When preparing biomolecular simulations with GROMACS, molecular modelers often run into a practical challenge: how to define custom index groups that don’t neatly fall into the default categories like protein, solvent, or ions. For example, what if you want to…

When working on molecular systems, small changes can have big consequences. Accidentally deleting an entire chain, misplacing a fragment, or tweaking a parameter too early in the workflow can compromise hours of careful work. What makes it worse is that…

When working with complex molecular systems, molecular modelers often need to alternate between creating, modifying, and analyzing structures. SAMSON provides a modular approach to streamline this workflow through the concept of editors: dedicated tools that let you perform specific interactive…

When working with protein structures from the Protein Data Bank (PDB), you often start with an asymmetric unit — just a portion of the full biological or crystallographic assembly. While this is sufficient for some analyses, many modeling and simulation…

Predicting how molecules transition from one state to another is at the heart of molecular modeling. Whether you’re studying protein folding, ligand binding, or conformational changes, knowing the minimum energy path (MEP) between two states can shed light on kinetics…

If you’ve ever tried installing scientific software in a university or institutional setting, you’ve likely run into a familiar obstacle: you don’t have admin rights. Maybe you’re working on shared lab computers, maybe IT is hard to reach, or maybe…

Anyone working in molecular modeling knows that navigating structural complexity is part of daily life. Whether building a model from scratch or modifying existing biomolecules, the ability to interactively edit molecular systems in a flexible, precise manner can dramatically reduce…

For many molecular modelers and cheminformatics researchers, going from a simple SMILES string to a complete 3D structure can involve cobbling together multiple tools, scripts, or web platforms. This can be time-consuming and disrupt workflow—especially when working with large datasets.…