SAMSON Blog – Page 114

Easily Filter Molecular Backbones by Atom Counts in SAMSON

Molecular modelers often need to identify specific structural patterns across large systems. Whether you’re working on large proteins, synthetic polymers, or coarse-grained models, it’s common to need quick answers to questions like: “Which backbones have more than 10 carbon atoms?”…

Speeding Up Molecular Visualization with Custom Visual Presets

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Setting up visualizations for complex molecular systems often takes time—especially when you want consistent style, clarity, and precision across multiple structures or sessions. Whether you’re preparing a publication figure, exploring protein-ligand interactions, or showing a dynamic process to students, you’ve…

Making Molecular Presentations Feel Like Slides

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When preparing presentations for molecular modeling work, researchers often face the challenge of controlling the pace of their animations. Whether you’re demonstrating a binding process, highlighting conformational changes, or transitioning between topics in a research talk, timing is critical. A…

Simplify Your Molecular Modeling Workflow by Customizing the SAMSON Interface

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When working on complex molecular systems, staying organized and minimizing distraction is key. Many molecular modelers struggle with cluttered interfaces or inefficient workflows because the tools they use don’t adapt to how they think or work. Fortunately, SAMSON offers extensive…

Always Keep Your Eyes on the Molecule: Using the ‘Look at atoms’ Animation in SAMSON

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When working with molecular dynamics or structural analysis, it can be frustrating to lose track of a key region in your model just because the camera drifts away during visualization. Whether you are analyzing a binding site over time or…

Synchronizing Your Views: A More Intuitive Way to Work with Molecular Sequences

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For many molecular modelers, managing complex biomolecular systems means jumping between multiple representations: 3D structures, sequences, and data tables. A frequent source of friction is the disconnect between these representations—particularly when selecting elements in one view doesn’t immediately reflect in…

How to Create Custom Index Groups in GROMACS Wizard Without Writing a Line of Code

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When running advanced molecular dynamics simulations, especially those involving pull groups or complex post-simulation analysis, it’s often necessary to define custom index groups. This is typically done using gmx make_ndx, which requires knowledge of GROMACS command-line syntax and selection strings.…

When Steepest Descent Isn’t Enough: Accelerating Molecular Relaxation with FIRE

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Geometry optimization is an essential step in molecular modeling workflows, whether you’re preparing initial configurations for simulations or cleaning up experimental structures. But if you’ve ever felt that your steepest descent minimizer just isn’t converging fast enough—especially in systems with…

Make sense of molecular visualizations by filtering visible nodes in SAMSON

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If you’ve ever worked on a large molecular system, you know how cluttered the visual scene can become. Whether you’re analyzing docking results, molecular dynamics trajectories, or assembling molecular systems, excessive visual complexity often slows down interpretation and leads to…

Avoid Solvent Clashes in Coarse-Grained MD Simulations by Adjusting van der Waals Distances

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One common frustration for molecular modelers preparing coarse-grained (CG) systems for molecular dynamics simulations is dealing with solvated structures where solvent beads overlap with solute atoms. These clashes often cause failed simulations or unphysical behavior. The root cause? The default…