When preparing coarse-grained molecular dynamics (MD) simulations with GROMACS, many users encounter an unexpected obstacle: solvent molecules too close to the solute. This typically results in unrealistic overlaps and density artifacts that force them to redo the setup or troubleshoot…

If you’ve ever spent valuable minutes reselecting the same parts of a molecular system over and over again during analysis or visualization, you’re not alone. Molecular modeling often requires switching focus between a ligand and its receptor, or zooming in…

When setting up covalent docking simulations, one of the most frequent and frustrating sources of error is neglecting to properly define the chemical structure of the ligand—especially if the ligand comes from a crystal structure where it is already covalently…

If you’ve worked with molecular simulations using the Universal Force Field (UFF), you’ve probably faced this common struggle: finding the right parameters to reflect the behavior of your specific system. Accurate simulation results often require tweaking below the surface—beyond simply…

For molecular modelers, one of the biggest challenges is bridging the gap between different computational tools, data formats, and specific modeling functionalities. Whether you’re preparing structures, performing simulations, or visualizing molecular systems, you may find yourself juggling many different software…

When working with molecular structures, atom selection can become a tedious and repetitive task, especially in large systems like crystals, biomolecules, or complex nanostructures. Often, modelers want to focus on specific regions — say, atoms with certain charges, atoms within…

Molecular modelers often have a favorite script, algorithm, or visualization routine they reach for—something they’ve fine-tuned to match their workflow. But integrating these custom tools into large, extensible platforms can feel out of reach without advanced programming setups, complicated builds,…

When working with large molecular assemblies, crystal structures, or intricate protein systems, selecting the right atoms can be surprisingly time-consuming. Graphical selection tools may work well for small molecules, but they tend to get messy when you’re dealing with thousands—or…