OneAngstrom – Page 30

When Your Laptop Needs a Break: Running GROMACS Simulations in the Cloud with SAMSON

Running molecular dynamics simulations can be resource-intensive. If you’ve ever started a GROMACS job only to watch your workstation crawl to a halt—or worse, crash—you’re not alone. For many researchers and students, limited computing power can be a major bottleneck…

A Smarter Way to Visualize Docking in Molecular Models

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Docking simulations are fundamental in molecular modeling, especially in drug design, where one often wants to visualize how ligands interact with receptors. However, presenting these docking events clearly and intuitively can be surprisingly tricky. If you’ve ever struggled to convey…

Tired of Reselecting the Same Atoms? Try Quick Groups in SAMSON

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If you often work with large molecular systems, you’ve likely found yourself repeatedly selecting the same groups of atoms, residues, or molecules. Whether it’s for applying display styles, running simulations, or preparing figures, manually reselecting the same regions adds friction…

Quickly Find and Filter Molecular Groups with NSL’s Node Group Attributes

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When working with complex molecular systems, molecular modelers often face the challenge of filtering and selecting specific groups of atoms, residues, or molecules. Whether you’re visualizing individual ligand families or bulk-editing selections in a simulation, quick and accurate selection is…

Fine-tuning Performance of Your Local GROMACS Runs in SAMSON

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If you run molecular dynamics simulations with GROMACS on your local machine, you’ve probably wondered how to get the best performance without overloading your system. The GROMACS Wizard in SAMSON includes a performance settings panel that helps you customize how…

Why Minimizing Ligands Before Docking Matters — And How to Do It in SAMSON

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If you’ve ever experienced strange docking results—ligands floating in space, distorted poses, or unrealistic interactions—it might not be a scoring function issue. In many cases, the problem originates from poorly prepared ligand structures. Whether your ligand library comes from a…

Exporting Molecular Structures: From SAMSON to PDB, XYZ, and Beyond

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One of the common challenges in molecular modeling is converting your molecular structures and visualizations into file formats suitable for sharing, publishing, or further analysis in other software. Whether you're preparing a structure for a publication, collaborating with teams using…

Adding Custom Index Groups in GROMACS Wizard: A Simple Way to Organize Your Selections

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When setting up a molecular simulation, small things can save hours down the line. One of those things is organizing your system with custom index groups. GROMACS automatically generates standard index groups like Protein, SOL, and IONS based on the…

Mastering Molecular Presentations: Adjusting Orbit Camera Positions with Precision

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Creating effective molecular presentations often requires more than static views. Animations can significantly improve the clarity and engagement of your visualizations. One common requirement researchers face is showcasing a protein, material, or interaction site from multiple angles without overwhelming the…

Hands-On Molecular Modeling: Learn by Doing in SAMSON

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One of the most common frustrations that new users face when starting with molecular modeling platforms is the sheer complexity of tools and workflows. Even with excellent documentation, the transition from reading about a feature to applying it on your…