OneAngstrom – Page 247

What Are Node Types in SAMSON, and Why Do They Matter in Molecular Modeling?

When building or analyzing molecular systems, researchers often have to manage highly complex structures composed of atoms, residues, chains, groups, and all sorts of simulation elements. Managing these efficiently is critical to working with large or dynamic molecular models. That’s…

Need to Zoom In Without Breaking Your Focus? Try the Zoom Camera Animation in SAMSON.

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When preparing molecular animations, especially for presentations or publications, clarity is everything. A common frustration among molecular modelers is trying to zoom in on a specific part of a system — such as a binding site or a reaction center…

Quickly Select Side Chains Based on Attributes in SAMSON

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When working with large molecular structures, isolating specific parts of interest—such as side chains with certain atomic properties—can save significant time. This is especially true if you’re preparing simulations, analyzing interactions, or cleaning up your models. In SAMSON, the Node…

A Quick Way to Instantly Enhance Molecular Visualizations in SAMSON

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When working with complex molecular systems, presentation matters. Whether you’re preparing visuals for a publication, a lecture, or simply navigating intricate molecular networks, creating compelling representations that are both meaningful and accessible can take time. 👍 This is where Visual…

Controlling Molecular Scene Appearance with Render Preset Attributes

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When you’re dealing with molecular modeling, presentation isn’t just aesthetic—it’s essential. Whether you’re preparing visuals for publication, sharing models with collaborators, or trying to quickly identify certain features in a complex scene, controlling how each part of your system is…

Making PMF Calculations Less Painful with GROMACS Wizard

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If you’ve ever run umbrella sampling simulations in molecular dynamics, you probably know the next step: extracting the Potential of Mean Force (PMF) to understand free energy profiles along a reaction coordinate. But actually going from simulation data to a…

Saving Time and Keeping It Clean: Using Visual Presets in SAMSON

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One of the recurring challenges in molecular modeling is ensuring visual consistency across figures and animations, especially when working with large, multi-scale systems or preparing presentations and publications. If you’ve ever spent too much time adjusting rendering settings, tweaking atom…

Why Your Simulation Density Is Wrong (and How to Fix It with NPT Equilibration)

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One of the most frequent stumbling blocks in molecular dynamics is achieving the desired system density before running a production simulation. You ran energy minimization, followed it up with NVT thermal equilibration—and yet the system’s density just won’t settle. Sound…

Tweak One Atom, Explore New Possibilities: Generating Molecular Analogs in SAMSON

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If you’ve ever worked on optimizing a lead compound, you know how valuable small molecular changes can be. What if you could quickly and systematically generate analogs by swapping a single atom or group—right from your molecular design platform? This…

From 3D to Clarity: Simplifying Protein-Ligand Analysis with 2D Interaction Diagrams

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Understanding the interactions between a protein and its ligand is essential in molecular modeling and drug discovery. But when analyzing complex 3D molecular structures, sometimes seeing what matters most—key interactions—can get visually overwhelming. If you’ve ever felt like you needed…