When preparing molecular dynamics simulations, researchers often work with multiple starting conformations of the same system. This is especially common in studies involving ligand binding, protein flexibility, or comparative dynamics. However, managing and configuring these conformations for batch simulations can…

One of the challenges molecular modelers often face when working with coarse-grained (CG) molecular dynamics simulations is properly setting up force fields—particularly for MARTINI-based systems. A mismatch in force field parameters can lead to hours of debugging, poor system stability,…

When working with large molecular structures, molecular modelers often face the challenge of isolating specific atoms for inspection or modification. Manually selecting these atoms can be tedious and error-prone—especially in systems with thousands or millions of atoms like biomolecular complexes,…

Working with molecular models often means juggling several types of files: structures, scripts, datasets, documents, and even code. Anyone who has ever transferred a molecular project from one machine to another—or tried to share it with a collaborator—knows how easy…

When creating molecular animations, effectively guiding your viewer’s attention is a major challenge. Whether you’re preparing an educational video, a presentation for colleagues, or a publication-grade animation, cleanly controlling when molecular systems appear and disappear can make your message clearer.…

Molecular modelers often spend a considerable amount of time simulating ligand unbinding pathways in protein-ligand systems. However, after the hard work of generating results, exporting and visualizing the actual ligand motions can still be confusing or time-consuming. If you’ve been…

In molecular modeling, selecting the right atoms can be crucial. Whether you’re preparing a simulation system, modifying a structure, or simply visualizing specific regions, being able to define custom selection rules can save both time and effort. If you’ve ever…