SAMSON Blog – Page 103

Exporting Ligand Trajectories Along Paths: A Practical Guide for Molecular Modelers

Understanding how ligands move through binding pockets is vital in molecular modeling, whether you’re simulating binding/unbinding events, preparing free energy calculations, or simply visualizing molecular mechanisms. If you’ve ever computed a path (e.g., using a method like parallel nudged elastic…

Quickly Find Conformations by Atom Count in SAMSON

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When working with molecular models that have multiple conformations, navigating and managing them efficiently becomes essential—especially when the system’s complexity grows. If you’ve ever wished for a faster way to pinpoint specific conformations within large molecular structures in SAMSON, you’re…

Quickly Find Molecular Conformations by Atom Count in SAMSON

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One common challenge in molecular modeling is navigating large datasets of conformations—especially when analyzing or comparing molecular structures with vastly different complexities. Sometimes all a modeler wants is to isolate conformations of similar complexity, or to filter out conformations that…

Make Your Molecular Animations Breathe: How to Pause for Clarity in SAMSON

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If you’ve ever built a molecular animation to explain a structural transformation, introduce a conformational change, or visualize a docking sequence, you know how quickly things can move. For viewers—whether students, colleagues, or collaborators—absorption takes time. But what if your…

Building a Lipid Bilayer Around a Protein in Minutes

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Creating realistic membrane-protein systems is a recurring challenge in molecular modeling. Membrane proteins play critical biological roles, but setting up simulations that combine them with appropriate lipid environments often involves multiple tools, file format conversions, and a fair amount of…

Simplify Your Molecular Models by Filtering Visible Properties Only

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When working with complex molecular systems, visualization quickly becomes a challenge. Property models are often cluttered with hidden or irrelevant data, making it hard to focus on what matters most. If you’re a molecular modeler using SAMSON, you’ve likely wanted…

How to Easily Reuse Your GROMACS Projects Without Re-entering File Paths

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Molecular dynamics simulations often require several steps before researchers can run a full production simulation. These include energy minimization, equilibration under various ensembles (NVT, NPT), and finally the production run itself. For those using GROMACS through the SAMSON GROMACS Wizard,…

Avoiding Repetitive Edits in Molecular Dynamics: Save and Reuse Custom GROMACS Parameters

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Many molecular modelers working with GROMACS simulations face the same repetitive issue: each time you run a new molecular dynamics simulation—whether it’s energy minimization, NVT/NPT equilibration, or production MD—you often find yourself re-entering the same set of custom parameters manually.…

Molecular Depth Made Clear: Ambient Occlusion in SAMSON

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When working with complex molecular structures, one common challenge is understanding the spatial relationships between different parts of a model. Proteins, ligands, and assemblies can quickly turn into a dense visual web where depth becomes hard to interpret. A powerful…

Creating Molecule Libraries by Replacing Fragments: A Practical Guide in SAMSON

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In drug design and molecular optimization, exploring structural variants of a given parent molecule is a common strategy to improve activity, solubility, or other properties. Manually generating all these variants, however, can be repetitive and error-prone—even before simulations begin. The…