OneAngstrom – Page 13

From Glass to Gold: Fine-Tuning Materials in Molecular Renderings

High-quality molecular renderings are more than just accurate representations; they’re also an important tool for communication, teaching, and research. A common challenge? Making molecules look realistic or stylized enough to effectively tell the story behind your data, while avoiding the…

From Conformations to Continuous Pathways: Choosing the Right NEB Strategy

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When studying transitions between molecular states, a common challenge in computational chemistry is building a reliable minimum energy path connecting two conformations. This is essential for exploring reaction mechanisms, ligand unbinding, or protein conformational changes. But what’s the most efficient…

Understanding Relative Positioning in SAMSON’s Inspector

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For many molecular modelers, adjusting the position of multiple atoms simultaneously is a common need — whether you’re setting up a complex structure, refining a model, or exploring conformational changes. But moving multiple nodes in 3D space without breaking the…

Avoiding Topology Errors When Creating CG Models of Protein Replicas

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When working with coarse-grained (CG) molecular dynamics simulations, one common scenario is modeling systems that contain multiple copies—or replicas—of the same protein. This is typical in studies involving protein aggregation, crowding effects, or multi-component assemblies using approaches like the MARTINI…

Finding Exactly the Atoms You Want: Using Atom Attributes in NSL

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When working with large molecular systems, identifying specific atoms with precision can be time-consuming and frustrating. Whether you’re cleaning up a model, extracting meaningful subsets, or analyzing specific substructures, selecting atoms by hand becomes inefficient and error-prone very quickly. This…

A quick way to select node groups using attributes in SAMSON

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When analyzing or designing complex molecular systems in SAMSON, molecular modelers often need to select specific sets of entities—whether that’s to analyze a protein region, assign visualization properties, or apply an operation just to a subset of the system. However,…

Stabilize Your Camera View While Molecules Move: A Quick Guide

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When visualizing molecular dynamics or structural rearrangements, it’s easy to lose track of the most important regions. A common frustration among molecular modelers is trying to follow specific atoms or domains while letting the surrounding system move — without endlessly…

Stop Spinning in Circles: Rotate Molecules with Purpose in SAMSON

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If you’ve ever recorded molecular animations for presentations or publications, you’ve probably wrestled with getting that perfect, meaningful rotation of your molecular system. It’s easy to spend too much time adjusting camera angles manually, only to end up with a…

Choosing the Right Discrete Color Palettes in Molecular Modeling

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When working on complex molecular visualizations, clarity matters. Whether you’re analyzing large biomolecular systems or creating compelling visual outputs for presentations or publications, the choice of color can dramatically impact how easily your audience interprets molecular structures. One of the…

Avoid Unexpected Simulation Failures: How to Check Energy Minimization Results in GROMACS Wizard

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Energy minimization is a crucial preparatory step in molecular simulations, especially before launching longer production runs such as molecular dynamics (MD). A poorly minimized system may result in unstable simulations, wasted computational resources, and misleading scientific conclusions. Yet many modelers…