OneAngstrom – Page 2

What Happens When Your Molecular File Won’t Open?

Anyone working in molecular modeling has likely run into a frustrating moment: a colleague sends a structure file, but when you try to open it—nothing happens. Or worse, you get a vague error message. Whether it’s a .pdb, .mol2, .cube,…

Understanding Visibility Flags to Simplify Molecular Model Management

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Molecular modelers often deal with complex scenes involving hundreds or thousands of molecular entities. Managing which components are visible in a project is key to staying organized and productive. However, sometimes toggling visibility feels chaotic, especially when visual models behave…

A Cleaner Way to Tweak GROMACS Parameters Without Editing .mdp Files

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Molecular dynamics simulations often require parameter adjustments tailored to the system at hand. For GROMACS users, editing these parameters typically means diving into the .mdp files manually—a task that, while flexible, can be error-prone and slows down experimentation. If you’re…

Filtering Backbone Structures Using NSL: A Practical Guide for Molecular Modelers

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If you’re working with complex molecular systems, you likely face the challenge of isolating specific structural groups or backbones based on their properties. Whether you’re performing coarse-grained modeling, refining selection in visualizations, or analyzing structural consistency, manually identifying and filtering…

Avoiding Steric Clashes in Molecular Simulations: A Quick Guide to Energy Minimization with GROMACS Wizard

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If you’re setting up molecular dynamics simulations, one of the essential – yet often underestimated – preprocessing steps is energy minimization. Skipping it, or doing it incorrectly, may lead to steric clashes, unrealistic geometries, or unstable simulations downstream. Fortunately, the…

Exploring Defects in Diamond Structures

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Small imperfections in crystal structures, known as defects, can have a big impact on materials’ physical properties—altering conductivity, stability, and even color in some cases. If you’re modeling materials like diamond at the atomic level, understanding and controlling defects is…

Keeping the Essential: Selective Removal of Crystal Waters for GROMACS Simulations

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When preparing a molecular system for simulation in GROMACS, one common yet delicate task is handling existing crystal water molecules. While some waters can safely be deleted, others—especially those tightly bound in functional sites—may be crucial to your system’s behavior.…

Pinpoint the Right Molecular Groups: A Practical Look at Node Group Selection in SAMSON

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When working with complex molecular models, one of the most recurring tasks is selecting the correct subset of structures. Whether you’re isolating a ligand, identifying functional groups, or analyzing a molecular sub-assembly, manual selection is tedious and error-prone. Fortunately, the…

What Does It Really Mean for a Node to Be Hidden in SAMSON?

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When working with complex molecular systems in SAMSON, controlling what you see—and what you don’t—is essential for clarity and focus. If you’ve ever found yourself wondering why some nodes appear invisible, seemingly at random, you’re not alone. In this post,…

How to Select Negatively Charged Residues in Seconds

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When working with biomolecular structures, identifying residues with specific properties—like charge—can be a recurring task. Whether you are focusing on the electrostatic interactions, preparing systems for simulation, or simply analyzing subsets of residues, quickly filtering negatively charged amino acids can…