OneAngstrom – Page 92

Why Molecular Modelers Shouldn’t Skip Their SAMSON Profile

When working in molecular design, collaboration and visibility can open many doors: partnerships, contributions, opportunities, recognition. Yet, many molecular modelers overlook a simple step that connects them to the global research community: creating their public profile on SAMSON Connect. If…

Making Molecular Geometry Feel Real: A Quick Guide to Interactive Simulations in SAMSON

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Molecular modelers spend considerable time optimizing molecular geometries – making sure atoms are in the right place, bonds have the correct length, and everything aligns with physical reality. But clicking through optimization steps and waiting for calculated results can feel…

Building Carbon Nanotubes by Hand in SAMSON: A Visual Approach to Mastering Patterns

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Creating custom carbon nanotube structures can be a time-consuming and repetitive task, especially when modeling them atom-by-atom. Fortunately, with the integrated pattern editors in SAMSON, you can build nanotubes from scratch in just a few steps — while staying in…

Easily Select Start and Goal Protein Conformations in SAMSON

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One common challenge in molecular modeling is creating meaningful transition pathways between two conformations of a protein. Whether you’re studying allosteric mechanisms, conformational flexibility, or receptor–ligand induced fit, identifying and selecting the correct starting and target shapes can be one…

Running GROMACS Simulations in the Cloud with SAMSON

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One frequent bottleneck in molecular modeling is computational power. While modern desktops can handle many local simulations, certain tasks such as large-scale MD simulations, enhanced sampling, or batch computations demand more resources. This is where cloud computing becomes a valuable…

Quickly Filter Complex Molecular Segments Without Writing Scripts

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When analyzing large biomolecular systems, molecular modelers often face a routine but time-consuming challenge: efficiently selecting the relevant segments based on their properties, such as number of atoms, residues, or specific elements like carbon or nitrogen. Manual selection or scripting…

Smarter Polymer Design with Custom Monomer Sequences

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For molecular modelers working with synthetic or biological polymers, flexibility in defining and reusing molecular building blocks is critical. When creating complex polymers—especially those with repeating units or custom architectures—managing monomer sequences efficiently can save time and reduce errors. This…

Freeze and Refine: Minimizing Just a Part of a Molecule in SAMSON

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When working with complex molecular systems, sometimes you only need to refine a small region of a structure — perhaps an active site, a flexible region, or a newly added side chain. Re-minimizing the entire molecule can be slow and…

Quickly Filter Visible Labels in Complex Models

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When working with large molecular systems, it’s easy for the workspace to become visually cluttered. Especially when label nodes—used for annotating or identifying parts of a system—are scattered across complex models. Finding which labels are visible, filtering out those that…

Tracking Molecular Motion with Center-of-Mass Pathlines in SAMSON

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Visualizing how molecules move over time is a recurring challenge in molecular modeling. Whether you’re studying ligand unbinding, domain shifts in proteins, or atom group trajectories, understanding motion is crucial. One particularly useful concept is the center of mass (COM)…