SAMSON Blog – Page 28

A Quick Way to Instantly Enhance Molecular Visualizations in SAMSON

When working with complex molecular systems, presentation matters. Whether you’re preparing visuals for a publication, a lecture, or simply navigating intricate molecular networks, creating compelling representations that are both meaningful and accessible can take time. 👍 This is where Visual…

Controlling Molecular Scene Appearance with Render Preset Attributes

OneAngstrom

When you’re dealing with molecular modeling, presentation isn’t just aesthetic—it’s essential. Whether you’re preparing visuals for publication, sharing models with collaborators, or trying to quickly identify certain features in a complex scene, controlling how each part of your system is…

Making PMF Calculations Less Painful with GROMACS Wizard

OneAngstrom

If you’ve ever run umbrella sampling simulations in molecular dynamics, you probably know the next step: extracting the Potential of Mean Force (PMF) to understand free energy profiles along a reaction coordinate. But actually going from simulation data to a…

Saving Time and Keeping It Clean: Using Visual Presets in SAMSON

OneAngstrom

One of the recurring challenges in molecular modeling is ensuring visual consistency across figures and animations, especially when working with large, multi-scale systems or preparing presentations and publications. If you’ve ever spent too much time adjusting rendering settings, tweaking atom…

Why Your Simulation Density Is Wrong (and How to Fix It with NPT Equilibration)

OneAngstrom

One of the most frequent stumbling blocks in molecular dynamics is achieving the desired system density before running a production simulation. You ran energy minimization, followed it up with NVT thermal equilibration—and yet the system’s density just won’t settle. Sound…

Tweak One Atom, Explore New Possibilities: Generating Molecular Analogs in SAMSON

OneAngstrom

If you’ve ever worked on optimizing a lead compound, you know how valuable small molecular changes can be. What if you could quickly and systematically generate analogs by swapping a single atom or group—right from your molecular design platform? This…

From 3D to Clarity: Simplifying Protein-Ligand Analysis with 2D Interaction Diagrams

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Understanding the interactions between a protein and its ligand is essential in molecular modeling and drug discovery. But when analyzing complex 3D molecular structures, sometimes seeing what matters most—key interactions—can get visually overwhelming. If you’ve ever felt like you needed…

Speed Up Protein Docking by Restricting the Search Domain

OneAngstrom

Protein-protein docking is one of the cornerstones of structural bioinformatics, but it can be computationally expensive – especially when conformational sampling is performed across broad orientations. One way to make docking significantly faster and more relevant is to limit the…

Quickly Find What You Need in Molecular Structures: Using Attribute Filtering in SAMSON

OneAngstrom

When working with complex molecular systems, it can be overwhelming to dig through countless properties just to make a small adjustment. Whether you’re modifying atom positions, checking chemical features, or exploring the hierarchy of nodes in your system, the ability…

Fast, Consistent Molecular Visuals with Visual Presets in SAMSON

OneAngstrom

Creating consistent and clear molecular illustrations can quickly become tedious when you have to manually adjust representations, colors, and rendering options every time. Whether you’re preparing multiple images for a publication, setting up visuals for a presentation, or just trying…