Author: OneAngstrom

Running molecular simulations, whether using AlphaFold, GROMACS, or other cloud services, often means juggling various workflows and outputs. Researchers and molecular modelers frequently face a common challenge: staying organized when simulations are executed at scale, especially in a collaborative setting.…

When preparing molecular animations and presentations in SAMSON, it’s not uncommon to run into a frustrating issue: unintentionally changed views. Perhaps you’re preparing a smooth transition through keyframes, each showing a specific molecular perspective, but suddenly your hard-earned camera angle…

When preparing molecular presentations or videos, one of the biggest challenges modelers face is showcasing how structures come together. Whether it’s to illustrate docking, self-assembly, or molecular design, it’s often difficult to animate clear, comprehensible transitions from individual parts to…

When working with molecular simulations, one of the most common goals is to visualize how a molecular system evolves over time. Whether you’re cycling through protein conformations or presenting the movement of atoms along a simulated trajectory, making the motion…

Have you ever labeled atoms, residues, or molecules in your molecular model, only to see those labels disappear as you zoom out? Or perhaps you wanted residue-level labels at high level, but atoms clutter your screen instead? This behavior, although…

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…