SAMSON Blog – Page 27

Running Molecular Dynamics in the Cloud Without Installing GROMACS

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

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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

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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

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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

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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

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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

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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…

Quickly Find Segments by Atom, Residue, or Charge Counts in SAMSON

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When working with complex molecular systems, molecular modelers often face a recurring challenge: filtering and selecting specific parts of large biomolecules for focused analysis or operations. Whether you’re interested in molecules with a high partial charge, specific atomic compositions, or…

Making key parts of your molecular scene disappear—on purpose

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Molecular animations are more than just eye candy—they’re essential for communicating structural transitions, mechanisms, and design ideas. But what happens when certain parts of a model clutter your scene or distract from the key mechanism you’re trying to convey? Whether…

A Molecular Modeler’s Guide to Camera Animations in SAMSON

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Communicating molecular mechanisms clearly can be a challenge. Whether you’re creating visuals for publications, lectures, or lab meetings, the way you represent the spatial context of your molecules—and how that context changes over time—really matters. This is where camera animations…