When preparing coarse-grained (CG) models for molecular dynamics (MD) simulations in GROMACS using the MARTINI force field, one common source of simulation instability is improper solvation. Users often follow the traditional pipeline for all-atom models, only to find that water…

When preparing molecular animations, one common challenge researchers and molecular modelers face is achieving a smooth, natural-looking zoom that follows a moving point of interest—without making the viewers feel disoriented. Whether you are visualizing active binding sites, tracking molecular pathways,…

When creating molecular animations for teaching, presentations, or publications, one common challenge is how to focus viewers’ attention on specific parts of a complex scene. Simply showing everything at once can overwhelm the viewer, making it difficult to follow the…

When working on complex molecular systems, identifying and modifying specific atomic properties can sometimes feel like searching for a needle in a haystack. Whether you’re adjusting atom positions, verifying assignments, or reviewing node properties across selections, having a fast and…

When creating molecular animations, timing is everything. Whether you’re showing a conformational change, a docking process, or a reaction pathway, there are moments when you want your audience to stop and observe. But how do you highlight a critical molecular…

Running NPT equilibration in molecular dynamics is often followed by another significant challenge: accessing and interpreting the results. For users working with GROMACS via SAMSON’s GROMACS Wizard, making sense of calculated outputs can sometimes feel daunting, especially for beginners or…

When working with complex molecular systems, it’s often important to visually follow dynamic changes while maintaining a consistent viewing perspective. For example, you may want to track the conformational motion of a ligand binding to a protein without rotating or…