When preparing biological systems for molecular dynamics simulations, one recurring pain point is deciding what to do with water molecules. Should you delete all of them? What if some are tightly bound and essential for protein function or ligand binding?…

When creating animations of molecular systems, you’re often focused on illustrating detailed transitions—like conformational changes, ligand docking, or energy minimizations. But there’s a subtle issue that many researchers encounter: the camera viewpoint can drift between frames unintentionally, especially if no…

Writing Python scripts for molecular modeling often involves switching between documentation, coding environments, and visualization tools. For researchers and students working with complex simulations, simple tasks—like transforming atoms or building interfaces—can become time-consuming due to repetitive coding and context switching.…

Preparing input files for free energy calculations can often be tedious, requiring custom scripts to extract atomic coordinates along a reaction path. Fortunately, SAMSON’s Export Along Paths extension streamlines this task through a user-friendly interface that allows you to export…

In molecular modeling, finding biologically relevant transition pathways between molecular states can be a challenge—especially when simulating ligand unbinding events. Often, you may already have a trajectory generated through sampling or interpolation, but need to make it more accurate from…

When preparing molecular systems for simulation, clean geometry isn’t optional—it’s essential. Poor atomic arrangements can lead to unrealistic behavior, convergence failures, or wasted compute time. That’s why optimizing geometries before launching simulations should be part of every molecular modeler’s workflow.…

When working on molecular animations, one of the most common frustrations that molecular modelers face is keeping parts of a molecule steady while the rest of the system moves. Whether you’re showcasing ligand docking, domain movement, or assembling large biomolecular…

When preparing molecular presentations, researchers often focus heavily on the scientific content—molecular structures, simulation results, docking poses—and understandably so. However, the presentation layer of that information is also crucial. Transitions that appear abrupt or distracting can reduce clarity or even…