When preparing a coarse-grained (CG) molecular system for simulations, a common frustration is the appearance of solvent clashes that can cause a simulation to fail. These clashes often originate during the solvation stage, especially for CG models using the MARTINI…

When studying molecular simulations, it can be frustrating to lose track of a molecule or region of interest as it moves during an animation. Maybe you’ve spent time perfectly positioning the viewpoint, only to have the target drift off screen…

Creating clear and compelling molecular animations can be challenging, especially when you’re trying to smoothly follow a system across frames. One common issue molecular modelers face is making camera movements that feel natural and professional, especially when visualizing structural changes…

When working with molecular structures, efficiency matters. Whether you’re adjusting positions or reviewing properties of atoms in bulk, you’re likely dealing with a flood of information. SAMSON’s Inspector is designed to help—but if you’re not filtering attributes, you might not…

If you’ve ever tried to illustrate a molecular motion — a protein conformational change, a nanotube twist, or a docking transition — chances are you’ve faced the challenge of producing a smooth, realistic animation. You may have asked yourself: how…

Tracking the motion of molecules in a system can be crucial for understanding mechanisms like ligand binding and unbinding, conformational changes, or for generating reaction coordinate files in free energy methods. If you’ve been manually extracting coordinates along a path,…

Watching molecular systems in motion can be incredibly helpful for understanding complex conformational changes, analyzing reaction mechanisms, or conveying structure-function relationships. But making professional animations from molecular paths can sometimes feel like a chore—especially when working with multiple trajectories that…