OneAngstrom – Page 102

Filtering molecular models by atom count in SAMSON

When working on large molecular systems, it can be useful – and sometimes necessary – to quickly identify models with a specific atom count. This is particularly relevant when preparing simulations (e.g., optimizing system size), simplifying visualizations, or evaluating model…

Precise Atom Selection with Math: Save Time with the Atoms Selector in SAMSON

OneAngstrom

In molecular modeling, selecting specific atoms from large molecular systems often becomes tedious—especially when spatial or chemical criteria are involved. For instance, extracting atoms from exact regions of crystal lattices or focusing on a subchain of a protein might require…

Find your visual style in SAMSON using Visual Presets

OneAngstrom

When working with complex molecular systems, visualization is more than aesthetic—it’s how we perceive patterns, make decisions, and communicate insights. But if you’re often switching between tasks—say, from analyzing molecular dynamics to preparing a figure for a publication—manually adjusting render…

Running Molecular Dynamics in the Cloud Without Installing GROMACS

OneAngstrom

For many molecular modelers, setting up and running simulations with GROMACS can be a time-consuming step that involves compiling complex code, managing dependencies, and tweaking performance settings for your local computer. And if you’re switching between different machines or collaborating…

Preserving Functional Waters While Cleaning Up Your Structure

OneAngstrom

When preparing molecular systems for simulation using GROMACS, one of the first steps is to remove unnecessary components like water molecules. However, a common concern for molecular modelers is accidentally deleting functional or tightly bound crystal waters from the active…

Pause, Explain, Proceed: Controlling Presentation Flow with Stop Animation in SAMSON

OneAngstrom

Whether you’re demonstrating a molecular mechanism to students or showcasing your latest simulation to collaborators, clarity matters. One underrated, yet important challenge in molecular presentations is controlling the pace at which your audience consumes dense visual information. Especially during complex…

Will SAMSON Run on Your Machine? Here’s What You Need to Know

OneAngstrom

If you’re a molecular modeler interested in exploring simulations, data visualization, or integrative design workflows, trying new software should be exciting—not a fight with system requirements or installation errors. That’s why it’s helpful to know upfront what it takes to…

Simplifying Molecular Arrangement: How to Align and Distribute Structures in SAMSON

OneAngstrom

Organizing molecular structures spatially is a routine yet critical part of molecular modeling. Whether you’re preparing systems for simulations, illustrating interactions between molecules, or assembling complex biomolecular environments, correctly aligning and distributing molecules can prevent downstream errors and enhance clarity…

Lost in Molecules? Here’s How to Easily Navigate 3D Structures in SAMSON

OneAngstrom

When starting with molecular modeling, one challenge that many researchers face is navigating complex 3D structures efficiently. Whether you’re analyzing a protein-ligand interaction or building nanostructures, getting lost in space—or worse, losing your molecule entirely—happens more often than you might…

Confidently Predict Protein Structures in Minutes with AlphaFold-2 in SAMSON

OneAngstrom

Predicting a protein’s 3D structure has often been a time-consuming step for molecular modelers. For many, setting up command-line environments, ensuring accurate input formatting, and managing computational resources can slow down early-stage research. If you’re looking for a more streamlined…