustrations of researchers working with molecular modeling software is having to adapt their workflow around fixed interfaces and rigid toolsets. Every project is different, and a one-size-fits-all solution rarely fits anyone well. What if your…

For molecular modelers working with Python scripts, context-switching between external editors and molecular modeling tools is common—and often frustrating. If you’ve ever wished that you could write, edit, and run your scripts without leaving your molecular design environment, SAMSON has…

For molecular modelers, one recurring challenge is integrating multiple computational tools and datasets into a smooth and productive workflow. Whether you’re running docking simulations, visualizing complex molecular structures, or using custom algorithms, jumping between tools can be a time sink—and…

One of the most common challenges for molecular modelers is finding the right tool for a specific task—especially when working with a complex system that requires specialized functionality. Whether it’s parsing a new file format, creating a unique visual model,…

Controlling the conformation of a biomolecule to open or close a binding site is often a challenging step in molecular modeling. Whether you’re setting up a drug docking simulation or analyzing conformational flexibility, being able to guide molecular motion toward…

When showcasing complex molecular systems, clarity is key. Elements in the foreground may obscure parts of the structure you want to highlight, and simply hiding them can feel too abrupt. That’s where the Disappear animation in SAMSON becomes valuable: it…

In molecular modeling and education, revealing just the right amount of detail at the right moment is crucial. Whether you’re preparing a presentation or building an instructional animation, visual clarity can make or break how well a concept is understood.…

When working with molecular simulations in GROMACS, you often rely on index groups to define subsets of atoms. GROMACS generates standard ones automatically—like protein, water, or ions—but what if you need more control? Whether you’re setting up biased simulations or…

Setting up center-of-mass pulling simulations in GROMACS often requires the definition of custom index groups—particularly when dealing with multi-chain protein systems. For many molecular modelers, this step introduces friction, especially if you’re switching between the command line and visualization tools.…