Author: OneAngstrom

Searching for the right molecule in a library can be a slow and frustrating process—especially when you’re dealing with substructures. Maybe you’re designing a compound with a specific functionality, or maybe you want to filter out only the molecules that…

Before jumping into docking simulations, there’s one crucial step that experienced molecular modelers know better than to skip: system preparation. While it might feel like a formality, not preparing your protein structures correctly can lead to misleading results or failed…

When working on molecular models, measurements are vital. Whether you’re calculating bond lengths, angles, or torsion, clarity and reproducibility are essential — especially when presenting your model, collaborating, or coming back to your work months later. This is where SAMSON’s…

When working on complex molecular systems, it’s common to repeatedly switch between different selections—ligands, protein pockets, water molecules, and more. But let’s face it: manually selecting the same nodes over and over is time-consuming and error-prone. Fortunately, SAMSON offers a…

Understanding how large molecular assemblies are organized can be challenging when all atoms and components are shown together. Complex biomolecular structures can appear crowded, making it harder to explain mechanisms, discuss design ideas, or create engaging visualizations during scientific presentations.…

Running umbrella sampling simulations to explore molecular interactions can be computationally expensive and time-consuming. But how can you be sure you’ve sampled enough of your reaction coordinate space? One of the most common pain points in molecular modeling is having…

When setting up molecular dynamics simulations, especially those involving biomolecules in solution, minimizing unnecessary computation is essential. One often-overlooked factor that can dramatically improve efficiency is the choice of unit cell shape when defining periodic boundary conditions (PBCs). If you’ve…

When studying molecular interactions, understanding how specific atoms move along a reaction or unbinding pathway can reveal critical insights. Whether you’re preparing reaction coordinate input files for enhanced sampling, or trying to isolate ligand movement for free energy calculations, exporting…

In molecular simulation and visualization, it’s common to animate a system over time—watching proteins fold, ligands bind, or large molecular assemblies rearrange themselves. As these events unfold, a typical viewer wants to stay focused on a particular region of interest—perhaps…