OneAngstrom – Page 21

Never Lose Sight of Key Molecules During Simulations

When running molecular dynamics or simulating binding events, one common frustration lies in losing track of what’s most important—the atoms or regions you’re examining. Camera movements can end up drifting, making it difficult to stay focused on key interactions or…

Choosing the Right Symmetry Group in Large Molecular Assemblies

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When modeling large protein complexes, viral capsids, or other biological assemblies, symmetry can be both a powerful ally and a source of confusion. One challenge commonly faced by molecular modelers is deciding which symmetry group to retain when a structure…

Switching Views Instantly: Using Multiple Cameras in SAMSON

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If you’ve ever worked on a complex molecular model and found yourself spending time manually rotating, zooming, and navigating to repeatedly reach the same viewpoints, you’re not alone. Navigating 3D structures to find the perfect angle or focusing on a…

Create Slide-Like Molecular Presentations in SAMSON with the Stop Animation

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If you’ve ever tried presenting molecular simulations or structural models in SAMSON, you’ve probably encountered a common challenge: how do you effectively break up your animation into clearly structured sequences, kind of like slides in a PowerPoint presentation? Whether you’re…

Tired of Managing Molecular Simulations Locally? Try This Alternative

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Running complex molecular modeling jobs—such as protein structure prediction or molecular dynamics simulations—often requires substantial computing power, software installations, and careful monitoring of progress. For researchers dealing with local system limits, slow workflows, or collaboration headaches, SAMSON’s cloud-based Job Manager…

Why Did My Labels Disappear? Understanding Label Visibility in SAMSON

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When building molecular models, placing informative labels can be crucial: whether it’s highlighting a specific atom, measuring a distance, or tagging a particular residue, labels guide the interpretation and communication of your models. But if you’ve ever zoomed in or…

Indexing Beyond the Defaults: Smarter GROMACS Simulations with Custom Groups

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Simulation experts using GROMACS often start by relying on automatically generated index groups—like protein, water, or ions. These built-in groups are handy for many standard tasks, but when simulations get more specific (like defining pull groups or focusing on certain…

From Repetition to Pattern: Designing Monomer Sequences with Polymer Builder

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Building custom polymers can quickly become complex—especially when you’re not just connecting one identical monomer after another, but working with patterned sequences. Many computational chemists and molecular designers struggle with modeling repeat units that reflect experimental conditions or functional motifs.…

Filtering Molecular Models by Partial Charge in SAMSON

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When working with complex molecular systems, identifying specific structural groups based on electrostatic properties can be essential. Whether you’re screening ligands, analyzing biomolecular systems, or designing new compounds, partial charges help determine how molecules interact. Yet, combing through thousands of…

Run GROMACS Simulations Without Local Setup: A Quick Look at Cloud Capabilities in SAMSON

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For molecular modelers, running a GROMACS simulation often comes with a big technical prerequisite: installing, compiling, and configuring everything correctly on your local machine. This can take hours—and might involve battling with dependencies, GPU compatibility, or queuing systems. What if…