OneAngstrom – Page 93

Filtering molecular folders by atom counts in SAMSON

When working with complex molecular systems, it’s not unusual to accumulate a large number of molecular folders—each potentially comprising various atoms, chains, and structural features. This can make it difficult to quickly isolate the folders you want to work with.…

Make Your Molecules Pop: Using Visual Presets in SAMSON

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If you’ve ever spent hours building a molecular model only to end up with a blurry, color-confusing visual that doesn’t quite communicate your findings, you’re not alone. For molecular modelers, visually conveying structure and interaction is often as important as…

What Happens After You Click “Simulate”? Understanding Your GROMACS Results

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Molecular modeling can be a meticulous process, and when a production molecular dynamics (MD) simulation wraps up, there’s often a big question: What did it produce, and how do I interpret it? The GROMACS Wizard in SAMSON makes life a…

Why Your Molecular Simulations Might Fail Before They Begin

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One of the most overlooked but absolutely essential steps in setting up a molecular dynamics simulation is Energy Minimization. If you’ve ever wondered why your simulation crashes or produces unstable trajectories, there’s a good chance the culprit lies in skipping…

Quickly Refining NMR Ensembles Without Topology Files

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One common challenge faced by structural biologists working with NMR-derived molecular structures is postprocessing. After initial structure generation with tools like CYANA, converting these NMR ensembles into high-quality, energy-minimized models suitable for publication or molecular design often requires manual setup…

Need to Play a Molecular Path Backwards? Here’s a Simple Approach in SAMSON

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When working with molecular trajectories, it’s often necessary to analyze not just how a system evolves forward, but also what happens when the process is reversed. For instance, in conformational studies or reaction reversibility checks, playing a path backward can…

Deciding Between Multiple Symmetries in Large Biological Assemblies

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When modeling large biological assemblies like virus capsids or multi-subunit complexes, symmetry can be a valuable asset. It helps identify repeating units, reduce simulation costs, and guide structural analysis. However, molecular modelers often encounter a common scenario: multiple symmetry groups…

Trouble with PMF Profiles? Try This Simple, Visual Workflow

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If you have ever struggled to make sense of noisy Potential of Mean Force (PMF) profiles or spent hours parsing simulation folders manually, you’re not alone. For many molecular modelers, processing umbrella sampling results into clear, interpretable energy landscapes can…

Quickly Generate Carbon Nanotubes with Precise Geometry Using SAMSON

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Constructing carbon nanotube (CNT) models for molecular simulation or nanoengineering projects often requires carefully tuning structure-defining parameters. For many molecular modelers, this becomes a bottleneck—especially when dealing with multi-walled CNTs or trying to replicate specific geometries using external modeling tools.…

Adding Breathing Room in Molecular Animations: Understanding the Pause Feature

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Molecular animations are powerful tools for communicating complex structural and dynamic concepts. Whether you’re presenting a conformational change, a docking event, or an interactive walkthrough of biomolecular interactions, every frame matters. But there’s a challenge many molecular modelers face: giving…