When setting up molecular simulations involving pulling, especially center-of-mass (COM) pulling in GROMACS, an often overlooked step can significantly affect the accuracy and reliability of your results: correctly defining the periodic simulation box. In this blog post, we’ll walk through…
One of the most frequent questions molecular modelers ask when using software platforms like SAMSON is: “How can I add features or modules without overcomplicating my workflow—or overspending?” If you’ve ever wondered whether a particular tool or extension is freely…
Animations are crucial in molecular modeling, not only for presentations but also for understanding complex dynamic processes. Whether you’re illustrating a ligand docking, protein folding, or a simple conformational change, organization and control over your animations are essential. In SAMSON,…
When working on complex molecular modeling projects, keeping track of multiple structures, simulations, and variations can become challenging. If you’ve ever found yourself digging through layers of molecules trying to remember where you left that optimized ligand structure, you’re not…
Visualizing molecular structures clearly is essential for effective communication in molecular modeling. Yet, even the most detailed molecular models can feel flat or ambiguous without the right rendering settings. One common challenge modelers face is understanding spatial depth, especially when…
When working with complex molecular systems, it’s easy to feel overwhelmed by the amount of data displayed on screen. Whether you’re building models, running simulations, or presenting results, one universal challenge for molecular modelers is figuring out exactly what you…
When working on complex molecular modeling projects, it’s easy to get lost in a sea of nodes, structures, ligands, ions, and metadata. You might load a protein structure or build a molecular system, only to quickly find that navigating and…
When running molecular dynamics simulations with GROMACS, index groups are often an overlooked but essential part of analyzing results and defining simulation subsets. Whether you’re calculating RMSD, defining pulling groups, or setting restraints, the flexibility to define your own index…
Visualizing and analyzing the symmetry of macromolecular assemblies can help streamline modeling workflows by focusing only on the essential asymmetric portion. However, what if your system doesn’t present a single, clear symmetry group? This is a common situation when working…
Designing DNA nanostructures virtually is an exciting and increasingly common task among molecular modelers, bioengineers, and synthetic biologists. But the practical challenge often arises at a critical moment: how do you take your virtual design and prepare it for simulation?…
