Author: OneAngstrom

Installing complex molecular modeling software can sometimes feel like a project of its own—especially in restricted computing environments like corporate or university networks. One of the common stumbling blocks modelers face is the need for admin rights to install software,…

Molecular modelers often spend hours perfecting animations that communicate complex mechanisms and structures with clarity. When showing a ligand docking process or a protein folding simulation, even a few fast-moving frames can disrupt the viewer’s ability to keep up. This…

Interactive molecular minimization in SAMSON is convenient and fast, but what if you’re only interested in minimizing part of a molecule—say, just a few atoms or a flexible side chain—without altering the rest of the structure? When setting up a…

When working on molecular presentations, especially those that involve atomic movements such as docking, assembly, or simulation, demonstrating atom trajectories can significantly improve clarity and understanding. But how do you precisely capture those trajectories for presentations and further analysis? This…

In molecular dynamics simulations, a well-managed NPT equilibration is only half the journey: importing the results correctly can be just as critical. Many researchers using GROMACS encounter confusion or inconsistencies at this stage—not because their simulation failed, but because pressure…

Molecular modelers studying protein-ligand interactions often get stuck after generating ligand unbinding paths: how do you analyze these trajectories, compare them, and extract valuable information such as energy barriers? If you’ve used the Ligand Path Finder in SAMSON, the good…

Molecular modelers often struggle with visual clutter when working with large biomolecular systems. Zooming in on an area of interest can still leave the background fully detailed and distracting, which makes presentations or publications less effective. A simple yet powerful…