OneAngstrom – Page 112

Simplify Your Molecular Models by Filtering Visible Properties Only

When working with complex molecular systems, visualization quickly becomes a challenge. Property models are often cluttered with hidden or irrelevant data, making it hard to focus on what matters most. If you’re a molecular modeler using SAMSON, you’ve likely wanted…

How to Easily Reuse Your GROMACS Projects Without Re-entering File Paths

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Molecular dynamics simulations often require several steps before researchers can run a full production simulation. These include energy minimization, equilibration under various ensembles (NVT, NPT), and finally the production run itself. For those using GROMACS through the SAMSON GROMACS Wizard,…

Avoiding Repetitive Edits in Molecular Dynamics: Save and Reuse Custom GROMACS Parameters

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Many molecular modelers working with GROMACS simulations face the same repetitive issue: each time you run a new molecular dynamics simulation—whether it’s energy minimization, NVT/NPT equilibration, or production MD—you often find yourself re-entering the same set of custom parameters manually.…

Molecular Depth Made Clear: Ambient Occlusion in SAMSON

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When working with complex molecular structures, one common challenge is understanding the spatial relationships between different parts of a model. Proteins, ligands, and assemblies can quickly turn into a dense visual web where depth becomes hard to interpret. A powerful…

Creating Molecule Libraries by Replacing Fragments: A Practical Guide in SAMSON

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In drug design and molecular optimization, exploring structural variants of a given parent molecule is a common strategy to improve activity, solubility, or other properties. Manually generating all these variants, however, can be repetitive and error-prone—even before simulations begin. The…

A Practical Guide to Managing Your SAMSON Extensions

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For molecular modelers using the SAMSON platform, organizing and turning the right features on or off at the right time can save both time and computational resources. Whether you’re switching between different projects, collaborating in a team, or simply exploring…

Spotting Hidden Molecular Backbones with SAMSON’s NSL

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When working with complex molecular systems, it’s common to end up with visual clutter. Backbones, structural groups, side chains, and other entities can overlap, coexist, and sometimes hide from view—literally. That’s when being able to find and filter out exactly…

Choosing the Right Symmetry Group in Large Protein Assemblies

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When working with large macromolecular complexes—such as viral capsids or multi-subunit protein assemblies—molecular modelers often encounter one frustrating question: What symmetry best represents this structure? Identifying the correct symmetry group is not just about visualization—it’s about improving the quality and…

Simulating Defects in Diamond with SAMSON’s Crystal Creator

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Understanding how defects impact the properties of crystalline materials is a crucial task for materials scientists, physicists, and molecular modelers. Defects in crystal lattices can significantly affect mechanical strength, conductivity, optical behavior, and other physical properties. However, visualizing and simulating…

Bringing Molecular Trajectories to Life with Play Path Animations

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One of the most common challenges faced by molecular modelers is visualizing changes in molecular conformations over time. Whether you’re working with molecular dynamics (MD) simulations, conformational sampling, or interactive modifications, seeing how a system evolves in space and time…