Author: OneAngstrom

Protein modelers frequently run into a recurring challenge: identifying and correcting residues with unfavorable backbone conformations. These problematic residues can undermine the structural integrity of simulations, reduce model accuracy, and even produce misleading results in docking or dynamics. Fortunately, SAMSON’s…

In molecular modeling, analyzing a trajectory is often just as important as running it. But sometimes, we only realize what we’re looking for when we see it from an unexpected perspective — like watching the movement happen in reverse. Whether…

If you’ve ever wished you could see how a molecule responds to changes as you make them—like dragging an atom and watching the rest rearrange in real time—then interactive simulation in SAMSON may be exactly what you’re looking for. One…

When creating scientific presentations or explanatory animations in molecular modeling, it’s often tempting to jump directly to full rotations to highlight structures. However, small periodic motions can be much more effective in some contexts, especially for drawing attention subtly or…

Setting up a molecular dynamics (MD) production run can be tedious when juggling multiple input files from earlier workflow steps. That’s especially true if you’re dealing with projects that go through energy minimization, NVT and NPT equilibration stages. Any mismatched…

When simulating ligand unbinding pathways in protein-ligand complexes, one surprisingly common source of difficulty isn’t always the algorithm or even the protein structure itself—it’s defining the sampling region. Many molecular modelers spend hours tuning energy parameters, refining force fields, and…

Creating smooth, compelling molecular animations can be time-consuming, especially when you want the camera to follow a specific path or highlight different regions in a scene. One challenge molecular modelers often face is figuring out how to direct attention dynamically—without…

Visual storytelling is essential when presenting molecular structures in a clear and accessible way—whether it’s for educational videos, research presentations, or collaboration. But have you ever had models just suddenly appear on screen, breaking the fluidity of your animation? That…

When working with complex molecular systems, the tools we use to interact with our models can greatly influence our productivity. A common frustration among molecular modelers is wasted time navigating through cluttered interfaces or endlessly rearranging windows after each session.…

One of the key challenges in molecular modeling is accurately and intuitively representing molecular properties. Whether you’re analyzing protein hydrophobicity, temperature factors, or charge distribution, visual clarity matters. This is where color palettes in SAMSON come into play. If you’ve…