OneAngstrom – Page 277

Easily Select Chains by Residue Count in Your Molecular Models

A common challenge when working with complex biomolecular systems is efficiently identifying and selecting chains based on their characteristics. Suppose you’re analyzing a protein–protein interaction, or refining a molecular assembly, and want to focus only on chains that are sufficiently…

When Temperature Matters: Navigating NVT Equilibration in GROMACS Wizard

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For molecular modelers preparing systems for molecular dynamics simulations, a key challenge is achieving accurate thermodynamic conditions before production runs. One critical step in this process is NVT equilibration, which brings the system to the desired temperature while maintaining constant…

Installing and Editing Local Python Packages Inside SAMSON

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Many molecular modelers and computational chemists have their own Python packages—for custom simulations, analysis pipelines, or even neural networks for property prediction. But using them often means jumping between development environments, terminal sessions, and structured molecule viewers. What if everything…

Quickly See or Hide Molecular Animation Nodes with SAMSON’s Visibility Attributes

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When working with complex molecular systems, animations can quickly become overwhelming. Whether you’re presenting a molecular mechanism or simply analyzing the evolution of conformations, showing or hiding individual animation nodes efficiently helps you stay focused on what really matters. In…

Quickly Stabilize Temperature in Molecular Simulations with NVT Equilibration in SAMSON

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One common challenge in molecular dynamics is ensuring that your system reaches and maintains the desired temperature before you proceed with production simulations. If the temperature isn’t properly stabilized, results can be unreliable or misleading. This is where NVT equilibration…

A Better Way to Navigate Your Molecular Scenes: Using Multiple Cameras in SAMSON

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If you’ve ever worked on complex molecular systems, you’ve likely faced the challenge of jumping between different regions of interest. Whether you need a bird’s-eye view of the entire molecular complex or a close-up on a catalytic site, switching views…

Quickly Target Node Groups in SAMSON with the Node Specification Language

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When working with large and complex molecular systems in SAMSON, finding and interacting with specific elements can become time-consuming. Imagine trying to select just the ligands, or isolate a set of residues from a cluster of chains, without accidentally selecting…

Modifying GROMACS parameters in SAMSON without breaking your workflow

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One of the recurring pain points for molecular modelers using GROMACS is managing and fine-tuning molecular dynamics parameters across simulations. Whether you’re running energy minimizations or full production MD simulations, adjusting .mdp files efficiently without making mistakes or interrupting your…

Working with Multiple Molecules in SAMSON: The Role of Document View

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Molecular modelers often juggle numerous molecules when working on simulations, analyses, or comparisons. Switching between them, copying structures, organizing data, and applying operations to specific groups without clutter can be a challenge. This is where Document View in SAMSON becomes…

Making Molecular Models Easier to Understand with Visual Models in SAMSON

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For many molecular modelers, one significant challenge isn’t running simulations or optimizing structures—it’s presenting their results in a way that is easy to understand. Whether you’re working in research, education, or communication, visual clarity can save time, reduce misinterpretation, and…