Author: OneAngstrom

Colors aren’t just visual flair in molecular modeling—they are crucial tools for understanding. When dealing with complex molecular structures, reaction networks, or simulation results, using clear, distinguishable colors helps avoid confusion and supports better decision-making. In SAMSON, discrete color palettes…

When preparing a molecular animation or presentation, visual clarity is key. Sometimes, the default or current background isn’t ideal: maybe it’s too distracting, maybe it doesn’t match the context, or maybe you simply want to guide the audience’s attention more…

One of the common challenges in molecular modeling is ensuring that a newly created structure is physically realistic. Molecules built manually or imported from other software often start in high-energy, non-equilibrium configurations. This can distort simulations and affect downstream analyses…

When working with molecular simulations, one of the most frequent causes of downstream issues is improperly prepared structural data. Whether you’re building coarse-grained models, simulating protein-ligand interactions, or setting up molecular dynamics runs, small inconsistencies in your input structures—like alternate…

Creating compelling molecular visualizations is an essential part of communicating molecular mechanisms, whether you’re preparing presentations, producing educational videos, or designing research figures. But there’s a frequent challenge molecular modelers face: how do you smoothly reveal or hide parts of…

When molecular modelers present complex systems, it’s essential to maintain clear, consistent visual perspectives. During animations—whether for presentations, simulations, or teaching—you may want to move the camera along a horizontal path, preserving orientation while scanning across a molecular structure. SAMSON’s…

When preparing animated molecular presentations, a common challenge researchers face is visualizing how atoms or molecules move across time. Just watching the animation may not give enough insight into the exact path atoms follow. This can be critical, especially when…

Defining custom index groups can often be one of the trickiest steps for molecular modellers when setting up pulling simulations in GROMACS. If you’re performing center-of-mass (COM) pulling, it’s crucial that the pulled and reference groups are properly defined. In…