Running molecular dynamics simulations can often feel like juggling. You launch one equilibration job… then another… and before you know it, you’re wondering what has finished, what is still running, and where the results were saved. If you’re using the…

Exploring complex molecular structures, such as large proteins or densely packed nanomaterials, often presents a recurring challenge for modelers: internal features get visually buried inside layers of atoms. Rotating and zooming might help, but more often than not, you lose…

If you’ve ever run a molecular dynamics simulation only to encounter unexpected behavior, there’s a good chance you’re not alone. While energy minimization and restraints can catch many issues, a far more visual—and proactive—tool can help with one common modeling…

When exploring ligand unbinding pathways from proteins, molecular modelers often find themselves struggling with a deceptively simple question: which atoms should I select as the ligand, the active motion drivers, or the fixed anchors? The outcome of your unbinding simulations…

When preparing molecular animations in SAMSON, timing is everything. Whether you’re building a smooth protein docking sequence or visualizing a complex reaction mechanism, it’s often helpful to draw attention to a particular moment. This is where the Pause animation effect…

Tracking the movement of specific molecular components across a simulation is a common task in molecular modeling and simulations. One particularly useful metric is the motion of the center of mass (COM) of a group of atoms — for instance,…

When preparing a coarse-grained (CG) system for molecular dynamics simulations, one of the most overlooked yet essential steps is setting the correct force field. In SAMSON’s GROMACS Wizard, the careful selection of the right coarse-grained force field can make or…