Author: OneAngstrom

One of the most common frustrations for molecular modelers after completing energy minimization is realizing that the simulation system is not yet stable enough for meaningful dynamics. Structures might fly apart, unphysical fluctuations could persist, or temperatures deviate wildly. This…

Protein conformational changes are at the heart of many essential biological processes, but capturing the motion between two known conformations can be challenging—especially when you need to analyze or reuse specific atom trajectories for downstream tasks like simulation analysis, machine…

Creating engaging molecular animations isn’t just about moving atoms. In many cases, how your camera behaves — how it orbits, zooms, or pauses — makes a huge difference in whether your audience follows the story you’re telling. If you’ve ever…

If you’re working with molecular systems and want to explore how a system moves between two known structures—like a bound and unbound conformation—there’s a good chance you’ve considered using the Nudged Elastic Band (NEB) method. It’s a powerful tool to…

One common bottleneck in molecular docking workflows is navigating and interpreting the results after a large-scale ligand screening run. You’ve set up your systems, launched your AutoDock Vina simulations, and now you’re left with dozens—or hundreds—of poses across multiple ligands.…

One of the most common challenges in molecular animation is conveying focus without distracting the viewer. Especially when zooming in to highlight a specific active site or molecular interaction, small shifts in camera orientation or unintended changes in depth-of-field settings…

When setting up molecular dynamics simulations for a series of molecular conformations, choosing the right periodic box parameters can lead to more efficient simulations and better results. In SAMSON’s GROMACS Wizard, users working with multiple conformations have two main options…

For researchers using GROMACS, setting up pulling simulations often requires creating custom index groups—say, to specify exactly which atoms or chains to pull. But writing index groups by hand in GROMACS can be awkward, especially when you’re dealing with complex…

Have you ever wanted to try out a new analysis workflow but hesitated because setting everything up from scratch seemed daunting? If you’re exploring how to predict protein-ligand complexes using NMR data, there’s a helpful shortcut in SAMSON worth knowing:…