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 working on complex molecular models, managing visualization elements such as lights can become overwhelming. Whether you’re lighting your scenes for rendering or just tidying up your workspace, it’s crucial to be able to filter and isolate visible elements efficiently.…
One common challenge faced by molecular modelers is isolating meaningful subsets of bonds in complex structures. Whether you’re designing a molecule, analyzing structural motifs, or customizing visualizations, you often need to select specific bond types without manually clicking through thousands…
Installing powerful software for molecular modeling often comes with a common challenge: administrator rights. For many students, researchers, or professionals working on institutional computers, the inability to install software without admin privileges can be a blocker. But if you’re looking…
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…
When working on complex molecular models, the scene can easily become cluttered with visual presets. Whether it’s different representations for various parts of a biomolecule, or custom shaders applied during visualization iterations, keeping track of render presets can slow you…
In real-life materials, perfection is rare. Crystalline structures, even of highly ordered materials like diamond, often contain imperfections known as defects. For molecular modelers and material scientists, being able to visualize and manipulate such defects is essential — both to…
