SAMSON Blog – Page 53

Faster Molecular Geometry Optimization with FIRE in SAMSON

When building or analyzing molecular structures, geometry optimization is essential to remove unrealistic geometries and prepare systems for simulations. However, classic approaches such as steepest descent can be time-consuming, especially when your structure requires large-scale structural relaxation. Fortunately, SAMSON offers…

From Structure to Simulation: Exporting DNA Nanostructures with Adenita

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For many molecular designers working on DNA nanostructures, a common workflow challenge lies in translating intricate 3D models into formats that are simulation-ready. This becomes especially critical when preparing systems for coarse-grained simulations like those run with oxDNA. Adenita, a…

Choosing the Right Symmetry Axis in Large Protein Assemblies

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In large protein assemblies, symmetry often plays a fundamental role in biological function and modeling workflows. However, when working with complex structures like viral capsids or multimeric proteins, automated symmetry detection tools may propose multiple symmetry groups. This can lead…

Instant Protein Assemblies: Exploring Symmetry Mates Without the Guesswork

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Understanding how proteins arrange themselves into larger structures is a recurring challenge in molecular modeling. Whether you’re studying quaternary structures or designing nanostructures, one issue always arises: how to easily visualize the full biological assembly from the asymmetric unit provided…

Editing GROMACS MDP Parameters in SAMSON Without Touching the Command Line

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If you’ve ever run molecular dynamics (MD) simulations with GROMACS, you know how crucial the .mdp file is. It defines all the parameters that control how your simulation behaves—from minimization settings to production dynamics. But editing this file manually can…

Why Your SAMSON Extensions May Not Load—and How to Make Sure They Do

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If you’ve ever launched SAMSON and found that one of your favorite Extensions wasn’t loaded, even though it worked last week, you’re not alone. Molecular modelers relying on Extensions for simulations, visualizations, or custom tools may sometimes encounter this frustration.…

Cleaning Protein Structures Before Docking: Why It Matters and How to Do It in SAMSON

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If you’ve ever tried protein-protein docking and encountered strange results — unexpected clashes, misaligned complexes, or long computation times — chances are your system wasn’t properly prepared. Protein preparation is foundational for successful docking, yet it’s often overlooked or done…

Fine-tuning Molecular Visuals with Custom Color Palettes in SAMSON

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Color is an essential tool for molecular modelers. Whether you’re communicating structural insights, visualizing properties like hydrophobicity or temperature factors, or simply enhancing the aesthetic clarity of a molecular scene, choosing the right color scheme makes a big difference. But…

Using Python Scripts with SAMSON: A Quick Guide for Molecular Modelers

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Molecular modelers increasingly rely on scripting to streamline repetitive tasks, automate analyses, or create custom simulations. If you use Python in your workflow, integrating scripts directly into your modeling environment can dramatically reduce friction and time. SAMSON, the integrative platform…

Skip the Repeats: Simulating Only the Asymmetric Unit in Large Protein Complexes

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Molecular modelers working with large symmetric assemblies—like viral capsids or multi-subunit protein complexes—often face a dilemma: Should I simulate the entire structure, or is there a smarter way? In many cases, the repetitive nature of these biological assemblies means you’re…