Author: OneAngstrom

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…

When performing molecular modeling, it’s common to want to optimize only a specific part of a molecule while keeping the rest unchanged—for example, when adjusting a binding site or relaxing a region around a mutation. However, many molecular modelers run…

When working on complex molecular modeling projects, there’s often a need to open and compare several molecular structures, run different types of simulations, or organize exploratory paths independently. For researchers using SAMSON, knowing how to work efficiently with multiple documents…