When setting up molecular dynamics simulations with GROMACS, a recurring pain point for researchers is managing index groups. These groups—collections of atoms used to define restraints, pulling, or analysis regions—often need to be manually created through command line inputs in…

Sharing clear and engaging molecular mechanisms is often a challenge in computational modeling. Whether you are preparing for a presentation, creating supplementary materials for a publication, or simply documenting your workflow, showing your molecular model in action can make a…

Searching for specific substructures across a library of molecules is a routine task in cheminformatics, but it can be tedious and error-prone when working with large datasets. If you’ve ever found yourself combing through countless SMILES strings looking for specific…

When studying molecular behavior such as ligand binding and unbinding, free energy calculations, or preparing animations of molecular motion, capturing atom trajectories along computed paths can be crucial. SAMSON’s Export Along Paths extension offers a practical way for molecular modelers…

For molecular modelers working on viral proteins, computing conformational transitions between known structures is a frequent challenge. Whether designing potential inhibitors, studying viral entry, or simply trying to understand structural dynamics, one practical problem remains: how to interpolate between two…

Creating clear and engaging scientific animations for molecular design can be a challenge, especially when you want to convey not only structural information but also guide your audience through a story. One often overlooked aspect that can improve the clarity…

When studying the dynamic behavior of molecules, it’s common to want the camera to stay focused on a certain region — a binding site, an atom group, a functional group in motion — while the rest of the molecular system…

If you’re a molecular modeler preparing visual materials for teaching, a research presentation, or a publication, you’ve likely struggled to clearly communicate the internal architecture of complex molecular assemblies. It’s common to want to highlight specific subunits or depict how…