SAMSON Blog – Page 246

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

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…

Navigating Focus: How Dolly Camera Animations Simplify Molecular Visualization

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Working with complex molecular systems often means working with complex visuals. In tools like SAMSON, being able to direct attention to a specific region of your model can make a real difference—whether it’s for analysis, teaching, or presentation. One of…

Why Did My Labels Disappear? Understanding Label Visibility in SAMSON

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You’re preparing a molecular model and carefully added a set of labels to atoms, residues, or molecules — only to find that they seem to vanish as you zoom out or pan across your system in SAMSON. If this sounds…

Working Together: Managing Collaborative Groups in Molecular Modeling

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In collaborative scientific environments — from academic labs to cross-institutional research teams — sharing models, simulations, and analysis workflows is critical. If you’re a molecular modeler using SAMSON, you might have faced challenges when organizing joint work: How do you…