One of the common frustrations in molecular modeling is having to stop and manually reassign bonds and atom types every time you make a structural edit. Whether you’re building a new molecule, modifying a reaction intermediate, or fine-tuning a structure,…

When working with large macromolecular assemblies like viral capsids or multimeric enzymes, identifying the correct symmetry group can be crucial. But what if your structure seems to support several possible symmetries? This is a common situation in molecular modeling. For…

When you’re creating animations of molecular systems, even the smallest unintended camera shift can disrupt the story you’re trying to tell. Have you ever carefully crafted a molecular animation, only to find your view angle jumping between frames—even when you…

When preparing coarse-grained (CG) molecular dynamics (MD) systems—especially with force fields like MARTINI—you might run into unexpected instabilities during equilibration or production runs. A common underlying cause? Forgetting to neutralize the system or set the proper ionic conditions. Fortunately, GROMACS…

If you work in molecular modeling, you’ve likely faced the challenge of simulating multiple states or conformations of the same molecular system. Maybe you generated a trajectory from a docking animation, or you explored conformational changes using normal mode analysis.…

Potential of Mean Force (PMF) calculations are a central tool in molecular dynamics for exploring the energetics along a reaction coordinate, such as ligand binding pathways, ion transport, or conformational changes. But as any molecular modeler knows, getting a reliable…

If you’re designing or analyzing molecular systems regularly, you’ve likely spent more time than you’d like adjusting atom sizes, tweaking colors, choosing rendering styles, and setting up views to get a clear and informative visualization. This overhead can be a…

When you’re creating molecular animations, clarity matters. Whether you’re preparing a molecular movie for a publication, a presentation, or a classroom, controlling exactly when elements appear or disappear can make the difference between an obscure or a crystal-clear explanation. Enter…

When preparing molecular systems for simulations with GROMACS, one often underappreciated step is defining custom index groups. These groups play a crucial role in advanced simulations such as umbrella sampling, free energy calculations, or restrained simulations, where specific atom sets…