Author: OneAngstrom

Molecular modelers often need to create presentations or teaching materials that explain complex molecular processes through dynamic visualizations. But even with good data, static views can limit the impact and clarity of your message. If you’ve ever wished for a…

Creating scientific presentations using static images can make it hard to clearly communicate complex molecular processes such as docking, folding, or dynamic interactions. For molecular modelers, visualizing a sequence of changes in molecular configurations is not just attractive—it’s often essential.…

One common challenge in molecular modeling is clearly and efficiently conveying dynamic behavior of systems, especially when preparing scientific presentations or instructional materials. Still images often fall short in highlighting spatial transformations, such as molecular rotations. This is where SAMSON’s…

When setting up molecular dynamics simulations in GROMACS, many researchers face a recurring hurdle: defining custom index groups to isolate specific molecular components—like protein chains—for analysis or for applying pulling forces. This can be tedious and error-prone when done manually…

Working with dynamic molecular systems often means watching specific atoms or regions as they evolve over time. Whether you’re observing a key residue in a protein, a ligand during docking, or a catalytic site in motion, it’s easy to lose…

Understanding how molecules move—whether during a drug unbinding event or a protein conformational change—is crucial in molecular modeling. But visualizing those motions in a clear and interpretable way can be a challenge. If you’ve ever tried to trace how a…

Long modeling sessions, late-night analysis, or extended scripting in SAMSON can take a toll on your eyes—especially in brightly-lit interface environments. Many molecular modelers have found themselves squinting at atomistic details under stark white UIs. Thankfully, SAMSON provides a simple…

If you’re using umbrella sampling in GROMACS to estimate free energy profiles, you probably already know how time-consuming the simulations can be. What’s even more frustrating is the uncertainty: did the sampling fully cover the reaction coordinate space? Were there…

Molecular dynamics simulations often require finer control over system components for applying specific actions like restraints, pulling, or analysis. In GROMACS, this is handled through index groups. While GROMACS automatically creates standard groups (like protein, water, ions), there are many…