When setting up molecular simulations in GROMACS, creating custom index groups can be incredibly useful—for example, to define specific groups of atoms for pulling simulations or detailed analyses. But things tend to get tricky when working on large or batch…

When preparing molecular animations or creating visual presentations, clarity is essential. Too many atoms or complex visualizations can make it difficult for a viewer to focus on the message a molecular modeler wants to convey. This is especially true for…

Creating compelling molecular animations can be challenging, especially when you’re trying to draw attention to specific regions of a complex system. A common frustration for molecular modelers is achieving smooth and expressive zooming effects that go beyond a simple magnification.…

Creating effective scientific animations often comes down to highlighting just the right parts of a molecular system at the right moment. If you’re preparing a presentation or a video to communicate your latest discovery, you probably don’t want all atoms…

As a molecular modeler working with DNA nanostructures, it’s common to design sophisticated geometries digitally, only to find yourself wondering how these can be simulated effectively. Bridging the gap between interactive design and coarse-grained simulation is essential — and this…

When starting out with molecular modeling in SAMSON, one of the first challenges you may encounter is how to make your molecular structures both informative and visually clear. Whether you’re preparing a figure for a publication or trying to make…

When simulating molecular systems, it’s common to analyze dynamic regions that are central to your research – such as active sites, interface regions, or specific complexes. But as the system evolves over time, how can you always keep your eyes…

When preparing a biomolecular system for simulation with GROMACS, removing existing crystal waters is often part of the workflow. But not all water molecules are equal—some are tightly bound and participate directly in biochemical function, especially near active sites. Removing…